Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase.

PubMed

Costa, Kyle C; Wong, Phoebe M; Wang, Tiansong; Lie, Thomas J; Dodsworth, Jeremy A; Swanson, Ingrid; Burn, June A; Hackett, Murray; Leigh, John A

2010-06-15

In methanogenic Archaea, the final step of methanogenesis generates methane and a heterodisulfide of coenzyme M and coenzyme B (CoM-S-S-CoB). Reduction of this heterodisulfide by heterodisulfide reductase to regenerate HS-CoM and HS-CoB is an exergonic process. Thauer et al. [Thauer, et al. 2008 Nat Rev Microbiol 6:579-591] recently suggested that in hydrogenotrophic methanogens the energy of heterodisulfide reduction powers the most endergonic reaction in the pathway, catalyzed by the formylmethanofuran dehydrogenase, via flavin-based electron bifurcation. Here we present evidence that these two steps in methanogenesis are physically linked. We identify a protein complex from the hydrogenotrophic methanogen, Methanococcus maripaludis, that contains heterodisulfide reductase, formylmethanofuran dehydrogenase, F(420)-nonreducing hydrogenase, and formate dehydrogenase. In addition to establishing a physical basis for the electron-bifurcation model of energy conservation, the composition of the complex also suggests that either H(2) or formate (two alternative electron donors for methanogenesis) can donate electrons to the heterodisulfide-H(2) via F(420)-nonreducing hydrogenase or formate via formate dehydrogenase. Electron flow from formate to the heterodisulfide rather than the use of H(2) as an intermediate represents a previously unknown path of electron flow in methanogenesis. We further tested whether this path occurs by constructing a mutant lacking F(420)-nonreducing hydrogenase. The mutant displayed growth equal to wild-type with formate but markedly slower growth with hydrogen. The results support the model of electron bifurcation and suggest that formate, like H(2), is closely integrated into the methanogenic pathway.

Electron-ion temperature equilibration in warm dense tantalum

DOE PAGES

Doppner, T; LePape, S.; Ma, T.; ...

2014-11-05

We present measurements of electron-ion temperature equilibration in proton-heated tantalum, under warm dense matter conditions. Our results agree with theoretical predictions for metals calculated using input data from ab initio simulations. Furthermore, the fast relaxation observed in the experiment contrasts with much longer equilibration times found in proton heated carbon, indicating that the energy flow pathways in warm dense matter are far from being fully understood.

Characterization of the biochemical-pathway of uranium (VI) reduction in facultative anaerobic bacteria.

PubMed

Mtimunye, Phalazane J; Chirwa, Evans M N

2014-10-01

Cultures of U(VI) reducing bacteria sourced from abandoned uranium mine tailing dam were evaluated for their ability to reduce U(VI) to U(IV). The species in the cultures reduced U(VI) in solutions with initial U(VI) concentration up to 400mgL(-)(1) under a near neutral pH of 6.5. The electron flow pathway and fate of reduced species was also analysed in the individual species in order to evaluate the potential for control and optimisation of the reduction potential at the biochemical level. The results showed that U(VI) reduction in live cells was completely blocked by the NADH-dehydrogenase inhibitor, rotenone (C23H22O6), and thioredoxin inhibitor, cadmium chloride (CdCl2), showing that U(VI) reduction involves the electron flow through NADH-dehydrogenase, a primary electron donor to the electron transport respiratory (ETR) system. Mass balance analysis of uranium species aided by visual and electron microscopy suggest that most U(VI) reduction occurred on the cell surface of the isolated species. This finding indicates the possibility of easy uranium recovery for beneficial use through biological remediation. Should the U(VI) be reduced inside the cell, recovery would require complete disruption of the cells and therefore would be difficult. The study contributes new knowledge on the underlying mechanisms in the U(VI) reduction in facultative anaerobes. Copyright © 2014 Elsevier Ltd. All rights reserved.

The oxidation of phenol by ferrate(VI) and ferrate(V). A pulse radiolysis and stopped-flow study.

PubMed

Rush, J D; Cyr, J E; Zhao, Z; Bielski, B H

1995-04-01

Potassium ferrate, K2FeO4, is found to oxidize phenol in aqueous solution (5.5 < or = pH < or = 10) by a process which is second order in both reactants; -d[FeVI]/dt=k1[FeVI][phenol], k1 = 10(7)M-1s-1. Product analysis by HPLC showed a mixture of hydroxylated products, principally paraquinone, and biphenols that indicate that oxidation of phenol occurs by both one-electron and two-electron pathways. The two-electron oxidant, producing both para- and ortho-hydroxylated phenols is considered to be ferrate(V) which is itself produced by the initial one-electron reduction of ferrate(VI). The rate of ferrate(V) reaction with phenol was determined by pre-mix stopped flow pulse-radiolysis and found to be k7 = (3.8 +/- 0.4) x 10(5)M-1s-1.

Steering liquid metal flow in microchannels using low voltages.

PubMed

Tang, Shi-Yang; Lin, Yiliang; Joshipura, Ishan D; Khoshmanesh, Khashayar; Dickey, Michael D

2015-10-07

Liquid metals based on gallium, such as eutectic gallium indium (EGaIn) and Galinstan, have been integrated as static components in microfluidic systems for a wide range of applications including soft electrodes, pumps, and stretchable electronics. However, there is also a possibility to continuously pump liquid metal into microchannels to create shape reconfigurable metallic structures. Enabling this concept necessitates a simple method to control dynamically the path the metal takes through branched microchannels with multiple outlets. This paper demonstrates a novel method for controlling the directional flow of EGaIn liquid metal in complex microfluidic networks by simply applying a low voltage to the metal. According to the polarity of the voltage applied between the inlet and an outlet, two distinct mechanisms can occur. The voltage can lower the interfacial tension of the metal via electrocapillarity to facilitate the flow of the metal towards outlets containing counter electrodes. Alternatively, the voltage can drive surface oxidation of the metal to form a mechanical impediment that redirects the movement of the metal towards alternative pathways. Thus, the method can be employed like a 'valve' to direct the pathway chosen by the metal without mechanical moving parts. The paper elucidates the operating mechanisms of this valving system and demonstrates proof-of-concept control over the flow of liquid metal towards single or multiple directions simultaneously. This method provides a simple route to direct the flow of liquid metal for applications in microfluidics, optics, electronics, and microelectromechanical systems.

Engineering Heteromaterials to Control Lithium Ion Transport Pathways

DOE PAGES

Liu, Yang; Vishniakou, Siarhei; Yoo, Jinkyoung; ...

2015-12-21

Safe and efficient operation of lithium ion batteries requires precisely directed flow of lithium ions and electrons to control the first directional volume changes in anode and cathode materials. Understanding and controlling the lithium ion transport in battery electrodes becomes crucial to the design of high performance and durable batteries. Some recent work revealed that the chemical potential barriers encountered at the surfaces of heteromaterials play an important role in directing lithium ion transport at nanoscale. We utilize in situ transmission electron microscopy to demonstrate that we can switch lithiation pathways from radial to axial to grain-by-grain lithiation through themore » systematic creation of heteromaterial combinations in the Si-Ge nanowire system. Furthermore, our systematic studies show that engineered materials at nanoscale can overcome the intrinsic orientation-dependent lithiation, and open new pathways to aid in the development of compact, safe, and efficient batteries.« less

Engineering Heteromaterials to Control Lithium Ion Transport Pathways

PubMed Central

Liu, Yang; Vishniakou, Siarhei; Yoo, Jinkyoung; Dayeh, Shadi A.

2015-01-01

Safe and efficient operation of lithium ion batteries requires precisely directed flow of lithium ions and electrons to control the first directional volume changes in anode and cathode materials. Understanding and controlling the lithium ion transport in battery electrodes becomes crucial to the design of high performance and durable batteries. Recent work revealed that the chemical potential barriers encountered at the surfaces of heteromaterials play an important role in directing lithium ion transport at nanoscale. Here, we utilize in situ transmission electron microscopy to demonstrate that we can switch lithiation pathways from radial to axial to grain-by-grain lithiation through the systematic creation of heteromaterial combinations in the Si-Ge nanowire system. Our systematic studies show that engineered materials at nanoscale can overcome the intrinsic orientation-dependent lithiation, and open new pathways to aid in the development of compact, safe, and efficient batteries. PMID:26686655

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

Alfonso Hernandez, Laura; Nelson, Tammie Renee; Gelin, Maxim F.

The interchromophoric energy-transfer pathways between weakly coupled units in a π-conjugated phenylene–ethynylene macrocycle and its half-ring analogue have been investigated using the nonadiabatic excited-state molecular dynamics approach. To track the flow of electronic transition density between macrocycle units, we formulate a transition density flux analysis adapted from the statistical minimum flow method previously developed to investigate vibrational energy flow. Following photoexcitation, transition density is primarily delocalized on two chromophore units and the system undergoes ultrafast energy transfer, creating a localized excited state on a single unit. In the macrocycle, distinct chromophore units donate transition density to a single acceptor unitmore » but do not interchange transition density among each other. We find that energy transfer in the macrocycle is slower than in the corresponding half ring because of the presence of multiple interfering energy-transfer pathways. Finally, simulation results are validated by modeling the fluorescence anisotropy decay.« less

Flow-induced immobilization of glucose oxidase in nonionic micellar nanogels for glucose sensing.

PubMed

Cardiel, Joshua J; Zhao, Ya; Tonggu, Lige; Wang, Liguo; Chung, Jae-Hyun; Shen, Amy Q

2014-10-21

A simple microfluidic platform was utilized to immobilize glucose oxidase (GOx) in a nonionic micellar scaffold. The immobilization of GOx was verified by using a combination of cryogenic electron microscopy (cryo-EM), scanning electron microscopy (SEM), and ultraviolet spectroscopy (UV) techniques. Chronoamperometric measurements were conducted on nanogel-GOx scaffolds under different glucose concentrations, exhibiting linear amperometric responses. Without impacting the lifetime and denaturation of GOx, the nonionic nanogel provides a favorable microenvironment for GOx in biological media. This flow-induced immobilization method in a nonionic nanogel host matrix opens up new pathways for designing a simple, fast, biocompatible, and cost-effective process to immobilize biomolecules that are averse to ionic environments.

First-principles investigation on transport properties of NiO monowire-based molecular device

NASA Astrophysics Data System (ADS)

Chandiramouli, R.; Sriram, S.

2014-08-01

The electronic transport properties of novel NiO monowire connected to the gold electrodes are investigated using density functional theory combined with nonequilibrium Green's functions formalism. The densities of states of the monowire under various bias conditions are discussed. The transport properties are discussed in terms of the transmission spectrum and current-voltage characteristics of NiO monowire. The transmission pathways provide the insight to the transmission of electrons along the monowire. With different bias voltages, current in the order of few microampere flows across the monowire. The applied voltage controls the flow of current through the monowire, which can be used to control the current efficiently in the low order of magnitude in the molecular device.

Bioenergetic reprogramming plasticity under nitrogen depletion by the unicellular green alga Scenedesmus obliquus.

PubMed

Papazi, Aikaterini; Korelidou, Anna; Andronis, Efthimios; Parasyri, Athina; Stamatis, Nikolaos; Kotzabasis, Kiriakos

2018-03-01

Simultaneous nitrogen depletion and 3,4-dichlorophenol addition induce a bioenergetic microalgal reprogramming, through strong Cyt b 6 f synthesis, that quench excess electrons from dichlorophenol's biodegradation to an overactivated photosynthetic electron flow and H 2 -productivity. Cellular energy management includes "rational" planning and operation of energy production and energy consumption units. Microalgae seem to have the ability to calculate their energy reserves and select the most profitable bioenergetic pathways. Under oxygenic mixotrophic conditions, microalgae invest the exogenously supplied carbon source (glucose) to biomass increase. If 3,4-dichlorophenol is added in the culture medium, then glucose is invested more to biodegradation rather than to growth. The biodegradation yield is enhanced in nitrogen-depleted conditions, because of an increase in the starch accumulation and a delay in the establishment of oxygen-depleted conditions in a closed system. In nitrogen-depleted conditions, starch cannot be invested in PSII-dependent and PSII-independent pathways for H 2 -production, mainly because of a strong decrease of the cytochrome b 6 f complex of the photosynthetic electron flow. For this reason, it seems more profitable for the microalga under these conditions to direct the metabolism to the synthesis of lipids as cellular energy reserves. Nitrogen-depleted conditions with exogenously supplied 3,4-dichlorophenol induce reprogramming of the microalgal bioenergetic strategy. Cytochrome b 6 f is strongly synthesized (mainly through catabolism of polyamines) to manage the electron bypass from the dichlorophenol biodegradation procedure to the photosynthetic electron flow (at the level of PQ pool) and consequently through cytochrome b 6 f and PSI to hydrogenase and H 2 -production. All the above showed that the selection of the appropriate cultivation conditions is the key for the manipulation of microalgal bioenergetic strategy that leads to different metabolic products and paves the way for a future microalgal "smart" biotechnology.

The cytochrome b6f complex at the crossroad of photosynthetic electron transport pathways.

PubMed

Tikhonov, Alexander N

2014-08-01

Regulation of photosynthetic electron transport at the level of the cytochrome b6f complex provides efficient performance of the chloroplast electron transport chain (ETC). In this review, after brief overview of the structural organization of the chloroplast ETC, the consideration of the problem of electron transport control is focused on the plastoquinone (PQ) turnover and its interaction with the b6f complex. The data available show that the rates of plastoquinol (PQH2) formation in PSII and its diffusion to the b6f complex do not limit the overall rate of electron transfer between photosystem II (PSII) and photosystem I (PSI). Analysis of experimental and theoretical data demonstrates that the rate-limiting step in the intersystem chain of electron transport is determined by PQH2 oxidation at the Qo-site of the b6f complex, which is accompanied by the proton release into the thylakoid lumen. The acidification of the lumen causes deceleration of PQH2 oxidation, thus impeding the intersystem electron transport. Two other mechanisms of regulation of the intersystem electron transport have been considered: (i) "state transitions" associated with the light-induced redistribution of solar energy between PSI and PSII, and (ii) redistribution of electron fluxes between alternative pathways (noncyclic electron transport and cyclic electron flow around PSI). Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Study of local currents in low dimension materials using complex injecting potentials

NASA Astrophysics Data System (ADS)

He, Shenglai; Covington, Cody; Varga, Kálmán

2018-04-01

A complex potential is constructed to inject electrons into the conduction band, mimicking electron currents in nanoscale systems. The injected electrons are time propagated until a steady state is reached. The local current density can then be calculated to show the path of the conducting electrons on an atomistic level. The method allows for the calculation of the current density vectors within the medium as a function of energy of the conducting electron. Using this method, we investigate the electron pathway of graphene nanoribbons in various structures, molecular junctions, and black phosphorus nanoribbons. By analyzing the current flow through the structures, we find strong dependence on the structural geometry and the energy of the injected electrons. This method may be of general use in the study of nano-electronic materials and interfaces.

Electronic Risk Assessment System as an Appropriate Tool for the Prevention of Cancer: a Qualitative Study.

PubMed

Javan Amoli, Amir Hossein; Maserat, Elham; Safdari, Reza; Zali, Mohammad Reza

2015-01-01

Decision making modalities for screening for many cancer conditions and different stages have become increasingly complex. Computer-based risk assessment systems facilitate scheduling and decision making and support the delivery of cancer screening services. The aim of this article was to survey electronic risk assessment system as an appropriate tool for the prevention of cancer. A qualitative design was used involving 21 face-to-face interviews. Interviewing involved asking questions and getting answers from exclusive managers of cancer screening. Of the participants 6 were female and 15 were male, and ages ranged from 32 to 78 years. The study was based on a grounded theory approach and the tool was a semi- structured interview. Researchers studied 5 dimensions, comprising electronic guideline standards of colorectal cancer screening, work flow of clinical and genetic activities, pathways of colorectal cancer screening and functionality of computer based guidelines and barriers. Electronic guideline standards of colorectal cancer screening were described in the s3 categories of content standard, telecommunications and technical standards and nomenclature and classification standards. According to the participations' views, workflow and genetic pathways of colorectal cancer screening were identified. The study demonstrated an effective role of computer-guided consultation for screening management. Electronic based systems facilitate real-time decision making during a clinical interaction. Electronic pathways have been applied for clinical and genetic decision support, workflow management, update recommendation and resource estimates. A suitable technical and clinical infrastructure is an integral part of clinical practice guidline of screening. As a conclusion, it is recommended to consider the necessity of architecture assessment and also integration standards.

A post Gurney quantum mechanical perspective on the electrolysis of water: ion neutralization in solution

NASA Astrophysics Data System (ADS)

Guo, Enyi; McKenzie, David R.

2017-11-01

Electron fluxes crossing the interface between a metallic conductor and an aqueous environment are important in many fields; hydrogen production, environmental scanning tunnelling microscopy, scanning electrochemical microscopy being some of them. Gurney (Gurney 1931 Proc. R. Soc. Lond. 134, 137 (doi:10.1098/rspa.1931.0187)) provided in 1931 a scheme for tunnelling during electrolysis and outlined conditions for it to occur. We measure the low-voltage current flows between gold electrodes in pure water and use the time-dependent behaviour at voltage switch-on and switch-off to evaluate the relative contribution to the steady current arising from tunnelling of electrons between the electrodes and ions in solution and from the neutralization of ions adsorbed onto the electrode surface. We ascribe the larger current contribution to quantum tunnelling of electrons to and from ions in solution near the electrodes. We refine Gurney's barrier scheme to include solvated electron states and quantify energy differences using updated information. We show that Gurney's conditions would prevent the current flow at low voltages we observe but outline how the ideas of Marcus (Marcus 1956 J. Chem. Phys. 24, 966-978 (doi:10.1063/1.1742723)) concerning solvation fluctuations enable the condition to be relaxed. We derive an average barrier tunnelling model and a multiple pathways tunnelling model and compare predictions with measurements of the steady-state current-voltage relation. The tunnelling barrier was found to be wide and low in agreement with other experimental studies. Applications as a biosensing mechanism are discussed that exploit the fast tunnelling pathways along molecules in solution.

Possible Dynamically Gated Conductance along Heme Wires in Bacterial Multiheme Cytochromes

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

Smith, Dayle MA; Rosso, Kevin M.

2014-07-24

The staggered cross decaheme configuration of electron transfer co-factors in the outer-membrane cytochrome MtrF may serve as a prototype for conformationally-gated multi-heme electron transport. Derived from the bacterium Shewanella oneidensis, the staggered cross configuration reveals intersecting c-type octaheme and tetraheme “wires” containing thermodynamic “hills” and “valleys”, suggesting that the protein structure may include a dynamical mechanism for conductance and pathway switching depending on enzymatic functional need. Recent molecular simulations have established the pair-wise electronic couplings, redox potentials, and reorganization energies to predict the maximum conductance along the various heme wire pathways by sequential hopping of a single electron (PNAS (2014)more » 11,611-616). Here, we expand this information with classical molecular and statistical mechanics calculations of large-amplitude protein dynamics in MtrF, to address its potential to modulate pathway conductance, including assessment of the effect of the total charge state. Explicit solvent molecular dynamics simulations of fully oxidized and fully reduced MtrF employing ten independent 50-ns simulations at 300 K and 1 atm showed that reduced MtrF is more expanded and explores more conformational space than oxidized MtrF, and that heme reduction leads to increased heme solvent exposure. The slowest mode of collective decaheme motion is 90% similar between the oxidized and reduced states, and consists primarily of inter-heme separation with minor rotational contributions. The frequency of this motion is 1.7×107 s 1 for fully-oxidized and fully-reduced MtrF, respectively, slower than the downhill electron transfer rates between stacked heme pairs at the octaheme termini and faster than the electron transfer rates between parallel hemes in the tetraheme chain. This implies that MtrF uses slow conformational fluctuations to modulate electron flow along the octaheme pathway, apparently for the purpose of increasing the residence time of electrons on lowest potential hemes 4 and 9. This apparent gating mechanism should increase the success rate of electron transfer from MtrF to low potential environmental acceptors via these two solvent-exposed hemes.« less

Induction of Photosynthetic Carbon Fixation in Anoxia Relies on Hydrogenase Activity and Proton-Gradient Regulation-Like1-Mediated Cyclic Electron Flow in Chlamydomonas reinhardtii.

PubMed

Godaux, Damien; Bailleul, Benjamin; Berne, Nicolas; Cardol, Pierre

2015-06-01

The model green microalga Chlamydomonas reinhardtii is frequently subject to periods of dark and anoxia in its natural environment. Here, by resorting to mutants defective in the maturation of the chloroplastic oxygen-sensitive hydrogenases or in Proton-Gradient Regulation-Like1 (PGRL1)-dependent cyclic electron flow around photosystem I (PSI-CEF), we demonstrate the sequential contribution of these alternative electron flows (AEFs) in the reactivation of photosynthetic carbon fixation during a shift from dark anoxia to light. At light onset, hydrogenase activity sustains a linear electron flow from photosystem II, which is followed by a transient PSI-CEF in the wild type. By promoting ATP synthesis without net generation of photosynthetic reductants, the two AEF are critical for restoration of the capacity for carbon dioxide fixation in the light. Our data also suggest that the decrease in hydrogen evolution with time of illumination might be due to competition for reduced ferredoxins between ferredoxin-NADP(+) oxidoreductase and hydrogenases, rather than due to the sensitivity of hydrogenase activity to oxygen. Finally, the absence of the two alternative pathways in a double mutant pgrl1 hydrogenase maturation factor G-2 is detrimental for photosynthesis and growth and cannot be compensated by any other AEF or anoxic metabolic responses. This highlights the role of hydrogenase activity and PSI-CEF in the ecological success of microalgae in low-oxygen environments. © 2015 American Society of Plant Biologists. All Rights Reserved.

The aerobic respiratory chain of the acidophilic archaeon Ferroplasma acidiphilum: A membrane-bound complex oxidizing ferrous iron.

PubMed

Castelle, Cindy J; Roger, Magali; Bauzan, Marielle; Brugna, Myriam; Lignon, Sabrina; Nimtz, Manfred; Golyshina, Olga V; Giudici-Orticoni, Marie-Thérèse; Guiral, Marianne

2015-08-01

The extremely acidophilic archaeon Ferroplasma acidiphilum is found in iron-rich biomining environments and is an important micro-organism in naturally occurring microbial communities in acid mine drainage. F. acidiphilum is an iron oxidizer that belongs to the order Thermoplasmatales (Euryarchaeota), which harbors the most extremely acidophilic micro-organisms known so far. At present, little is known about the nature or the structural and functional organization of the proteins in F. acidiphilum that impact the iron biogeochemical cycle. We combine here biochemical and biophysical techniques such as enzyme purification, activity measurements, proteomics and spectroscopy to characterize the iron oxidation pathway(s) in F. acidiphilum. We isolated two respiratory membrane protein complexes: a 850 kDa complex containing an aa3-type cytochrome oxidase and a blue copper protein, which directly oxidizes ferrous iron and reduces molecular oxygen, and a 150 kDa cytochrome ba complex likely composed of a di-heme cytochrome and a Rieske protein. We tentatively propose that both of these complexes are involved in iron oxidation respiratory chains, functioning in the so-called uphill and downhill electron flow pathways, consistent with autotrophic life. The cytochrome ba complex could possibly play a role in regenerating reducing equivalents by a reverse ('uphill') electron flow. This study constitutes the first detailed biochemical investigation of the metalloproteins that are potentially directly involved in iron-mediated energy conservation in a member of the acidophilic archaea of the genus Ferroplasma. Copyright © 2015 Elsevier B.V. All rights reserved.

The End of the Line: Can Ferredoxin and Ferredoxin NADP(H) Oxidoreductase Determine the Fate of Photosynthetic Electrons?

PubMed Central

Goss, Tatjana; Hanke, Guy

2014-01-01

At the end of the linear photosynthetic electron transfer (PET) chain, the small soluble protein ferredoxin (Fd) transfers electrons to Fd:NADP(H) oxidoreductase (FNR), which can then reduce NADP+ to support C assimilation. In addition to this linear electron flow (LEF), Fd is also thought to mediate electron flow back to the membrane complexes by different cyclic electron flow (CEF) pathways: either antimycin A sensitive, NAD(P)H complex dependent, or through FNR located at the cytochrome b6f complex. Both Fd and FNR are present in higher plant genomes as multiple gene copies, and it is now known that specific Fd iso-proteins can promote CEF. In addition, FNR iso-proteins vary in their ability to dynamically interact with thylakoid membrane complexes, and it has been suggested that this may also play a role in CEF. We will highlight work on the different Fd-isoproteins and FNR-membrane association found in the bundle sheath (BSC) and mesophyll (MC) cell chloroplasts of the C4 plant maize. These two cell types perform predominantly CEF and LEF, and the properties and activities of Fd and FNR in the BSC and MC are therefore specialized for CEF and LEF respectively. A diversity of Fd isoproteins and dynamic FNR location has also been recorded in C3 plants, algae and cyanobacteria. This indicates that the principles learned from the extreme electron transport situations in the BSC and MC of maize might be usefully applied to understanding the dynamic transition between these states in other systems. PMID:24678667

Flow-Directed Crystallization for Printed Electronics.

PubMed

Qu, Ge; Kwok, Justin J; Diao, Ying

2016-12-20

The solution printability of organic semiconductors (OSCs) represents a distinct advantage for materials processing, enabling low-cost, high-throughput, and energy-efficient manufacturing with new form factors that are flexible, stretchable, and transparent. While the electronic performance of OSCs is not comparable to that of crystalline silicon, the solution processability of OSCs allows them to complement silicon by tackling challenging aspects for conventional photolithography, such as large-area electronics manufacturing. Despite this, controlling the highly nonequilibrium morphology evolution during OSC printing remains a challenge, hindering the achievement of high electronic device performance and the elucidation of structure-property relationships. Many elegant morphological control methodologies have been developed in recent years including molecular design and novel processing approaches, but few have utilized fluid flow to control morphology in OSC thin films. In this Account, we discuss flow-directed crystallization as an effective strategy for controlling the crystallization kinetics during printing of small molecule and polymer semiconductors. Introducing the concept of flow-directed crystallization to the field of printed electronics is inspired by recent advances in pharmaceutical manufacturing and flow processing of flexible-chain polymers. Although flow-induced crystallization is well studied in these areas, previous findings may not apply directly to the field of printed electronics where the molecular structures (i.e., rigid π-conjugated backbone decorated with flexible side chains) and the intermolecular interactions (i.e., π-π interactions, quadrupole interactions) of OSCs differ substantially from those of pharmaceuticals or flexible-chain polymers. Another critical difference is the important role of solvent evaporation in open systems, which defines the flow characteristics and determines the crystallization kinetics and pathways. In other words, flow-induced crystallization is intimately coupled with the mass transport processes driven by solvent evaporation during printing. In this Account, we will highlight these distinctions of flow-directed crystallization for printed electronics. In the context of solution printing of OSCs, the key issue that flow-directed crystallization addresses is the kinetics mismatch between crystallization and various transport processes during printing. We show that engineering fluid flows can tune the kinetics of OSC crystallization by expediting the nucleation and crystal growth processes, significantly enhancing thin film morphology and device performance. For small molecule semiconductors, nucleation can be enhanced and patterned by directing the evaporative flux via contact line engineering, and defective crystal growth can be alleviated by enhancing mass transport to yield significantly improved coherence length and reduced grain boundaries. For conjugated polymers, extensional and shear flow can expedite nucleation through flow-induced conformation change, facilitating the control of microphase separation, degree of crystallinity, domain alignment, and percolation. Although the nascent concept of flow-directed solution printing has not yet been widely adopted in the field of printed electronics, we anticipate that it can serve as a platform technology in the near future for improving device performance and for systematically tuning thin film morphology to construct structure-property relationships. From a fundamental perspective, it is imperative to develop a better understanding of the effects of fluid flow and mass transport on OSC crystallization as these processes are ubiquitous across all solution processing techniques and can critically impact charge transport properties.

LEAN SIX SIGMA TECHNIQUES TO IMPROVE OPHTHALMOLOGY CLINIC EFFICIENCY.

PubMed

Ciulla, Thomas A; Tatikonda, Mohan V; ElMaraghi, Yehya A; Hussain, Rehan M; Hill, Amanda L; Clary, Julie M; Hattab, Eyas

2017-07-18

Ophthalmologists serve an increasing volume of a growing elderly population undergoing increasingly complex outpatient medical care, including extensive diagnostic testing and treatment. The resulting prolonged patient visit times ("patient flow times") limit quality, patient and employee satisfaction, and represent waste. Lean Six Sigma process improvement was used in a vitreoretinal practice to decrease patient flow time, demonstrating that this approach can yield significant improvement in health care. Process flow maps were created to determine the most common care pathways within clinic. Three months' visits from the electronic medical record system, which tracks patient task times at each process step in the office were collected. Care tasks and care pathways consuming the greatest time and variation were identified and modified. Follow-up analysis from 6 weeks' visits was conducted to assess improvement. Nearly all patients took one of five paths through the office. Patient flow was redesigned to reduce waiting room time by having staff members immediately start patients into one of those five paths; staffing was adjusted to address high demand tasks, and scheduling was optimized around derived predictors of patient flow times. Follow-up analysis revealed a statistically significant decline in mean patient flow time by 18% and inpatient flow time SD by 4.6%. Patient and employee satisfaction scores improved. Manufacturing industry techniques, such as Lean and Six Sigma, can be used to improve patient care, minimize waste, and enhance patient and staff satisfaction in outpatient clinics.

Appearance of an Alternate Pathway Cyanide-resistant during Germination of Seeds of Cicer arietinum

PubMed Central

Burguillo, Placido De La Fuente; Nicolás, Gregorio

1977-01-01

The combined action of the inhibitors antimycin A and cyanide with benzohydroxamic acid indicates the presence of a cyanide-resistant pathway of respiration in chick pea (Cicer arietinum L.) seeds. The appearance of this pathway takes place during germination. During the first 12 hours of germination, the respiration is predominantly cyanide-sensitive, showing after this time a shift to an “alternate” respiration which is sensitive to benzohydroxamic acid, reaching the maximal cyanide resistance between 72 and 96 hours of germination. The appearance of the alternate pathway is initiated by high O2 concentrations and depends on cytoplasmic protein synthesis, since its appearance is inhibited by cycloheximide but not by chloramphenicol. Actinomycin D has no effect on the appearance of the alternate pathway. Our results indicate, in agreement with other authors, that the branching point is located between the flavoproteins and cytochromes b, probably at the level of ubiquinone, but the possibility of more than one branching point of the electron flow is also considered. PMID:16660130

Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans

DOE PAGES

Nazem-Bokaee, Hadi; Gopalakrishnan, Saratram; Ferry, James G.; ...

2016-01-17

Methanosarcina acetivorans is a model archaeon with renewed interest due to its unique reversible methane production pathways. However, the mechanism and relevant pathways implicated in (co)utilizing novel carbon substrates in this organism are still not fully understood. This paper provides a comprehensive inventory of thermodynamically feasible routes for anaerobic methane oxidation, co-reactant utilization, and maximum carbon yields of major biofuel candidates by M. acetivorans. Here, an updated genome-scale metabolic model of M. acetivorans is introduced (iMAC868 containing 868 genes, 845 reactions, and 718 metabolites) by integrating information from two previously reconstructed metabolic models (i.e., iVS941 and iMB745), modifying 17 reactions,more » adding 24 new reactions, and revising 64 gene-proteinreaction associations based on newly available information. The new model establishes improved predictions of growth yields on native substrates and is capable of correctly predicting the knockout outcomes for 27 out of 28 gene deletion mutants. By tracing a bifurcated electron flow mechanism, the iMAC868 model predicts thermodynamically feasible (co)utilization pathway of methane and bicarbonate using various terminal electron acceptors through the reversal of the aceticlastic pathway. In conclusion, this effort paves the way in informing the search for thermodynamically feasible ways of (co)utilizing novel carbon substrates in the domain Archaea.« less

Removing organic matter from sulfate-rich wastewater via sulfidogenic and methanogenic pathways.

PubMed

Vilela, Rogerio Silveira; Damianovic, Márcia Helena Rissato Zamariolli; Foresti, Eugenio

2014-01-01

The simultaneous organic matter removal and sulfate reduction in synthetic sulfate-rich wastewater was evaluated for various chemical oxygen demand (COD)/sulfate ratios applied in a horizontal-flow anaerobic immobilized sludge (HAIS) reactor. At higher COD/sulfate ratios (12.5 and 7.5), the removal of organic matter was stable, likely due to methanogenesis. A combination of sulfate reduction and methanogenesis was clearly established at COD/sulfate ratios of 3.0 and 1.9. At a COD/sulfate ratio of 1.0, the organic matter removal was likely influenced by methanogenesis inhibition. The quantity of sulfate removed at a COD/sulfate ratio of 1.0 was identical to that obtained at a ratio of 1.9, indicating a lack of available electron donors for sulfidogenesis. The sulfate reduction and organic matter removal were not maximized at the same COD/sulfate ratio; therefore, competitive inhibition must be the predominant mechanism in establishing an electron flow.

Dissolution-Driven Permeability Reduction of a Fractured Carbonate Caprock

PubMed Central

Ellis, Brian R.; Fitts, Jeffrey P.; Bromhal, Grant S.; McIntyre, Dustin L.; Tappero, Ryan; Peters, Catherine A.

2013-01-01

Abstract Geochemical reactions may alter the permeability of leakage pathways in caprocks, which serve a critical role in confining CO2 in geologic carbon sequestration. A caprock specimen from a carbonate formation in the Michigan sedimentary Basin was fractured and studied in a high-pressure core flow experiment. Inflowing brine was saturated with CO2 at 40°C and 10 MPa, resulting in an initial pH of 4.6, and had a calcite saturation index of −0.8. Fracture permeability decreased during the experiment, but subsequent analyses did not reveal calcite precipitation. Instead, experimental observations indicate that calcite dissolution along the fracture pathway led to mobilization of less soluble mineral particles that clogged the flow path. Analyses of core sections via electron microscopy, synchrotron-based X-ray diffraction imaging, and the first application of microbeam Ca K-edge X-ray absorption near edge structure, provided evidence that these occlusions were fragments from the host rock rather than secondary precipitates. X-ray computed tomography showed a significant loss of rock mass within preferential flow paths, suggesting that dissolution also removed critical asperities and caused mechanical closure of the fracture. The decrease in fracture permeability despite a net removal of material along the fracture pathway demonstrates a nonintuitive, inverse relationship between dissolution and permeability evolution in a fractured carbonate caprock. PMID:23633894

Control of electron transport routes through redox-regulated redistribution of respiratory complexes

PubMed Central

Liu, Lu-Ning; Bryan, Samantha J.; Huang, Fang; Yu, Jianfeng; Nixon, Peter J.; Rich, Peter R.; Mullineaux, Conrad W.

2012-01-01

In cyanobacteria, respiratory electron transport takes place in close proximity to photosynthetic electron transport, because the complexes required for both processes are located within the thylakoid membranes. The balance of electron transport routes is crucial for cell physiology, yet the factors that control the predominance of particular pathways are poorly understood. Here we use a combination of tagging with green fluorescent protein and confocal fluorescence microscopy in live cells of the cyanobacterium Synechococcus elongatus PCC 7942 to investigate the distribution on submicron scales of two key respiratory electron donors, type-I NAD(P)H dehydrogenase (NDH-1) and succinate dehydrogenase (SDH). When cells are grown under low light, both complexes are concentrated in discrete patches in the thylakoid membranes, about 100–300 nm in diameter and containing tens to hundreds of complexes. Exposure to moderate light leads to redistribution of both NDH-1 and SDH such that they become evenly distributed within the thylakoid membranes. The effects of electron transport inhibitors indicate that redistribution of respiratory complexes is triggered by changes in the redox state of an electron carrier close to plastoquinone. Redistribution does not depend on de novo protein synthesis, and it is accompanied by a major increase in the probability that respiratory electrons are transferred to photosystem I rather than to a terminal oxidase. These results indicate that the distribution of complexes on the scale of 100–300 nm controls the partitioning of reducing power and that redistribution of electron transport complexes on these scales is a physiological mechanism to regulate the pathways of electron flow. PMID:22733774

[Molecular responses of photosynthetic apparatus of plants to long term irradiance changes].

PubMed

Adamiec, Małgorzata; Jackowski, Grzegorz

2008-01-01

In response to long term (at least 1-3 h) irradiance changes the responses are elicited at the level of structure and function of photosynthetic apparatus of plants which are thought to be aimed to keep the balance between the level of excitation energy funneled to the reaction centers of the photosystems by energetic antennae and the utilization of this energy in the form of photosynthetic electron transfer and dark reactions. At high vs medium irradiances the rate of excitation energy transfer via LHCII is reduced while the rate of electron flow and photosynthetic dark reactions is increased. The reaction at LHCII level stems from the reduction of its pool per PSII reaction center and the regulatory events comprise changes in the expression of LHCII apoproteins and/or chi b biosynthesis. The basis for higher electron flow capabilities lies in significant increases in the content of some electron carriers and the catalytic activity of ATP synthase. The upregulation of photosynthetic dark reaction in turn is due to the activation of signaling pathways leading to the increase in the pool and catalytic activities of rubisco and other Calvin cycle enzymes.

Atomic Resolution Modeling of the Ferredoxin:[FeFe] Hydrogenase Complex from Chlamydomonas reinhardtii

PubMed Central

Chang, Christopher H.; King, Paul W.; Ghirardi, Maria L.; Kim, Kwiseon

2007-01-01

The [FeFe] hydrogenases HydA1 and HydA2 in the green alga Chlamydomonas reinhardtii catalyze the final reaction in a remarkable metabolic pathway allowing this photosynthetic organism to produce H2 from water in the chloroplast. A [2Fe-2S] ferredoxin is a critical branch point in electron flow from Photosystem I toward a variety of metabolic fates, including proton reduction by hydrogenases. To better understand the binding determinants involved in ferredoxin:hydrogenase interactions, we have modeled Chlamydomonas PetF1 and HydA2 based on amino-acid sequence homology, and produced two promising electron-transfer model complexes by computational docking. To characterize these models, quantitative free energy calculations at atomic resolution were carried out, and detailed analysis of the interprotein interactions undertaken. The protein complex model we propose for ferredoxin:HydA2 interaction is energetically favored over the alternative candidate by 20 kcal/mol. This proposed model of the electron-transfer complex between PetF1 and HydA2 permits a more detailed view of the molecular events leading up to H2 evolution, and suggests potential mutagenic strategies to modulate electron flow to HydA2. PMID:17660315

Atomic resolution modeling of the ferredoxin:[FeFe] hydrogenase complex from Chlamydomonas reinhardtii.

PubMed

Chang, Christopher H; King, Paul W; Ghirardi, Maria L; Kim, Kwiseon

2007-11-01

The [FeFe] hydrogenases HydA1 and HydA2 in the green alga Chlamydomonas reinhardtii catalyze the final reaction in a remarkable metabolic pathway allowing this photosynthetic organism to produce H(2) from water in the chloroplast. A [2Fe-2S] ferredoxin is a critical branch point in electron flow from Photosystem I toward a variety of metabolic fates, including proton reduction by hydrogenases. To better understand the binding determinants involved in ferredoxin:hydrogenase interactions, we have modeled Chlamydomonas PetF1 and HydA2 based on amino-acid sequence homology, and produced two promising electron-transfer model complexes by computational docking. To characterize these models, quantitative free energy calculations at atomic resolution were carried out, and detailed analysis of the interprotein interactions undertaken. The protein complex model we propose for ferredoxin:HydA2 interaction is energetically favored over the alternative candidate by 20 kcal/mol. This proposed model of the electron-transfer complex between PetF1 and HydA2 permits a more detailed view of the molecular events leading up to H(2) evolution, and suggests potential mutagenic strategies to modulate electron flow to HydA2.

PSI Mehler reaction is the main alternative photosynthetic electron pathway in Symbiodinium sp., symbiotic dinoflagellates of cnidarians.

PubMed

Roberty, Stéphane; Bailleul, Benjamin; Berne, Nicolas; Franck, Fabrice; Cardol, Pierre

2014-10-01

Photosynthetic organisms have developed various photoprotective mechanisms to cope with exposure to high light intensities. In photosynthetic dinoflagellates that live in symbiosis with cnidarians, the nature and relative amplitude of these regulatory mechanisms are a matter of debate. In our study, the amplitude of photosynthetic alternative electron flows (AEF) to oxygen (chlororespiration, Mehler reaction), the mitochondrial respiration and the Photosystem I (PSI) cyclic electron flow were investigated in strains belonging to three clades (A1, B1 and F1) of Symbiodinium. Cultured Symbiodinium strains were maintained under identical environmental conditions, and measurements of oxygen evolution, fluorescence emission and absorption changes at specific wavelengths were used to evaluate PSI and PSII electron transfer rates (ETR). A light- and O2 -dependent ETR was observed in all strains. This electron transfer chain involves PSII and PSI and is insensitive to inhibitors of mitochondrial activity and carbon fixation. We demonstrate that in all strains, the Mehler reaction responsible for photoreduction of oxygen by the PSI under high light, is the main AEF at the onset and at the steady state of photosynthesis. This sustained photosynthetic AEF under high light intensities acts as a photoprotective mechanism and leads to an increase of the ATP/NADPH ratio. © 2014 The Authors New Phytologist © 2014 New Phytologist Trust.

Hydrogeophysical imaging of deposit heterogeneity and groundwater chemistry changes during DNAPL source zone bioremediation.

PubMed

Chambers, J E; Wilkinson, P B; Wealthall, G P; Loke, M H; Dearden, R; Wilson, R; Allen, D; Ogilvy, R D

2010-10-21

Robust characterization and monitoring of dense nonaqueous phase liquid (DNAPL) source zones is essential for designing effective remediation strategies, and for assessing the efficacy of treatment. In this study high-resolution cross-hole electrical resistivity tomography (ERT) was evaluated as a means of monitoring a field-scale in-situ bioremediation experiment, in which emulsified vegetable oil (EVO) electron donor was injected into a trichloroethene source zone. Baseline ERT scans delineated the geometry of the interface between the contaminated alluvial aquifer and the underlying mudstone bedrock, and also the extent of drilling-induced physical heterogeneity. Time-lapse ERT images revealed major preferential flow pathways in the source and plume zones, which were corroborated by multiple lines of evidence, including geochemical monitoring and hydraulic testing using high density multilevel sampler arrays within the geophysical imaging planes. These pathways were shown to control the spatial distribution of the injected EVO, and a bicarbonate buffer introduced into the cell for pH control. Resistivity signatures were observed within the preferential flow pathways that were consistent with elevated chloride levels, providing tentative evidence from ERT of the biodegradation of chlorinated solvents. Copyright © 2010 S. Yamamoto. Published by Elsevier B.V. All rights reserved.

Involvement of cyclic electron flow in irradiance stress responding and its potential regulation of the mechanisms in Pyropia yezoensis

NASA Astrophysics Data System (ADS)

Niu, Jianfeng; Feng, Jianhua; Xie, Xiujun; Gao, Shan; Wang, Guangce

2016-07-01

Pyropia yezoensis, belongs to the genus of Porphyra before 2011, inhabit on intertidal zone rocks where irradiation changes dramatically, implying that the seaweed has gained certain mechanisms to survive a harsh environment. Based on the photosynthetic parameters with or without the inhibitors determined by a Dual-PAM-100 apparatus, we investigated the photosynthetic performance and the changes in electron flow that occurred during the algae were stressed with different light intensities previously. When the irradiation saturation was approaching, the CEF around PS I became crucial since the addition of inhibitors usually led to an increase in non-photochemical quenching. The inhibitor experiments showed that there were at least three different CEF pathways in Py. yezoensis and these pathways compensated each other. In addition to maintaining a proper ratio of ATP/NAD(P)H to support efficient photosynthesis, the potential roles of CEF might also include the regulation of different photoprotective mechanisms in Py. yezoensis. Under the regulation of CEF, chlororespiration is thought to transport electrons from the reduced plastoquinone (PQ) pool to oxygen in order to mitigate the reduction in the electron transfer chain. When irradiation was up to the high-grade stress conditions, the relative value of CEF began to decrease, which implied that the NADP+ pool or PQ+ pool was very small and that the electrons were transferred from reduced PS I to oxygen. The scavenging enzymes might be activated and the water-water cycle probably became an effective means of removing the active oxygen produced by the irradiation stressed Py. yezoensis. We believe that the different mechanisms could make up the photoprotective network to allow Py. yezoensis for survival in a highly variable light stress habitat, which may enlighten scientists in future studies on irradiance stress in other algae species.

Impacts of genetically engineered alterations in carbon sink pathways on photosynthetic performance

DOE PAGES

Holland, Steven C.; Artier, Juliana; Miller, Neil T.; ...

2016-10-05

Genetic engineering of photosynthetic organisms typically redirects native metabolism towards desirable products, which thereby represent new metabolic sinks. There is limited information on how these modifications impact the evolved mechanisms of photosynthetic energy metabolism and cellular growth. Two engineered strains of Synechocystis sp. PCC 6803 with altered carbon sink capacity were assayed for their photosynthetic and CO 2 concentrating mechanism properties in conditions of high and low inorganic carbon (Ci) availability. In the ΔglgC mutant, glycogen cannot be synthesized and a carbon sink pathway has been effectively removed. The JU547 strain has been engineered by integration of the Pseudomonas syringaemore » ethylene forming enzyme and provides a new sink. When cultured under high carbon conditions, ΔglgC displayed diminished photochemical efficiency, a more reduced NADPH pool, delayed initiation of the Calvin-Benson-Bassham cycle, and impairment of linear and cyclic electron flows. It also exhibited a large decrease in photochemical quenching indicative of the accumulation of Q A-, normally associated with a reduced PQ pool, but appears instead to be the result of an undefined dissipative mechanism to spill excess energy. In the case of carbon sink integration, JU547 displayed slightly more oxidized PQ and NADPH pools and increased rates of cyclic electron flow and an enhanced demand for inorganic carbon as suggested by increase in the expression of the bicarbonate transporter, SbtA. Overall, the results highlight the importance of the native regulatory network of autotrophic metabolism in governing photosynthetic performance and provide cogent examples of both predicable and difficult to predict phenotypic consequences upon installation of new pathways in autotrophs.« less

Microelectrode-based technology for the detection of low levels of bacteria

NASA Technical Reports Server (NTRS)

Rogers, Tom D.; Hitchens, G. D.; Mishra, S. K.; Pierson, D. L.

1992-01-01

A microelectrode-based electrochemical detection method was used for quantitation of bacteria in water samples. The redox mediator, benzoquinone, was used to accept electrons from the bacterial metabolic pathway to create a flow of electrons by reducing the mediator. Electrochemical monitoring electrodes detected the reduced mediator as it diffused out of the cells and produced a small electrical current. By using a combination of microelectrodes and monitoring instrumentation, the cumulative current generated by a particular bacterial population could be monitored. Using commercially available components, an electrochemical detection system was assembled and tested to evaluate its potential as an emerging technology for rapid detection and quantitation of bacteria in water samples.

Importance of the alternative oxidase (AOX) pathway in regulating cellular redox and ROS homeostasis to optimize photosynthesis during restriction of the cytochrome oxidase pathway in Arabidopsis thaliana

PubMed Central

Vishwakarma, Abhaypratap; Tetali, Sarada Devi; Selinski, Jennifer; Scheibe, Renate; Padmasree, Kollipara

2015-01-01

Background and Aims The importance of the alternative oxidase (AOX) pathway, particularly AOX1A, in optimizing photosynthesis during de-etiolation, under elevated CO2, low temperature, high light or combined light and drought stress is well documented. In the present study, the role of AOX1A in optimizing photosynthesis was investigated when electron transport through the cytochrome c oxidase (COX) pathway was restricted at complex III. Methods Leaf discs of wild-type (WT) and aox1a knock-out mutants of Arabidopsis thaliana were treated with antimycin A (AA) under growth-light conditions. To identify the impact of AOX1A deficiency in optimizing photosynthesis, respiratory O2 uptake and photosynthesis-related parameters were measured along with changes in redox couples, reactive oxygen species (ROS), lipid peroxidation and expression levels of genes related to respiration, the malate valve and the antioxidative system. Key Results In the absence of AA, aox1a knock-out mutants did not show any difference in physiological, biochemical or molecular parameters compared with WT. However, after AA treatment, aox1a plants showed a significant reduction in both respiratory O2 uptake and NaHCO3-dependent O2 evolution. Chlorophyll fluorescence and P700 studies revealed that in contrast to WT, aox1a knock-out plants were incapable of maintaining electron flow in the chloroplastic electron transport chain, and thereby inefficient heat dissipation (low non-photochemical quenching) was observed. Furthermore, aox1a mutants exhibited significant disturbances in cellular redox couples of NAD(P)H and ascorbate (Asc) and consequently accumulation of ROS and malondialdehyde (MDA) content. By contrast, WT plants showed a significant increase in transcript levels of CSD1, CAT1, sAPX, COX15 and AOX1A in contrast to aox1a mutants. Conclusions These results suggest that AOX1A plays a significant role in sustaining the chloroplastic redox state and energization to optimize photosynthesis by regulating cellular redox homeostasis and ROS generation when electron transport through the COX pathway is disturbed at complex III. PMID:26292995

Modeling a Field Application of In Situ Bioremediation of Perchlorate-Contaminated Groundwater Using Horizontal Flow Treatment Wells (HFTWs)

DTIC Science & Technology

2004-03-01

the side effects of chemotherapy (Urbansky, 1998). As a result of several cases of aplastic anemia having been discovered in patients who were...Cl-) and oxygen (O2). The first two of 7 these reductive steps requires the presence of an electron donor, such as acetate, lactate , ethanol... Chile , is the only confirmed natural source of perchlorate (Bohlke et al., 1997; USEPA, 2001; Urbansky, 2002). The principal pathway by which

Malignant human cell transformation of Marcellus Shale gas drilling flow back water

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

Yao, Yixin; Department of Environmental Medicine, New York University School of Medicine, Tuxedo, NY 10987; Chen, Tingting

The rapid development of high-volume horizontal hydraulic fracturing for mining natural gas from shale has posed potential impacts on human health and biodiversity. The produced flow back waters after hydraulic stimulation are known to carry high levels of saline and total dissolved solids. To understand the toxicity and potential carcinogenic effects of these wastewaters, flow back waters from five Marcellus hydraulic fracturing oil and gas wells were analyzed. The physicochemical nature of these samples was analyzed by inductively coupled plasma mass spectrometry and scanning electron microscopy/energy dispersive X-ray spectroscopy. A cytotoxicity study using colony formation as the endpoint was carriedmore » out to define the LC{sub 50} values of test samples using human bronchial epithelial cells (BEAS-2B). The BEAS-2B cell transformation assay was employed to assess the carcinogenic potential of the samples. Barium and strontium were among the most abundant metals in these samples and the same metals were found to be elevated in BEAS-2B cells after long-term treatment. BEAS-2B cells treated for 6 weeks with flow back waters produced colony formation in soft agar that was concentration dependent. In addition, flow back water-transformed BEAS-2B cells show better migration capability when compared to control cells. This study provides information needed to assess the potential health impact of post-hydraulic fracturing flow back waters from Marcellus Shale natural gas mining. - Highlights: • This is the first report of potential cytotoxicity and transforming activity of Marcellus shale gas mining flow back to mammalian cells. • Barium and Strontium were elevated in flow back water exposed cells. • Flow back water malignantly transformed cells and formed tumor in athymic nude mice. • Flow back transformed cells exhibited altered transcriptome with dysregulated cell migration pathway and adherent junction pathway.« less

Extremely efficient internal exciton dissociation through edge states in layered 2D perovskites

NASA Astrophysics Data System (ADS)

Blancon, J.-C.; Tsai, H.; Nie, W.; Stoumpos, C. C.; Pedesseau, L.; Katan, C.; Kepenekian, M.; Soe, C. M. M.; Appavoo, K.; Sfeir, M. Y.; Tretiak, S.; Ajayan, P. M.; Kanatzidis, M. G.; Even, J.; Crochet, J. J.; Mohite, A. D.

2017-03-01

Understanding and controlling charge and energy flow in state-of-the-art semiconductor quantum wells has enabled high-efficiency optoelectronic devices. Two-dimensional (2D) Ruddlesden-Popper perovskites are solution-processed quantum wells wherein the band gap can be tuned by varying the perovskite-layer thickness, which modulates the effective electron-hole confinement. We report that, counterintuitive to classical quantum-confined systems where photogenerated electrons and holes are strongly bound by Coulomb interactions or excitons, the photophysics of thin films made of Ruddlesden-Popper perovskites with a thickness exceeding two perovskite-crystal units (>1.3 nanometers) is dominated by lower-energy states associated with the local intrinsic electronic structure of the edges of the perovskite layers. These states provide a direct pathway for dissociating excitons into longer-lived free carriers that substantially improve the performance of optoelectronic devices.

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

Blancon, Jean -Christophe Robert; Tsai, Hsinhan; Nie, Wanyi

Understanding and controlling charge and energy flow in state-of-the-art semiconductor quantum wells has enabled high-efficiency optoelectronic devices. Two-dimensional (2D) Ruddlesden-Popper perovskites are solution-processed quantum wells wherein the band gap can be tuned by varying the perovskite-layer thickness, which modulates the effective electron-hole confinement. We report that, counterintuitive to classical quantum-confined systems where photogenerated electrons and holes are strongly bound by Coulomb interactions or excitons, the photophysics of thin films made of Ruddlesden-Popper perovskites with a thickness exceeding two perovskite-crystal units (>1.3 nanometers) is dominated by lower-energy states associated with the local intrinsic electronic structure of the edges of the perovskitemore » layers. Furthermore, these states provide a direct pathway for dissociating excitons into longer-lived free carriers that substantially improve the performance of optoelectronic devices.« less

[Regulation effects of short sunlight on two electron transport pathways in nectarine flower bud during dormancy induction].

PubMed

Li, Dong-Mei; Zhang, Hai-Sen; Tan, Qiu-Ping; Li, Ling; Yu, Qin; Gao, Dong-Sheng

2011-11-01

Taking the nectarine variety 'Shuguang' (Prunus persica var. nectariana cv. Shuguang) as test material, and by using respiration inhibitors KCN and SHAM, this paper studied the cytochrome electron transport pathway and the alternative respiration pathway in nectarine flower bud during dormancy induction under the effects of short sunlight. Both the total respiration rate (V(t)) and the cytochrome electron transport pathway respiration rate (rho' V(cyt)) presented double hump-shaped variation. Short sunlight brought the first-hump of V(t) and rho' V(cyt), forward and delayed the second-hump synchronously, inhibited the rho' V(cyt), but had no significant effects on the V(t). The capacity (V(alt)) and activity (rho V (alt)) of alternative respiration pathway also varied in double hump-shape, and the variation was basically in synchronous. Short sunlight made the first climax of V(alt) and rhoV(alt) advanced, but had little effects on the later period climax. The inhibition of cytochrome electron transport pathway and the enhancement of alternative respiration pathway were the important features of nectarine flower bud during dormancy induction, and according to the respective contributions of the two electron transport pathways to the total respiration rate, the cytochrome electron transport pathway was still the main pathway of electron transport, whereas the alternative respiration pathway played an auxiliary and branched role.

Connection between the membrane electron transport system and Hyn hydrogenase in the purple sulfur bacterium, Thiocapsa roseopersicina BBS.

PubMed

Tengölics, Roland; Mészáros, Lívia; Győri, E; Doffkay, Zsolt; Kovács, Kornél L; Rákhely, Gábor

2014-10-01

Thiocapsa. roseopersicina BBS has four active [NiFe] hydrogenases, providing an excellent opportunity to examine their metabolic linkages to the cellular redox processes. Hyn is a periplasmic membrane-associated hydrogenase harboring two additional electron transfer subunits: Isp1 is a transmembrane protein, while Isp2 is located on the cytoplasmic side of the membrane. In this work, the connection of HynSL to various electron transport pathways is studied. During photoautotrophic growth, electrons, generated from the oxidation of thiosulfate and sulfur, are donated to the photosynthetic electron transport chain via cytochromes. Electrons formed from thiosulfate and sulfur oxidation might also be also used for Hyn-dependent hydrogen evolution which was shown to be light and proton motive force driven. Hyn-linked hydrogen uptake can be promoted by both sulfur and nitrate. The electron flow from/to HynSL requires the presence of Isp2 in both directions. Hydrogenase-linked sulfur reduction could be inhibited by a QB site competitive inhibitor, terbutryne, suggesting a redox coupling between the Hyn hydrogenase and the photosynthetic electron transport chain. Based on these findings, redox linkages of Hyn hydrogenase are modeled. Copyright © 2014 Elsevier B.V. All rights reserved.

The Response of Nannochloropsis gaditana to Nitrogen Starvation Includes De Novo Biosynthesis of Triacylglycerols, a Decrease of Chloroplast Galactolipids, and Reorganization of the Photosynthetic Apparatus

PubMed Central

Simionato, Diana; Block, Maryse A.; La Rocca, Nicoletta; Jouhet, Juliette; Maréchal, Eric

2013-01-01

Microalgae of the genus Nannochloropsis are capable of accumulating triacylglycerols (TAGs) when exposed to nutrient limitation (in particular, nitrogen [N]) and are therefore considered promising organisms for biodiesel production. Here, after nitrogen removal from the medium, Nannochloropsis gaditana cells showed extensive triacylglycerol accumulation (38% TAG on a dry weight basis). Triacylglycerols accumulated during N deprivation harbored signatures, indicating that they mainly stemmed from freshly synthesized fatty acids, with a small proportion originating from a recycling of membrane glycerolipids. The amount of chloroplast galactoglycerolipids, which are essential for the integrity of thylakoids, decreased, while their fatty acid composition appeared to be unaltered. In starved cells, galactolipids were kept at a level sufficient to maintain chloroplast integrity, as confirmed by electron microscopy. Consistently, N-starved Nannochloropsis cells contained less photosynthetic membranes but were still efficiently performing photosynthesis. N starvation led to a modification of the photosynthetic apparatus with a change in pigment composition and a decrease in the content of all the major electron flow complexes, including photosystem II, photosystem I, and the cytochrome b6f complex. The photosystem II content was particularly affected, leading to the inhibition of linear electron flow from water to CO2. Such a reduction, however, was partially compensated for by activation of alternative electron pathways, such as cyclic electron transport. Overall, these changes allowed cells to modify their energetic metabolism in order to maintain photosynthetic growth. PMID:23457191

Extremely efficient internal exciton dissociation through edge states in layered 2D perovskites

DOE PAGES

Blancon, Jean -Christophe Robert; Tsai, Hsinhan; Nie, Wanyi; ...

2017-03-09

Understanding and controlling charge and energy flow in state-of-the-art semiconductor quantum wells has enabled high-efficiency optoelectronic devices. Two-dimensional (2D) Ruddlesden-Popper perovskites are solution-processed quantum wells wherein the band gap can be tuned by varying the perovskite-layer thickness, which modulates the effective electron-hole confinement. We report that, counterintuitive to classical quantum-confined systems where photogenerated electrons and holes are strongly bound by Coulomb interactions or excitons, the photophysics of thin films made of Ruddlesden-Popper perovskites with a thickness exceeding two perovskite-crystal units (>1.3 nanometers) is dominated by lower-energy states associated with the local intrinsic electronic structure of the edges of the perovskitemore » layers. Furthermore, these states provide a direct pathway for dissociating excitons into longer-lived free carriers that substantially improve the performance of optoelectronic devices.« less

Statistical Distribution of Inflation on Lava Flows: Analysis of Flow Surfaces on Earth and Mars

NASA Technical Reports Server (NTRS)

Glazel, L. S.; Anderson, S. W.; Stofan, E. R.; Baloga, S.

2003-01-01

The surface morphology of a lava flow results from processes that take place during the emplacement of the flow. Certain types of features, such as tumuli, lava rises and lava rise pits, are indicators of flow inflation or endogenous growth of a lava flow. Tumuli in particular have been identified as possible indicators of tube location, indicating that their distribution on the surface of a lava flow is a junction of the internal pathways of lava present during flow emplacement. However, the distribution of tumuli on lava flows has not been examined in a statistically thorough manner. In order to more rigorously examine the distribution of tumuli on a lava flow, we examined a discrete flow lobe with numerous lava rises and tumuli on the 1969 - 1974 Mauna Ulu flow at Kilauea, Hawaii. The lobe is located in the distal portion of the flow below Holei Pali, which is characterized by hummocky pahoehoe flows emplaced from tubes. We chose this flow due to its discrete nature allowing complete mapping of surface morphologies, well-defined boundaries, well-constrained emplacement parameters, and known flow thicknesses. In addition, tube locations for this Mauna Ulu flow were mapped by Holcomb (1976) during flow emplacement. We also examine the distribution of tumuli on the distal portion of the hummocky Thrainsskjoldur flow field provided by Rossi and Gudmundsson (1996). Analysis of the Mauna Ulu and Thrainsskjoldur flow lobes and the availability of high-resolution MOC images motivated us to look for possible tumuli-dominated flow lobes on the surface of Mars. We identified a MOC image of a lava flow south of Elysium Mons with features morphologically similar to tumuli. The flow is characterized by raised elliptical to circular mounds, some with axial cracks, that are similar in size to the tumuli measured on Earth. One potential avenue of determining whether they are tumuli is to look at the spatial distribution to see if any patterns similar to those of tumuli-dominated terrestrial flows can be identified. Since tumuli form by the injection of lava beneath a crust, the distribution of tumuli on a flow should represent the distribution of thermally preferred pathways beneath the surface of the crust. That distribution of thermally preferred pathways may be a function of the evolution of a basaltic lava flow. As a longer-lived flow evolves, initially broad thermally preferred pathways would evolve to narrower, more well-defined tube-like pathways. The final flow morphology clearly preserves the growth of the flow over time, with inflation features indicating pathways that were not necessarily contemporaneously active. Here, we test using statistical analysis whether this final flow morphology produces distinct distributions that can be used to readily determine the distribution of thermally preferred pathways beneath the surface of the crust.

Distal [FeS]-Cluster Coordination in [NiFe]-Hydrogenase Facilitates Intermolecular Electron Transfer

PubMed Central

Petrenko, Alexander; Stein, Matthias

2017-01-01

Biohydrogen is a versatile energy carrier for the generation of electric energy from renewable sources. Hydrogenases can be used in enzymatic fuel cells to oxidize dihydrogen. The rate of electron transfer (ET) at the anodic side between the [NiFe]-hydrogenase enzyme distal iron–sulfur cluster and the electrode surface can be described by the Marcus equation. All parameters for the Marcus equation are accessible from Density Functional Theory (DFT) calculations. The distal cubane FeS-cluster has a three-cysteine and one-histidine coordination [Fe4S4](His)(Cys)3 first ligation sphere. The reorganization energy (inner- and outer-sphere) is almost unchanged upon a histidine-to-cysteine substitution. Differences in rates of electron transfer between the wild-type enzyme and an all-cysteine mutant can be rationalized by a diminished electronic coupling between the donor and acceptor molecules in the [Fe4S4](Cys)4 case. The fast and efficient electron transfer from the distal iron–sulfur cluster is realized by a fine-tuned protein environment, which facilitates the flow of electrons. This study enables the design and control of electron transfer rates and pathways by protein engineering. PMID:28067774

Structure and stability of hexa-aqua V(III) cations in vanadium redox flow battery electrolytes.

PubMed

Vijayakumar, M; Li, Liyu; Nie, Zimin; Yang, Zhenguo; Hu, JianZhi

2012-08-07

The vanadium(III) cation structure in mixed acid based electrolyte solution from vanadium redox flow batteries is studied by (17)O and (35/37)Cl nuclear magnetic resonance (NMR) spectroscopy, electronic spectroscopy and density functional theory (DFT) based computational modelling. Both computational and experimental results reveal that the V(III) species can complex with counter anions (sulfate/chlorine) depending on the composition of its solvation sphere. By analyzing the powder precipitate it was found that the formation of sulfate complexed V(III) species is the crucial process in the precipitation reaction. The precipitation occurs through nucleation of neutral species formed through deprotonation and ion-pair formation process. However, the powder precipitate shows a multiphase nature which warrants multiple reaction pathways for precipitation reaction.

Epi-illumination optical design for fluorescence polarization measurements in flow systems.

PubMed Central

Eisert, W G; Beisker, W

1980-01-01

An epi-illumination design for fluorescence polarization measurements is introduced in flow cytometry with the optical axis orthogonally aligned to the cell stream. Various optical components and designs are discussed with respect to their influence on polarization measurements. Using the epi-configuration, paired measurements with the direction of polarization of the exciting light changed orthogonally are proposed for the compensation of system anisotropies and electronic mismatch. Large aperture corrections are employed for the excitation as well as for the emission pathway. Additional parameters such as fluorescence at 90 degrees, multiangle light scattering, and high precision cell-sizing by internally calibrated time of the flight measurements, as described previously, remain available with the design proposed here. Fluorescent latex microspheres, stained intracellular DNA, and algae have been used to test performance. PMID:7023562

Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs.

PubMed

Le, Nguyen-Quoc-Khanh; Ou, Yu-Yen

2016-07-30

Cellular respiration is a catabolic pathway for producing adenosine triphosphate (ATP) and is the most efficient process through which cells harvest energy from consumed food. When cells undergo cellular respiration, they require a pathway to keep and transfer electrons (i.e., the electron transport chain). Due to oxidation-reduction reactions, the electron transport chain produces a transmembrane proton electrochemical gradient. In case protons flow back through this membrane, this mechanical energy is converted into chemical energy by ATP synthase. The convert process is involved in producing ATP which provides energy in a lot of cellular processes. In the electron transport chain process, flavin adenine dinucleotide (FAD) is one of the most vital molecules for carrying and transferring electrons. Therefore, predicting FAD binding sites in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells. We used an independent data set to evaluate the performance of the proposed method, which had an accuracy of 69.84 %. We compared the performance of the proposed method in analyzing two newly discovered electron transport protein sequences with that of the general FAD binding predictor presented by Mishra and Raghava and determined that the accuracy of the proposed method improved by 9-45 % and its Matthew's correlation coefficient was 0.14-0.5. Furthermore, the proposed method enabled reducing the number of false positives significantly and can provide useful information for biologists. We developed a method that is based on PSSM profiles and SAAPs for identifying FAD binding sites in newly discovered electron transport protein sequences. This approach achieved a significant improvement after we added SAAPs to PSSM features to analyze FAD binding proteins in the electron transport chain. The proposed method can serve as an effective tool for predicting FAD binding sites in electron transport proteins and can help biologists understand the functions of the electron transport chain, particularly those of FAD binding sites. We also developed a web server which identifies FAD binding sites in electron transporters available for academics.

Tapping the Unused Potential of Photosynthesis with a Heterologous Electron Sink.

PubMed

Berepiki, Adokiye; Hitchcock, Andrew; Moore, C Mark; Bibby, Thomas S

2016-12-16

Increasing the efficiency of the conversion of light energy to products by photosynthesis represents a grand challenge in biotechnology. Photosynthesis is limited by the carbon-fixing enzyme Rubisco resulting in much of the absorbed energy being wasted as heat or fluorescence or lost as excess reductant via alternative electron dissipation pathways. To harness this wasted reductant, we engineered the model cyanobacterium Synechococcus PCC 7002 to express the mammalian cytochrome P450 CYP1A1 to serve as an artificial electron sink for excess electrons derived from light-catalyzed water-splitting. This improved photosynthetic efficiency by increasing the maximum rate of photosynthetic electron flow by 31.3%. A simple fluorescent assay for CYP1A1 activity demonstrated that the P450 was functional in the absence of its native reductase, that activity was light-dependent and scaled with irradiance. We show for the first time in live cells that photosynthetic reductant can be redirected to power a heterologous cytochrome P450. Furthermore, Synechococcus PCC 7002 expressing CYP1A1 degraded the herbicide atrazine, which is a widespread environmental pollutant.

Regulation of Photosynthetic Electron Transport and Photoinhibition

PubMed Central

Roach, Thomas; Krieger-Liszkay, Anja Krieger

2014-01-01

Photosynthetic organisms and isolated photosystems are of interest for technical applications. In nature, photosynthetic electron transport has to work efficiently in contrasting environments such as shade and full sunlight at noon. Photosynthetic electron transport is regulated on many levels, starting with the energy transfer processes in antenna and ending with how reducing power is ultimately partitioned. This review starts by explaining how light energy can be dissipated or distributed by the various mechanisms of non-photochemical quenching, including thermal dissipation and state transitions, and how these processes influence photoinhibition of photosystem II (PSII). Furthermore, we will highlight the importance of the various alternative electron transport pathways, including the use of oxygen as the terminal electron acceptor and cyclic flow around photosystem I (PSI), the latter which seem particularly relevant to preventing photoinhibition of photosystem I. The control of excitation pressure in combination with the partitioning of reducing power influences the light-dependent formation of reactive oxygen species in PSII and in PSI, which may be a very important consideration to any artificial photosynthetic system or technical device using photosynthetic organisms. PMID:24678670

Scenarios for Demand Growth of Metals in Electricity Generation Technologies, Cars, and Electronic Appliances

PubMed Central

2018-01-01

This study provides scenarios toward 2050 for the demand of five metals in electricity production, cars, and electronic appliances. The metals considered are copper, tantalum, neodymium, cobalt, and lithium. The study shows how highly technology-specific data on products and material flows can be used in integrated assessment models to assess global resource and metal demand. We use the Shared Socio-economic Pathways as implemented by the IMAGE integrated assessment model as a starting point. This allows us to translate information on the use of electronic appliances, cars, and renewable energy technologies into quantitative data on metal flows, through application of metal content estimates in combination with a dynamic stock model. Results show that total demand for copper, neodymium, and tantalum might increase by a factor of roughly 2 to 3.2, mostly as a result of population and GDP growth. The demand for lithium and cobalt is expected to increase much more, by a factor 10 to more than 20, as a result of future (hybrid) electric car purchases. This means that not just demographics, but also climate policies can strongly increase metal demand. This shows the importance of studying the issues of climate change and resource depletion together, in one modeling framework. PMID:29533657

Scenarios for Demand Growth of Metals in Electricity Generation Technologies, Cars, and Electronic Appliances.

PubMed

Deetman, Sebastiaan; Pauliuk, Stefan; van Vuuren, Detlef P; van der Voet, Ester; Tukker, Arnold

2018-04-17

This study provides scenarios toward 2050 for the demand of five metals in electricity production, cars, and electronic appliances. The metals considered are copper, tantalum, neodymium, cobalt, and lithium. The study shows how highly technology-specific data on products and material flows can be used in integrated assessment models to assess global resource and metal demand. We use the Shared Socio-economic Pathways as implemented by the IMAGE integrated assessment model as a starting point. This allows us to translate information on the use of electronic appliances, cars, and renewable energy technologies into quantitative data on metal flows, through application of metal content estimates in combination with a dynamic stock model. Results show that total demand for copper, neodymium, and tantalum might increase by a factor of roughly 2 to 3.2, mostly as a result of population and GDP growth. The demand for lithium and cobalt is expected to increase much more, by a factor 10 to more than 20, as a result of future (hybrid) electric car purchases. This means that not just demographics, but also climate policies can strongly increase metal demand. This shows the importance of studying the issues of climate change and resource depletion together, in one modeling framework.

Importance of the alternative oxidase (AOX) pathway in regulating cellular redox and ROS homeostasis to optimize photosynthesis during restriction of the cytochrome oxidase pathway in Arabidopsis thaliana.

PubMed

Vishwakarma, Abhaypratap; Tetali, Sarada Devi; Selinski, Jennifer; Scheibe, Renate; Padmasree, Kollipara

2015-09-01

The importance of the alternative oxidase (AOX) pathway, particularly AOX1A, in optimizing photosynthesis during de-etiolation, under elevated CO2, low temperature, high light or combined light and drought stress is well documented. In the present study, the role of AOX1A in optimizing photosynthesis was investigated when electron transport through the cytochrome c oxidase (COX) pathway was restricted at complex III. Leaf discs of wild-type (WT) and aox1a knock-out mutants of Arabidopsis thaliana were treated with antimycin A (AA) under growth-light conditions. To identify the impact of AOX1A deficiency in optimizing photosynthesis, respiratory O2 uptake and photosynthesis-related parameters were measured along with changes in redox couples, reactive oxygen species (ROS), lipid peroxidation and expression levels of genes related to respiration, the malate valve and the antioxidative system. In the absence of AA, aox1a knock-out mutants did not show any difference in physiological, biochemical or molecular parameters compared with WT. However, after AA treatment, aox1a plants showed a significant reduction in both respiratory O2 uptake and NaHCO3-dependent O2 evolution. Chlorophyll fluorescence and P700 studies revealed that in contrast to WT, aox1a knock-out plants were incapable of maintaining electron flow in the chloroplastic electron transport chain, and thereby inefficient heat dissipation (low non-photochemical quenching) was observed. Furthermore, aox1a mutants exhibited significant disturbances in cellular redox couples of NAD(P)H and ascorbate (Asc) and consequently accumulation of ROS and malondialdehyde (MDA) content. By contrast, WT plants showed a significant increase in transcript levels of CSD1, CAT1, sAPX, COX15 and AOX1A in contrast to aox1a mutants. These results suggest that AOX1A plays a significant role in sustaining the chloroplastic redox state and energization to optimize photosynthesis by regulating cellular redox homeostasis and ROS generation when electron transport through the COX pathway is disturbed at complex III. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Modular electron transfer circuits for synthetic biology

PubMed Central

Agapakis, Christina M

2010-01-01

Electron transfer is central to a wide range of essential metabolic pathways, from photosynthesis to fermentation. The evolutionary diversity and conservation of proteins that transfer electrons makes these pathways a valuable platform for engineered metabolic circuits in synthetic biology. Rational engineering of electron transfer pathways containing hydrogenases has the potential to lead to industrial scale production of hydrogen as an alternative source of clean fuel and experimental assays for understanding the complex interactions of multiple electron transfer proteins in vivo. We designed and implemented a synthetic hydrogen metabolism circuit in Escherichia coli that creates an electron transfer pathway both orthogonal to and integrated within existing metabolism. The design of such modular electron transfer circuits allows for facile characterization of in vivo system parameters with applications toward further engineering for alternative energy production. PMID:21468209

Near-Vent, Fissure-Fed Lava Channel Network Morphologies in the Kīlauea December 1974 Flow: Implications for Differentiating Lava Construction From Fluvial Erosion on Planets

NASA Astrophysics Data System (ADS)

Bleacher, J. E.

2015-12-01

Streamlined islands are often assumed to be the product of erosion by water and are cited as evidence of aqueous flows on Mars. However, lava can build streamlined islands in a manner that is more easily explained by flow thickening followed by partial drainage of preferred lava pathways. Kīlauea's December 1974 (D1974) flow was emplaced as a broad sheet-like flow from a series of en echelon fissures across an older hummocky pāhoehoe tumulus field. The lavas surrounded the tumuli and coalesced to fill a topographic low near the basal scarp of the Koae Fault System. As these obstacles were inundated by the D1974 flow, the lava preferentially cooled around the tumuli to form a higher viscosity zone beneath a smooth crust. Stagnation of these thinner, cooler, and more viscous zones focused the flow into a series of preferred lava pathways located between the stagnant islands. Changes in the local discharge rate disrupted the crust of the flow above the lower viscosity pathways. Older tumuli adjacent to the D1974 flow display the same relief as the flow's islands and uncovered portions of this older flow are exposed at the tops of many islands, supporting an interpretation that islands were anchored by high-standing pre-flow tumuli. As the local lava supply waned, partial drainage of the preferred pathways occurred between the higher-standing surfaces anchored to the older tumuli. The resulting morphology consists of a relatively smooth flow field with thin margins that is dissected by depressed pathways or channels. This morphology resembles an erosional surface incised into a smooth plain, but actually represents an initial constructional process followed by partial drainage within a viscous lava flow. Many other Hawaiian rift zone, fissure-fed flow fields display comparable morphologies in the near vent facies, including islands, terraces, thin flow margins and a lack of well defined topographic levees along channels. Thus, branching channel networks and streamlined islands within fissure-fed flow fields on Mars could have resulted from a combination of initial flow thickening followed by partial drainage of preferred lava pathways, and therefore do not necessarily imply substrate erosion or modification by fluvial processes.

Molecular mechanism of NDMA formation from N,N-dimethylsulfamide during ozonation: quantum chemical insights into a bromide-catalyzed pathway.

PubMed

Trogolo, Daniela; Mishra, Brijesh Kumar; Heeb, Michèle B; von Gunten, Urs; Arey, J Samuel

2015-04-07

During ozonation of drinking water, the fungicide metabolite N,N-dimethylsulfamide (DMS) can be transformed into a highly toxic product, N-nitrosodimethylamine (NDMA). We used quantum chemical computations and stopped-flow experiments to evaluate a chemical mechanism proposed previously to describe this transformation. Stopped-flow experiments indicate a pK(a) = 10.4 for DMS. Experiments show that hypobromous acid (HOBr), generated by ozone oxidation of naturally occurring bromide, brominates the deprotonated DMS(-) anion with a near-diffusion controlled rate constant (7.1 ± 0.6 × 10(8) M(-1) s(-1)), forming Br-DMS(-) anion. According to quantum chemical calculations, Br-DMS has a pK(a) ∼ 9.0 and thus remains partially deprotonated at neutral pH. The anionic Br-DMS(-) bromamine can react with ozone with a high rate constant (10(5 ± 2.5) M(-1) s(-1)), forming the reaction intermediate (BrNO)(SO2)N(CH3)2(-). This intermediate resembles a loosely bound complex between an electrophilic nitrosyl bromide (BrNO) molecule and an electron-rich dimethylaminosulfinate ((SO2)N(CH3)2(-)) fragment, based on inspection of computed natural charges and geometric parameters. This fragile complex undergoes immediate (10(10 ± 2.5) s(-1)) reaction by two branches: an exothermic channel that produces NDMA, and an entropy-driven channel giving non-NDMA products. Computational results bring new insights into the electronic nature, chemical equilibria, and kinetics of the elementary reactions of this pathway, enabled by computed energies of structures that are not possible to access experimentally.

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

Holland, Steven C.; Artier, Juliana; Miller, Neil T.

Genetic engineering of photosynthetic organisms typically redirects native metabolism towards desirable products, which thereby represent new metabolic sinks. There is limited information on how these modifications impact the evolved mechanisms of photosynthetic energy metabolism and cellular growth. Two engineered strains of Synechocystis sp. PCC 6803 with altered carbon sink capacity were assayed for their photosynthetic and CO 2 concentrating mechanism properties in conditions of high and low inorganic carbon (Ci) availability. In the ΔglgC mutant, glycogen cannot be synthesized and a carbon sink pathway has been effectively removed. The JU547 strain has been engineered by integration of the Pseudomonas syringaemore » ethylene forming enzyme and provides a new sink. When cultured under high carbon conditions, ΔglgC displayed diminished photochemical efficiency, a more reduced NADPH pool, delayed initiation of the Calvin-Benson-Bassham cycle, and impairment of linear and cyclic electron flows. It also exhibited a large decrease in photochemical quenching indicative of the accumulation of Q A-, normally associated with a reduced PQ pool, but appears instead to be the result of an undefined dissipative mechanism to spill excess energy. In the case of carbon sink integration, JU547 displayed slightly more oxidized PQ and NADPH pools and increased rates of cyclic electron flow and an enhanced demand for inorganic carbon as suggested by increase in the expression of the bicarbonate transporter, SbtA. Overall, the results highlight the importance of the native regulatory network of autotrophic metabolism in governing photosynthetic performance and provide cogent examples of both predicable and difficult to predict phenotypic consequences upon installation of new pathways in autotrophs.« less

ULTRASTRUCTURAL STUDIES OF VASOPRESSIN EFFECT ON ISOLATED PERFUSED RENAL COLLECTING TUBULES OF THE RABBIT

PubMed Central

Ganote, Charles E.; Grantham, Jared J.; Moses, Harold L.; Burg, Maurice B.; Orloff, Jack

1968-01-01

Isolated cortical collecting tubules from rabbit kidney were studied during perfusion with solutions made either isotonic or hypotonic to the external bathing medium. Examination of living tubules revealed a reversible increase in thickness of the cellular layer, prominence of lateral cell membranes, and formation of intracellular vacuoles during periods of vasopressin-induced osmotic water transport. Examination in the electron microscope revealed that vasopressin induced no changes in cell structure in collecting tubules in the absence of an osmotic difference and significant bulk water flow across the tubule wall. In contrast, tubules fixed during vasopressin-induced periods of high osmotic water transport showed prominent dilatation of lateral intercellular spaces, bulging of apical cell membranes into the tubular lumen, and formation of intracellular vacuoles. It is concluded that the ultrastructural changes are secondary to transepithelial bulk water flow and not to a direct effect of vasopressin on the cells, and that vasopressin induces osmotic flow by increasing water permeability of the luminal cell membrane. The lateral intercellular spaces may be part of the pathway for osmotically induced transepithelial bulk water flow. PMID:4867134

Analysis of the magnetically induced current density of molecules consisting of annelated aromatic and antiaromatic hydrocarbon rings.

PubMed

Sundholm, Dage; Berger, Raphael J F; Fliegl, Heike

2016-06-21

Magnetically induced current susceptibilities and current pathways have been calculated for molecules consisting of two pentalene groups annelated with a benzene (1) or naphthalene (2) moiety. Current strength susceptibilities have been obtained by numerically integrating separately the diatropic and paratropic contributions to the current flow passing planes through chosen bonds of the molecules. The current density calculations provide novel and unambiguous current pathways for the unusual molecules with annelated aromatic and antiaromatic hydrocarbon moieties. The calculations show that the benzene and naphthalene moieties annelated with two pentalene units as in molecules 1 and 2, respectively, are unexpectedly antiaromatic sustaining only a local paratropic ring current around the ring, whereas a weak diatropic current flows around the C-H moiety of the benzene ring. For 1 and 2, the individual five-membered rings of the pentalenes are antiaromatic and a slightly weaker semilocal paratropic current flows around the two pentalene rings. Molecules 1 and 2 do not sustain any net global ring current. The naphthalene moiety of the molecule consisting of a naphthalene annelated with two pentalene units (3) does not sustain any strong ring current that is typical for naphthalene. Instead, half of the diatropic current passing the naphthalene moiety forms a zig-zag pattern along the C-C bonds of the naphthalene moiety that are not shared with the pentalene moieties and one third of the current continues around the whole molecule partially cancelling the very strong paratropic semilocal ring current of the pentalenes. For molecule 3, the pentalene moieties and the individual five-membered rings of the pentalenes are more antiaromatic than for 1 and 2. The calculated current patterns elucidate why the compounds with formally [4n + 2] π-electrons have unusual aromatic properties violating the Hückel π-electron count rule. The current density calculations also provide valuable information for interpreting the measured (1)H NMR spectra.

On-line metabolic pathway analysis based on metabolic signal flow diagram.

PubMed

Shi, H; Shimizu, K

In this work, an integrated modeling approach based on a metabolic signal flow diagram and cellular energetics was used to model the metabolic pathway analysis for the cultivation of yeast on glucose. This approach enables us to make a clear analysis of the flow direction of the carbon fluxes in the metabolic pathways as well as of the degree of activation of a particular pathway for the synthesis of biomaterials for cell growth. The analyses demonstrate that the main metabolic pathways of Saccharomyces cerevisiae change significantly during batch culture. Carbon flow direction is toward glycolysis to satisfy the increase of requirement for precursors and energy. The enzymatic activation of TCA cycle seems to always be at normal level, which may result in the overflow of ethanol due to its limited capacity. The advantage of this approach is that it adopts both virtues of the metabolic signal flow diagram and the simple network analysis method, focusing on the investigation of the flow directions of carbon fluxes and the degree of activation of a particular pathway or reaction loop. All of the variables used in the model equations were determined on-line; the information obtained from the calculated metabolic coefficients may result in a better understanding of cell physiology and help to evaluate the state of the cell culture process. Copyright 1998 John Wiley & Sons, Inc.

The minute virus of mice exploits different endocytic pathways for cellular uptake

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

Garcin, Pierre O.; Panté, Nelly, E-mail: pante@zoology.ubc.ca

The minute virus of mice, prototype strain (MVMp), is a non-enveloped, single-stranded DNA virus of the family Parvoviridae. Unlike other parvoviruses, the mechanism of cellular uptake of MVMp has not been studied in detail. We analyzed MVMp endocytosis in mouse LA9 fibroblasts and a tumor cell line derived from epithelial–mesenchymal transition through polyomavirus middle T antigen transformation in transgenic mice. By a combination of immunofluorescence and electron microscopy, we found that MVMp endocytosis occurs at the leading edge of migrating cells in proximity to focal adhesion sites. By using drug inhibitors of various endocytic pathways together with immunofluorescence microscopy andmore » flow cytometry analysis, we discovered that MVMp can use a number of endocytic pathways, depending on the host cell type. At least three different mechanisms were identified: clathrin-, caveolin-, and clathrin-independent carrier-mediated endocytosis, with the latter occurring in transformed cells but not in LA9 fibroblasts. - Highlights: • MVMp uptake takes place at the leading edge of migrating cells. • MVMp exploits a variety of endocytic pathways. • MVMp could use clathrin- and caveolin-mediated endocytosis. • MVMp could also use clathrin-independent carriers for cellular uptake.« less

Carbon-dependent control of electron transfer and central carbon pathway genes for methane biosynthesis in the Archaean, Methanosarcina acetivorans strain C2A

PubMed Central

2010-01-01

Background The archaeon, Methanosarcina acetivorans strain C2A forms methane, a potent greenhouse gas, from a variety of one-carbon substrates and acetate. Whereas the biochemical pathways leading to methane formation are well understood, little is known about the expression of the many of the genes that encode proteins needed for carbon flow, electron transfer and/or energy conservation. Quantitative transcript analysis was performed on twenty gene clusters encompassing over one hundred genes in M. acetivorans that encode enzymes/proteins with known or potential roles in substrate conversion to methane. Results The expression of many seemingly "redundant" genes/gene clusters establish substrate dependent control of approximately seventy genes for methane production by the pathways for methanol and acetate utilization. These include genes for soluble-type and membrane-type heterodisulfide reductases (hdr), hydrogenases including genes for a vht-type F420 non-reducing hydrogenase, molybdenum-type (fmd) as well as tungsten-type (fwd) formylmethanofuran dehydrogenases, genes for rnf and mrp-type electron transfer complexes, for acetate uptake, plus multiple genes for aha- and atp-type ATP synthesis complexes. Analysis of promoters for seven gene clusters reveal UTR leaders of 51-137 nucleotides in length, raising the possibility of both transcriptional and translational levels of control. Conclusions The above findings establish the differential and coordinated expression of two major gene families in M. acetivorans in response to carbon/energy supply. Furthermore, the quantitative mRNA measurements demonstrate the dynamic range for modulating transcript abundance. Since many of these gene clusters in M. acetivorans are also present in other Methanosarcina species including M. mazei, and in M. barkeri, these findings provide a basis for predicting related control in these environmentally significant methanogens. PMID:20178638

Impaired Mitochondrial Transcription Termination Disrupts the Stromal Redox Poise in Chlamydomonas1[OPEN

PubMed Central

Uhmeyer, Andreas

2017-01-01

In photosynthetic eukaryotes, the metabolite exchange between chloroplast and mitochondria ensures efficient photosynthesis under saturating light conditions. The Chlamydomonas reinhardtii mutant stm6 is devoid of the mitochondrial transcription termination factor MOC1 and aberrantly expresses the mitochondrial genome, resulting in enhanced photosynthetic hydrogen production and diminished light tolerance. We analyzed the modulation of mitochondrial and chlororespiration during the acclimation of stm6 and the MOC1-complemented strain to excess light. Although light stress stimulated mitochondrial respiration via the energy-conserving cytochrome c pathway in both strains, the mutant was unable to fine-tune the expression and activity of oxidative phosphorylation complex I in excess light, which was accompanied by an increased mitochondrial respiration via the alternative oxidase pathway. Furthermore, stm6 failed to fully activate chlororespiration and cyclic electron flow due to a more oxidized state of the chloroplast stroma, which is caused by an increased mitochondrial electron sink capacity. Increased susceptibility to photoinhibition of PSII in stm6 demonstrates that the MOC1-dependent modulation of mitochondrial respiration helps control the stromal redox poise as a crucial part of high-light acclimation in C. reinhardtii. PMID:28500267

NDH-Mediated Cyclic Electron Flow Around Photosystem I is Crucial for C4 Photosynthesis.

PubMed

Ishikawa, Noriko; Takabayashi, Atsushi; Noguchi, Ko; Tazoe, Youshi; Yamamoto, Hiroshi; von Caemmerer, Susanne; Sato, Fumihiko; Endo, Tsuyoshi

2016-10-01

C 4 photosynthesis exhibits efficient CO 2 assimilation in ambient air by concentrating CO 2 around ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) through a metabolic pathway called the C 4 cycle. It has been suggested that cyclic electron flow (CEF) around PSI mediated by chloroplast NADH dehydrogenase-like complex (NDH), an alternative pathway of photosynthetic electron transport (PET), plays a crucial role in C 4 photosynthesis, although the contribution of NDH-mediated CEF is small in C 3 photosynthesis. Here, we generated NDH-suppressed transformants of a C 4 plant, Flaveria bidentis, and showed that the NDH-suppressed plants grow poorly, especially under low-light conditions. CO 2 assimilation rates were consistently decreased in the NDH-suppressed plants under low and medium light intensities. Measurements of non-photochemical quenching (NPQ) of Chl fluorescence, the oxidation state of the reaction center of PSI (P700) and the electrochromic shift (ECS) of pigment absorbance indicated that proton translocation across the thylakoid membrane is impaired in the NDH-suppressed plants. Since proton translocation across the thylakoid membrane induces ATP production, these results suggest that NDH-mediated CEF plays a role in the supply of ATP which is required for C 4 photosynthesis. Such a role is more crucial when the light that is available for photosynthesis is limited and the energy production by PET becomes rate-determining for C 4 photosynthesis. Our results demonstrate that the physiological contribution of NDH-mediated CEF is greater in C 4 photosynthesis than in C 3 photosynthesis, suggesting that the mechanism of PET in C 4 photosynthesis has changed from that in C 3 photosynthesis accompanying the changes in the mechanism of CO 2 assimilation. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Land cover effects on infiltration and preferential flow pathways in the high rainfall zone of Madagascar

NASA Astrophysics Data System (ADS)

Zwartendijk, Bob; van Meerveld, Ilja; Ravelona, Maafaka; Razakamanarivo, Herintsitohaina; Ghimire, Chandra; Bruijnzeel, Sampurno; Jones, Julia

2015-04-01

Shortened slash-and-burn cycles exhaust agricultural land and have resulted in extensive tracts of highly degraded land across the tropics. Land degradation typically results in decreased rainfall infiltration due to a reduced field-saturated hydraulic conductivity of the topsoil because of a progressive decline in soil organic matter, exposure to raindrop impact, surface sealing and compaction. This results, in turn, in enhanced surface runoff and erosion, and consequently less subsurface flow and groundwater recharge. On the other hand, natural vegetation regrowth or active reforestation can lead to a renewed accumulation of soil organic matter, macropore development and increased infiltration rates. As part of the P4GES project (Can Paying 4 Global Ecosystem Services values reduce poverty?; www.p4ges.org), we study the effects of land use change and reforestation on water resources in the Corridor Ankeniheny-Zahamena (CAZ) in eastern Madagascar. In this poster, we present the results of infiltration and preferential flow measurements in four different land uses in the southern part of the CAZ: (i) closed canopy forest, (ii) 3-14 year-old regrowth on fallow land (savokas), (iii) exhausted and severely degraded land (tany maty), and (iv) recently reforested sites (6-8 years old). The results show that infiltrability increases significantly after several years of forest regrowth after land abandonment, but it remains unclear whether active replanting decreases the time required for restoration of soil hydrological functioning. Preferential flow pathways differed strikingly between the respective land cover types: infiltration in mature forests was predominantly characterized by macropore flow (preferential flow pathways), whereas infiltration in exhausted agricultural land was dominated by matrix flow (few preferential flow pathways). Occurrence of preferential flow pathways in reforestation and fallow sites varied considerably. These results suggest that land cover significantly affects hydrological flow pathways and that natural regeneration and active reforestation of degraded land can result in increased infiltration and a reduced likelihood for surface runoff.

An Inner Membrane Cytochrome Required Only for Reduction of High Redox Potential Extracellular Electron Acceptors

PubMed Central

Levar, Caleb E.; Chan, Chi Ho; Mehta-Kolte, Misha G.

2014-01-01

ABSTRACT Dissimilatory metal-reducing bacteria, such as Geobacter sulfurreducens, transfer electrons beyond their outer membranes to Fe(III) and Mn(IV) oxides, heavy metals, and electrodes in electrochemical devices. In the environment, metal acceptors exist in multiple chelated and insoluble forms that span a range of redox potentials and offer different amounts of available energy. Despite this, metal-reducing bacteria have not been shown to alter their electron transfer strategies to take advantage of these energy differences. Disruption of imcH, encoding an inner membrane c-type cytochrome, eliminated the ability of G. sulfurreducens to reduce Fe(III) citrate, Fe(III)-EDTA, and insoluble Mn(IV) oxides, electron acceptors with potentials greater than 0.1 V versus the standard hydrogen electrode (SHE), but the imcH mutant retained the ability to reduce Fe(III) oxides with potentials of ≤−0.1 V versus SHE. The imcH mutant failed to grow on electrodes poised at +0.24 V versus SHE, but switching electrodes to −0.1 V versus SHE triggered exponential growth. At potentials of ≤−0.1 V versus SHE, both the wild type and the imcH mutant doubled 60% slower than at higher potentials. Electrodes poised even 100 mV higher (0.0 V versus SHE) could not trigger imcH mutant growth. These results demonstrate that G. sulfurreducens possesses multiple respiratory pathways, that some of these pathways are in operation only after exposure to low redox potentials, and that electron flow can be coupled to generation of different amounts of energy for growth. The redox potentials that trigger these behaviors mirror those of metal acceptors common in subsurface environments where Geobacter is found. PMID:25425235

An inner membrane cytochrome required only for reduction of high redox potential extracellular electron acceptors

DOE PAGES

Levar, Caleb E.; Chan, Chi Ho; Mehta-Kolte, Misha G.; ...

2014-10-28

Dissimilatory metal-reducing bacteria, such as Geobacter sulfurreducens, transfer electrons beyond their outer membranes to Fe(III) and Mn(IV) oxides, heavy metals, and electrodes in electrochemical devices. In the environment, metal acceptors exist in multiple chelated and insoluble forms that span a range of redox potentials and offer different amounts of available energy. Despite this, metal-reducing bacteria have not been shown to alter their electron transfer strategies to take advantage of these energy differences. Disruption of imcH, encoding an inner membrane c-type cytochrome, eliminated the ability of G. sulfurreducens to reduce Fe(III) citrate, Fe(III)-EDTA, and insoluble Mn(IV) oxides, electron acceptors with potentialsmore » greater than 0.1 V versus the standard hydrogen electrode (SHE), but the imcH mutant retained the ability to reduce Fe(III) oxides with potentials of ≤–0.1 V versus SHE. The imcH mutant failed to grow on electrodes poised at +0.24 V versus SHE, but switching electrodes to –0.1 V versus SHE triggered exponential growth. At potentials of ≤–0.1 V versus SHE, both the wild type and the imcH mutant doubled 60% slower than at higher potentials. Electrodes poised even 100 mV higher (0.0 V versus SHE) could not trigger imcH mutant growth. These results demonstrate that G. sulfurreducens possesses multiple respiratory pathways, that some of these pathways are in operation only after exposure to low redox potentials, and that electron flow can be coupled to generation of different amounts of energy for growth. Redox potentials that trigger these behaviors mirror those of metal acceptors common in subsurface environments where Geobacter is found.« less

Reactive transport simulations of alternative flow pathways in the ambient unsaturated zone at Yucca Mountain, Nevada

NASA Astrophysics Data System (ADS)

Browning, L.; Murphy, W.; Manepally, C.; Fedors, R.

2003-04-01

Uncertainties in simulated ambient system unsaturated zone flow could have a significant impact on performance evaluations of the proposed nuclear waste repository at Yucca Mountain, Nevada. In addition to determining variations in the quantity of water available to corrode engineered materials and transport radionuclides, model assumptions regarding flow pathways may significantly affect estimates of groundwater chemistry. The manner and extent to which groundwater compositions evolve along a flow pathway are determined mainly by thermohydrologic conditions, the types of reactive materials encountered, and the interaction times with those materials. Simulated groundwater compositions can thus vary significantly depending on whether or not the flow model includes lateral diversion of infiltrating waters, or preferential flow pathways in variably-saturated materials. To assist a regulatory review of a potential license application for a geologic repository for high-level waste, we developed a reactive transport model for the ambient hydrogeochemical system at Yucca Mountain. The model simulates two phase, nonisothermal, advective and diffusive flow and transport through a one dimensional, matrix and fracture continua (dual permeability) containing ten kinetically reactive hydrostatigraphic layers in the vicinity of the SD-9 borehole at Yucca Mountain. In this presentation, we describe how the model was used to evaluate alternative ambient unsaturated zone flow pathways proposed by the U.S. Department of Energy. This abstract is an independent product of the CNWRA and does not necessarily reflect the views or regulatory position of the NRC.

RLIP76-dependent suppression of PI3K/AKT/Bcl-2 pathway by miR-101 induces apoptosis in prostate cancer

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

Yang, Jing; Song, Qi; Cai, Yi

MicroRNA-101 (miR-101) participates in carcinogenesis and tumor progression in various cancers. However, its biological functions in prostate cancer are still unclear. Here, we demonstrate that miR-101 represents a critical role in regulating cell apoptosis in prostate cancer cells. We first demonstrated that miR-101 treatment promoted apoptosis in DU145 and PC3 cells by using flow cytometric analysis and transmission electron microscopy (TEM). To verify the mechanisms, we identified a novel miR-101 target, Ral binding protein 1 (RLIP76). We found miR-101 transfection significantly suppresses RLIP76 expression, which can transactivate phosphorylation of PI3K-Akt signaling, and resulted in an amplification of Bcl2-induced apoptosis. Furthermore,more » we demonstrated that RLIP76 overexpression could reverse the anti-tumor effects of miR-101 in DU145 and PC3 cells by using flow cytometry assay and MTT assay. Taken together, our results revealed that the effect of miR-101 on prostate cancer cell apoptosis was due to RLIP76 regulation of the PI3K/Akt/Bcl-2 signaling pathway. - Highlights: • miR-101 inhibited prostate cancer cell proliferation and enhanced apoptosis. • miR-101 directly targeted and regulated RLIP76 expression. • miR-101 suppressed PI3K/Akt/Bcl-2 signaling pathway by targeting RLIP76.« less

Alternative mitochondrial electron transfer for the treatment of neurodegenerative diseases and cancers: Methylene blue connects the dots.

PubMed

Yang, Shao-Hua; Li, Wenjun; Sumien, Nathalie; Forster, Michael; Simpkins, James W; Liu, Ran

2017-10-01

Brain has exceptional high requirement for energy metabolism with glucose as the exclusive energy source. Decrease of brain energy metabolism and glucose uptake has been found in patients of Alzheimer's, Parkinson's and other neurodegenerative diseases, providing a clear link between neurodegenerative disorders and energy metabolism. On the other hand, cancers, including glioblastoma, have increased glucose uptake and rely on aerobic glycolysis for energy metabolism. The switch of high efficient oxidative phosphorylation to low efficient aerobic glycolysis pathway (Warburg effect) provides macromolecule for biosynthesis and proliferation. Current research indicates that methylene blue, a century old drug, can receive electron from NADH in the presence of complex I and donates it to cytochrome c, providing an alternative electron transfer pathway. Methylene blue increases oxygen consumption, decrease glycolysis, and increases glucose uptake in vitro. Methylene blue enhances glucose uptake and regional cerebral blood flow in rats upon acute treatment. In addition, methylene blue provides protective effect in neuron and astrocyte against various insults in vitro and in rodent models of Alzheimer's, Parkinson's, and Huntington's disease. In glioblastoma cells, methylene blue reverses Warburg effect by enhancing mitochondrial oxidative phosphorylation, arrests glioma cell cycle at s-phase, and inhibits glioma cell proliferation. Accordingly, methylene blue activates AMP-activated protein kinase, inhibits downstream acetyl-coA carboxylase and cyclin-dependent kinases. In summary, there is accumulating evidence providing a proof of concept that enhancement of mitochondrial oxidative phosphorylation via alternative mitochondrial electron transfer may offer protective action against neurodegenerative diseases and inhibit cancers proliferation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Heterogeneous catalytic ozonation of hydroquinone using sewage sludge-derived carbonaceous catalysts.

PubMed

Xu, Jinglu; Yu, Yang; Ding, Kang; Liu, Zhiying; Wang, Lei; Xu, Yanhua

2018-03-01

This study converted sewage sludge into a carbonaceous catalyst via pyrolysis and employed it in the ozonation of hydroquinone. The catalyst was characterized by Mössbauer spectroscopy, X-ray photoelectron spectroscopy, temperature programmed desorption, scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy and X-ray diffraction. Intermediate products were detected by gas chromatography-mass spectrometry, and a pathway for hydroquinone degradation was proposed. The results showed that sludge pyrolyzed at 700 °C promoted hydroquinone degradation, compared with commercial activated carbon derived from coal. When the catalyst dose was 0.5 g/L, the hydroquinone (200 mg/L) removal rate reached 97.86% after exposure to ozone (the ozone concentration was 17 mg/L and the flow rate was 50 mL/min) for 60 min. The results indicated that basic groups contributed to the catalysis.

Cobalt-doped carbon xerogel with different initial pH values toward oxygen reduction

NASA Astrophysics Data System (ADS)

Fitri, Azim; Loh, Kee Shyuan; Puspasari, Ifa; Mohamad, Abu Bakar

2017-12-01

In this study, cobalt-doped carbon xerogel (Co-CX) was synthesized via sol-gel polymerization resorcinol-formaldehyde, catalyzed with cobalt nitrate, followed by drying and carbonization process under nitrogen gas flow. The effect of initial pH value (5.5, 6.5 and 7.5) and the type of carbon precursors on the morphology of Co-CX have been investigated with Field Emission-Transmission Electron Microscopy (FESEM). The catalytic activity of Co-CX for the oxygen reduction reaction (ORR) in 0.1 M KOH has been studied by using a rotating ring-disk electrode (RRDE) technique. FESEM revealed that Co doping promotes the formation of more pores. While the conditions allow obtaining xerogel with higher porosity at pH 7.5. The RRDE result display that Co-CX exhibited good catalytic activity tends to favor two electrons pathway.

Cellular trafficking of low molecular weight heparin incorporated in layered double hydroxide nanoparticles in rat vascular smooth muscle cells.

PubMed

Gu, Zi; Rolfe, Barbara E; Thomas, Anita C; Campbell, Julie H; Lu, G Q Max; Xu, Zhi P

2011-10-01

This paper reports a clear elucidation of the pathway for the cellular delivery of layered double hydroxide (LDH) nanoparticles intercalated with anti-restenotic low molecular weight heparin (LMWH). Cellular uptake of LMWH-LDH conjugates into cultured rat vascular smooth muscle cells (SMCs) measured via flow cytometry was more than ten times greater than that of LMWH alone. Confocal and transmission electron microscopy showed LMWH-LDH conjugates taken up by endosomes, then released into the cytoplasm. We propose that LMWH-LDH is taken up via a unique 'modified endocytic' pathway, whereby the conjugate is internalized by SMCs in early endosomes, sorted in late endosomes, and quickly released from late endosomes/lysosomes, avoiding degradation. Treatment of cells with LMWH-LDH conjugates suppressed the activation of ERK1/2 in response to foetal calf serum (FCS) for up to 24h, unlike unconjugated LMWH which had no significant effect at 24h. Improved understanding of the intracellular pathway of LMWH-LDH nanohybrids in SMC will allow for refinement of design for LDH nanomedicine applications. Copyright © 2011 Elsevier Ltd. All rights reserved.

Communication: Probing non-equilibrium vibrational relaxation pathways of highly excited C≡N stretching modes following ultrafast back-electron transfer.

PubMed

Lynch, Michael S; Slenkamp, Karla M; Khalil, Munira

2012-06-28

Fifth-order nonlinear visible-infrared spectroscopy is used to probe coherent and incoherent vibrational energy relaxation dynamics of highly excited vibrational modes indirectly populated via ultrafast photoinduced back-electron transfer in a trinuclear cyano-bridged mixed-valence complex. The flow of excess energy deposited into four C≡N stretching (ν(CN)) modes of the molecule is monitored by performing an IR pump-probe experiment as a function of the photochemical reaction (τ(vis)). Our results provide experimental evidence that the nuclear motions of the molecule are both coherently and incoherently coupled to the electronic charge transfer process. We observe that intramolecular vibrational relaxation dynamics among the highly excited ν(CN) modes change significantly en route to equilibrium. The experiment also measures a 7 cm(-1) shift in the frequency of a ∼57 cm(-1) oscillation reflecting a modulation of the coupling between the probed high-frequency ν(CN) modes for τ(vis) < 500 fs.

Inhibition of ERK1/2 or AKT Activity Equally Enhances Radiation Sensitization in B16F10 Cells.

PubMed

Kalal, Bhuvanesh Sukhlal; Fathima, Faraz; Pai, Vinitha Ramanath; Sanjeev, Ganesh; Krishna, Chilakapati Murali; Upadhya, Dinesh

2018-02-01

The aim of the study was to evaluate the radiation sensitizing ability of ERK1/2, PI3K-AKT and JNK inhibitors in highly radiation resistant and metastatic B16F10 cells which carry wild-type Ras and Braf . Mouse melanoma cell line B16F10 was exposed to 1.0, 2.0 and 3.0 Gy of electron beam radiation. Phosphorylated ERK1/2, AKT and JNK levels were estimated by ELISA. Cells were exposed to 2.0 and 3.0 Gy of radiation with or without prior pharmacological inhibition of ERK1/2, AKT as well as JNK pathways. Cell death induced by radiation as well as upon inhibition of these pathways was measured by TUNEL assay using flow cytometry. Exposure of B16F10 cells to 1.0, 2.0 and 3.0 Gy of electron beam irradiation triggered an increase in all the three phosphorylated proteins compared to sham-treated and control groups. B16F10 cells pre-treated with either ERK1/2 or AKT inhibitors equally enhanced radiation-induced cell death at 2.0 as well as 3.0 Gy (P < 0.001), while inhibition of JNK pathway increased radiation-induced cell death to a lesser extent. Interestingly combined inhibition of ERK1/2 or AKT pathways did not show additional cell death compared to individual ERK1/2 or AKT inhibition. This indicates that ERK1/2 or AKT mediates radiation resistance through common downstream molecules in B16F10 cells. Even without activating mutations in Ras or Braf genes, ERK1/2 and AKT play a critical role in B16F10 cell survival upon radiation exposure and possibly act through common downstream effector/s.

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

21 CFR 880.2420 - Electronic monitor for gravity flow infusion systems.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Electronic monitor for gravity flow infusion... and Personal Use Monitoring Devices § 880.2420 Electronic monitor for gravity flow infusion systems. (a) Identification. An electronic monitor for gravity flow infusion systems is a device used to...

21 CFR 880.2420 - Electronic monitor for gravity flow infusion systems.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Electronic monitor for gravity flow infusion... and Personal Use Monitoring Devices § 880.2420 Electronic monitor for gravity flow infusion systems. (a) Identification. An electronic monitor for gravity flow infusion systems is a device used to...

21 CFR 880.2420 - Electronic monitor for gravity flow infusion systems.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Electronic monitor for gravity flow infusion... and Personal Use Monitoring Devices § 880.2420 Electronic monitor for gravity flow infusion systems. (a) Identification. An electronic monitor for gravity flow infusion systems is a device used to...

21 CFR 880.2420 - Electronic monitor for gravity flow infusion systems.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Electronic monitor for gravity flow infusion... and Personal Use Monitoring Devices § 880.2420 Electronic monitor for gravity flow infusion systems. (a) Identification. An electronic monitor for gravity flow infusion systems is a device used to...

21 CFR 880.2420 - Electronic monitor for gravity flow infusion systems.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Electronic monitor for gravity flow infusion... and Personal Use Monitoring Devices § 880.2420 Electronic monitor for gravity flow infusion systems. (a) Identification. An electronic monitor for gravity flow infusion systems is a device used to...

Quantum Electron Tunneling in Respiratory Complex I1

PubMed Central

Hayashi, Tomoyuki; Stuchebrukhov, Alexei A.

2014-01-01

We have simulated the atomistic details of electronic wiring of all Fe/S clusters in complex I, a key enzyme in the respiratory electron transport chain. The tunneling current theory of many-electron systems is applied to the broken-symmetry (BS) states of the protein at the ZINDO level. One-electron tunneling approximation is found to hold in electron tunneling between the anti-ferromagnetic binuclear and tetranuclear Fe/S clusters with moderate induced polarization of the core electrons. Calculated tunneling energy is about 3 eV higher than Fermi level in the band gap of the protein, which supports that the mechanism of electron transfer is quantum mechanical tunneling, as in the rest of electron transport chain. Resulting electron tunneling pathways consist of up to three key contributing protein residues between neighboring Fe/S clusters. A distinct signature of the wave properties of electrons is observed as quantum interferences when multiple tunneling pathways exist. In N6a-N6b, electron tunnels along different pathways depending on the involved BS states, suggesting possible fluctuations of the tunneling pathways driven by the local protein environment. The calculated distance dependence of the electron transfer rates with internal water molecules included are in good agreement with a reported phenomenological relation. PMID:21495666

Identification of Preferential Groundwater Flow Pathways from Local Tracer Breakthrough Curves

NASA Astrophysics Data System (ADS)

Kokkinaki, A.; Sleep, B. E.; Dearden, R.; Wealthall, G.

2009-12-01

Characterizing preferential groundwater flow paths in the subsurface is a key factor in the design of in situ remediation technologies. When applying reaction-based remediation methods, such as enhanced bioremediation, preferential flow paths result in fast solute migration and potentially ineffective delivery of reactants, thereby adversely affecting treatment efficiency. The presence of such subsurface conduits was observed at the SABRe (Source Area Bioremediation) research site. Non-uniform migration of contaminants and electron donor during the field trials of enhanced bioremediation supported this observation. To better determine the spatial flow field of the heterogeneous aquifer, a conservative tracer test was conducted. Breakthrough curves were obtained at a reference plane perpendicular to the principal groundwater flow direction. The resulting dataset was analyzed using three different methods: peak arrival times, analytical solution fitting and moment analysis. Interpretation using the peak arrival time method indicated areas of fast plume migration. However, some of the high velocities are supported by single data points, thus adding considerable uncertainty to the estimated velocity distribution. Observation of complete breakthrough curves indicated different types of solute breakthrough, corresponding to different transport mechanisms. Sharp peaks corresponded to high conductivity preferential flow pathways, whereas more dispersed breakthrough curves with long tails were characteristic of significant dispersive mixing and dilution. While analytical solutions adequately quantified flow characteristics for the first type of curves, they failed to do so for the second type, in which case they gave unrealistic results. Therefore, a temporal moment analysis was performed to obtain complete spatial distributions of mass recovery, velocity and dispersivity. Though the results of moment analysis qualitatively agreed with the results of previous methods, more realistic estimates of velocities were obtained and the presence of one major preferential flow pathway was confirmed. However, low mass recovery and deviations from the 10% scaling rule for dispersivities indicate that insufficient spatial and temporal monitoring, as well as interpolation and truncation errors introduced uncertainty in the flow and transport parameters estimated by the method of moments. The results of the three analyses are valuable for enhancing the understanding of mass transport and remediation performance. Comparing the different interpretation methods, increasing the amount of concentration data considered in the analysis, the derived velocity fields were smoother and the estimated local velocities and dispersivities became more realistic. In conclusion, moment analysis is a method that represents a smoothed average of the velocity across the entire breakthrough curve, whereas the peak arrival time, which may be a less well constrained estimate, represents the physical peak arrival and typically yields a higher velocity than the moment analysis. This is an important distinction when applying the results of the tracer test to field sites.

Nature and mechanisms of hepatocyte apoptosis induced by D-galactosamine/lipopolysaccharide challenge in mice.

PubMed

Wu, Yi-Hang; Hu, Shao-Qing; Liu, Jun; Cao, Hong-Cui; Xu, Wei; Li, Yong-Jun; Li, Lan-Juan

2014-06-01

Apoptosis plays a role in the normal development of liver. However, overactivation thereof may lead to hepatocellular damage. The aim of this study was to assess D-galactosamine (D-GalN)/lipopolysaccharide (LPS)-induced hepatocyte apoptotic changes in mice and clarify the mechanisms involved in this process. DNA ladder detection was employed to determine the induction condition of hepatic apoptosis. An initial test indicated that typical hepatocyte apoptosis was observed at 6-10 h after the intraperitoneal injection of D-GalN (700 mg/kg) and LPS (10 µg/kg). Subsequently, we evaluated hepatocyte apoptosis at 8 h after administering D-GalN/LPS by histopathological analysis, terminal deoxynucleotidyl transferase-mediated dUTP nick end‑labeling (TUNEL) detection, flow cytometry and electron microscopy analysis. To clarify the apoptosis-related gene expression, the expression levels of tumor necrosis factor-α (TNF-α), transforming growth factor-β1 (TGF-β1), caspase-3, and Fas/Fas ligand (FasL) were determined by serum enzyme immunoassay, immunohistochemistry and western blot analysis. Strong apoptotic positive signals following D-GalN/LPS injection were observed from the results of the serum analysis, histopathological and immunohistochemical analyses, DNA ladder detection, TUNEL detection, flow cytometry and electron microscopy analysis. Additionally, apoptotic hepatocytes were mainly at the late stage of cell apoptosis. The expression of TNF-α, TGF-β1, caspase-3 and Fas/FasL was significantly increased. In conclusion, this study evaluated the D-GalN/LPS-induced hepatocyte apoptotic changes and clarified the apoptosis-related gene expression in mice. The hepatocyte apoptosis induced by D-GalN/LPS may be mainly regulated by the death receptor pathway. TGF-β signaling pathway may also play a vital role in this process of hepatocyte apoptosis.

Quantum electron tunneling in respiratory complex I.

PubMed

Hayashi, Tomoyuki; Stuchebrukhov, Alexei A

2011-05-12

We have simulated the atomistic details of electronic wiring of all Fe/S clusters in complex I, a key enzyme in the respiratory electron transport chain. The tunneling current theory of many-electron systems is applied to the broken-symmetry (BS) states of the protein at the ZINDO level. While the one-electron tunneling approximation is found to hold in electron tunneling between the antiferromagnetic binuclear and tetranuclear Fe/S clusters without major orbital or spin rearrangement of the core electrons, induced polarization of the core electrons contributes significantly to decrease the electron transfer rates to 19-56 %. Calculated tunneling energy is about 3 eV higher than Fermi level in the band gap of the protein, which supports that the mechanism of electron transfer is quantum mechanical tunneling, as in the rest of the electron transport chain. Resulting electron tunneling pathways consist of up to three key contributing protein residues between neighboring Fe/S clusters. A signature of the wave properties of electrons is observed as distinct quantum interferences when multiple tunneling pathways exist. In N6a-N6b, electron tunnels along different pathways depending on the involved BS states, suggesting possible fluctuations of the tunneling pathways driven by the local protein environment. The calculated distance dependence of the electron transfer rates with internal water molecules included is in good agreement with a reported phenomenological relation.

A novel central pathway links arterial baroreceptors and pontine parasympathetic neurons in cerebrovascular control.

PubMed

Agassandian, Khristofor; Fazan, Valeria P S; Margaryan, Naira; Dragon, Deidre Nitschke; Riley, Jeffrey; Talman, William T

2003-10-01

1. We tested the hypothesis that arterial baroreceptor reflexes modulate cerebrovascular tone through a pathway that connects the cardiovascular nucleus tractus solitarii with parasympathetic preganglionic neurons in the pons. 2. Anesthetized rats were used in all studies. Laser flowmetry was used to measure cerebral blood flow. We assessed cerebrovascular responses to increases in arterial blood pressure in animals with lesions of baroreceptor nerves, the nucleus tractus solitarii itself, the pontine preganglionic parasympathetic neurons, or the parasympathetic ganglionic nerves to the cerebral vessels. Similar assessments were made in animals after blockade of synthesis of nitric oxide, which is released by the parasympathetic nerves from the pterygopalatine ganglia. Finally the effects on cerebral blood flow of glutamate stimulation of pontine preganglionic parasympathetic neurons were evaluated. 3. We found that lesions at any one of the sites in the putative pathway or interruption of nitric oxide synthesis led to prolongation of autoregulation as mean arterial pressure was increased to levels as high as 200 mmHg. Conversely, stimulation of pontine parasympathetic preganglionic neurons led to cerebral vasodilatation. The second series of studies utilized classic anatomical tracing methods to determine at the light and electron microscopic level whether neurons in the cardiovascular nucleus tractus solitarii, the site of termination of baroreceptor afferents, projected to the pontine preganglionic neurons. Fibers were traced with anterograde tracer from the nucleus tractus solitarii to the pons and with retrograde tracer from the pons to the nucleus tractus solitarii. Using double labeling techniques we further studied synapses made between labeled projections from the nucleus tractus solitarii and preganglionic neurons that were themselves labeled with retrograde tracer placed into the pterygopalatine ganglion. 4. These anatomical studies showed that the nucleus tractus solitarii directly projects to pontine preganglionic neurons and makes asymmetric, seemingly excitatory, synapses with those neurons. These studies provide strong evidence that arterial baroreceptors may modulate cerebral blood flow through direct connections with pontine parasympathetic neurons. Further study is needed to clarify the role this pathway plays in integrative physiology.

Molecular Basis for Electron Flow Within Metal-and Electrode-Reducing Biofilms

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

Bond, Daniel R.

2016-11-01

Electrochemical, spectral, genetic, and biochemical techniques were developed to reveal that a diverse suite of redox proteins and structural macromolecules outside the cell work together to move electrons long distances between Geobacter cells to metals and electrodes. In this project, we greatly expanded the known participants in the electron transfer pathway of Geobacter. For example, in addition to well-studied pili, polysaccharides contribute to anchoring, different cytochromes are required under different conditions, strategies change with redox potential, and the localization of these components can change depending on where cells are located in a biofilm. By inventing new electrodes compatible with real-timemore » spectral measurements, we were able to visualize the redox status of biofilms in action, leading to a hypothesis that long-distance electron transfer is ultimately limiting in these systems and redox potentials change within biofilms. The goals of this project were met, as we were able to 1) identify new elements crucial to the expression, assembly and function of the extracellular electron transfer phenotype 2) expand spectral and electrochemical techniques to define the mechanism and route of electron transfer through the matrix, and 3) combine this knowledge to build the next generation of genetic tools for study of this complex process.« less

Flow Pathways of Snow and Ground Ice Melt Water During Initial Seasonal Thawing of the Active Layer on Continuous Permafrost

NASA Astrophysics Data System (ADS)

Sjoberg, Y.; Johansson, E.; Rydberg, J.

2017-12-01

In most arctic environments, the snowmelt is the main hydrologic event of the year as a large fraction of annual precipitation rapidly moves through the catchment. Flow can occur on top of the frozen ground surface or through the developing active layer, and flow pathways are critical determinants for biogeochemical transport. We study the linkages between micro topography, active layer thaw, and water partitioning on a hillslope in Greenland during late snowmelt season to explore how seasonal subsurface flow pathways develop. During snowmelt, a parallel surface drainage pattern appears across the slope, consisting of small streams, and water also collects in puddles across the slope. Thaw rates in the active layer were significantly higher (T-test p<0.01) on wet parts of the slope (0.8 cm/day), compared to drier parts of the slope (0.6 cm/day). Analyses of stable water isotopic composition show that snow had the lightest isotopic signatures, but with a large spread of values, while seasonally frozen ground and standing surface water (puddles) were heavier. The stream water became heavier over the two-week sampling period, suggesting an increasing fraction of melted soil water input over time. In contrast, standing surface water (puddles) isotopic composition did not change over time. In boreal catchments, seasonal frost has previously been found to not significantly influence flow pathways during most snowmelt events, and pre-event groundwater make out most of the stream water during snowmelt. Our results from a continuous permafrost environment show that both surface (overland) and subsurface flow pathways in the active layer are active, and that a large fraction of the water moving on the hillslope comes from melted ground ice rather than snow in the late snowmelt season. This suggests a possibility that flow pathways during snowmelt could shift to deeper subsurface flow following degradation of continuous permafrost.

Thermal convection currents in NMR: flow profiles and implications for coherence pathway selection

PubMed

Jerschow

2000-07-01

Rayleigh-Benard convection currents are visualized in a vertical cylindrical tube by means of magnetic resonance imaging. Axially antisymmetric flow, multiple vertical rolls, and twisted node planes are observed. The flow can also be induced by strong RF irradiation. Its effects on the coherence pathways in NMR experiments employing field gradients are discussed. Copyright 2000 Academic Press.

Steady and transient fluid shear stress stimulate NO release in osteoblasts through distinct biochemical pathways

NASA Technical Reports Server (NTRS)

McAllister, T. N.; Frangos, J. A.

1999-01-01

Fluid flow has been shown to be a potent stimulus in osteoblasts and osteocytes and may therefore play an important role in load-induced bone remodeling. The objective of this study was to investigate the characteristics of flow-activated pathways. Previously we reported that fluid flow stimulates rapid and continuous release of nitric oxide (NO) in primary rat calvarial osteoblasts. Here we demonstrate that flow-induced NO release is mediated by shear stress and that this response is distinctly biphasic. Transients in shear stress associated with the onset of flow stimulated a burst in NO production (8.2 nmol/mg of protein/h), while steady flow stimulated sustained NO production (2.2 nmol/mg of protein/h). Both G-protein inhibition and calcium chelation abolished the burst phase but had no effect on sustained production. Activation of G-proteins stimulated dose-dependent NO release in static cultures of both calvarial osteoblasts and UMR-106 osteoblast-like cells. Pertussis toxin had no effect on NO release. Calcium ionophore stimulated low levels of NO production within 15 minutes but had no effect on sustained production. Taken together, these data suggest that fluid shear stress stimulates NO release by two distinct pathways: a G-protein and calcium-dependent phase sensitive to flow transients, and a G-protein and calcium-independent pathway stimulated by sustained flow.

The Role of Electronic Excitations on Chemical Reaction Dynamics at Metal, Semiconductor and Nanoparticle Surfaces

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

Tully, John C.

Chemical reactions are often facilitated and steered when carried out on solid surfaces, essential for applications such as heterogeneous catalysis, solar energy conversion, corrosion, materials processing, and many others. A critical factor that can determine the rates and pathways of chemical reactions at surfaces is the efficiency and specificity of energy transfer; how fast does energy move around and where does it go? For reactions on insulator surfaces energy transfer generally moves in and out of vibrations of the adsorbed molecule and the underlying substrate. By contrast, on metal surfaces, metallic nanoparticles and semiconductors, another pathway for energy flow opensmore » up, excitation and de-excitation of electrons. This so-called “nonadiabatic” mechanism often dominates the transfer of energy and can directly impact the course of a chemical reaction. Conventional computational methods such as molecular dynamics simulation do not account for this nonadiabatic behavior. The current DOE-BES funded project has focused on developing the underlying theoretical foundation and the computational methodology for the prediction of nonadiabatic chemical reaction dynamics at surfaces. The research has successfully opened up new methodology and new applications for molecular simulation. In particular, over the last three years, the “Electronic Friction” theory, pioneered by the PI, has now been developed into a stable and accurate computational method that is sufficiently practical to allow first principles “on-the-fly” simulation of chemical reaction dynamics at metal surfaces.« less

Transgressive physiological and transcriptomic responses to light stress in allopolyploid Glycine dolichocarpa (Leguminosae).

PubMed

Coate, J E; Powell, A F; Owens, T G; Doyle, J J

2013-02-01

Allopolyploidy is often associated with increased photosynthetic capacity as well as enhanced stress tolerance. Excess light is a ubiquitous plant stress associated with photosynthetic light harvesting. We show that under chronic excess light, the capacity for non-photochemical quenching (NPQ(max)), a photoprotective mechanism, was higher in a recently formed natural allotetraploid (Glycine dolichocarpa, designated 'T2') than in its diploid progenitors (G. tomentella, 'D3'; and G. syndetika, 'D4'). This enhancement in NPQ(max) was due to an increase in energy-dependent quenching (qE) relative to D3, combined with an increase in zeaxanthin-dependent quenching (qZ) relative to D4. To explore the genetic basis for this phenotype, we profiled D3, D4 and T2 leaf transcriptomes and found that T2 overexpressed genes of the water-water cycle relative to both diploid progenitors, as well as genes involved in cyclic electron flow around photosystem I (CEF-PSI) and the xanthophyll cycle, relative to D4. Xanthophyll pigments have critical roles in NPQ, and the water-water cycle and CEF-PSI are non-photosynthetic electron transport pathways believed to facilitate NPQ formation. In the absence of CO(2), T2 also exhibited greater quantum yield of photosystem II than either diploid, indicating a greater capacity for non-photosynthetic electron transport. We postulate that, relative to its diploid progenitors, T2 is able to achieve higher NPQ(max) due to an increase in xanthophyll pigments coupled with enhanced electron flow through the water-water cycle and CEF-PSI.

Electron tunneling through covalent and noncovalent pathways in proteins

NASA Technical Reports Server (NTRS)

Beratan, David N.; Onuchic, Jose Nelson; Hopfield, J. J.

1987-01-01

A model is presented for electron tunneling in proteins which allows the donor-acceptor interaction to be mediated by the covalent bonds between amino acids and noncovalent contacts between amino acid chains. The important tunneling pathways are predicted to include mostly bonded groups with less favorable nonbonded interactions being important when the through bond pathway is prohibitively long. In some cases, vibrational motion of nonbonded groups along the tunneling pathway strongly influences the temperature dependence of the rate. Quantitative estimates for the sizes of these noncovalent interactions are made and their role in protein mediated electron transport is discussed.

Flow pathways in the Slapton Wood catchment using temperature as a tracer

NASA Astrophysics Data System (ADS)

Birkinshaw, Stephen J.; Webb, Bruce

2010-03-01

SummaryThis study investigates the potential of temperature as a tracer to provide insights into flow pathways. The approach couples fieldwork and modelling experiments for the Eastergrounds Hollow within the Slapton Wood catchment, South Devon, UK. Measurements in the Eastergrounds Hollow were carried out for soil temperature, spring temperature, and the stream temperature and use was made of an existing 1989-1991 data set for the entire Slapton Wood catchment. The predominant flow in this hollow is a result of subsurface stormflow, and previous work has suggested that the water flows vertically down through the soil and then subsurface stormflow occurs at the soil/bedrock interface where the water is deflected laterally. The depth of the subsurface stormflow was previously thought to be around 2.2 m. However, analysis of the new spring, stream and soil temperature data suggests a deeper pathway for the subsurface stormflow. Modelling of water flow and heat transport was carried out using SHETRAN and this was calibrated to reproduce the water flow in the entire Slapton Wood catchment and soil temperatures in the Eastergrounds Hollow. The model was tested for the entire Eastergrounds Hollow with two different soil depths. A depth of 2.2 m, based on previous knowledge, was unable to reproduce the Eastergrounds spring temperature. A depth of 3.7 m produced an excellent comparison between measured and simulated stream and spring temperatures in the Eastergrounds Hollow. This work suggests that the depth of the flow pathways that produce the subsurface stormflow are deeper than previously thought. It also provides a demonstration on the use of temperature as a tracer to understand flow pathways.

Physical properties of electricity.

PubMed

Thomson, Angus J M

2013-01-01

Electricity is the flow of electrons through a conductor. The amount of current (amps) is related to the voltage (volts) pushing the electrons and the degree of resistance to flow (ohms). During their flow around a circuit, electrons can be used to create a number of useful byproducts such as heat and light. As electrons flow, they alter the charge of the matter they flow through, which may also generate electromagnetic effects. Copyright © 2013 AAGL. Published by Elsevier Inc. All rights reserved.

Structure of a CLC chloride ion channel by cryo-electron microscopy

PubMed Central

Park, Eunyong; Campbell, Ernest B.; MacKinnon, Roderick

2017-01-01

CLC proteins transport chloride (Cl−) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC proteins are channels that conduct Cl− ions passively, whereas others are secondary active transporters that exchange two Cl− ions for one H+. The structural basis underlying these distinctive transport mechanisms is puzzling because CLC channels and transporters are expected to share the same architecture based on sequence homology. To solve this puzzle we determined the structure of a mammalian CLC channel (CLC-K) using cryo-electron microscopy. A conserved loop in the Cl− transport pathway shows a structure markedly different from that of CLC transporters. Consequently, the cytosolic constriction for Cl− passage is widened in CLC-K such that the kinetic barrier previously postulated for Cl−/H+ transporter function would be reduced. Thus, reduction of a kinetic barrier in CLC channels enables fast flow of Cl− down its electrochemical gradient. PMID:28002411

Vibrational energy flow controls internal conversion in a transition metal complex.

PubMed

Hedley, Gordon J; Ruseckas, Arvydas; Samuel, Ifor D W

2010-09-02

Internal conversion (IC) between excited electronic states is a fundamental photophysical process that is important for understanding protection from UV radiation, energy transfer pathways and electron injection in artificial photosynthetic systems and organic solar cells. We have studied IC between three singlet MLCT states in an iridium complex using femtosecond fluorescence spectroscopy. Very fast IC with a time constant of <20 fs is observed from the highest state and a much slower relaxation to the lowest energy singlet state on a 70 fs time scale. The abrupt slowdown of the relaxation rate occurs when there is >0.6 eV of vibrational energy stored in the complex that has to be dissipated by intramolecular vibrational redistribution before further IC to the lower energy states can occur. These results show that the ability to dissipate vibrational energy can control the relaxation process in this class of materials.

Characterization of return flow pathways during flood irrigation

NASA Astrophysics Data System (ADS)

Claes, N.; Paige, G. B.; Parsekian, A.; Gordon, B. L.; Miller, S. N.

2015-12-01

With a decline in water resources available for private consumption and irrigation, the importance of sustainable water management practices is increasing. Local management decisions, based on models may affect the availability of water both locally and downstream, causing a ripple effect. It is therefore important that the models that these local management decisions are based on, accurately quantify local hydrological processes and the timescales at which they happen. We are focusing on return flow from flood irrigation, which can occur via different pathways back to the streams: overland flow, near-surface return flow and return flow via pathways below the vadose zone. The question addressed is how these different pathways each contribute to the total amount of return flow and the dynamics behind them. We used time-lapse ERT measurements in combination with an ensemble of ERT and seismic lines to answer this question via (1) capturing the process of gradual fragmentation of aqueous environments in the vadose zone during drying stages at field scale; (2) characterization of the formation of preferential flow paths from infiltrating wetting fronts during wetting cycles at field scale. The time-lapse ERT provides the possibility to capture the dynamic processes involved during the occurrence of finger flow or macro-pores when an intensive wetting period during flood irrigation occurs. It elucidates the dynamics of retention in the vadose zone during drying and wetting periods at field scale. This method provides thereby a link to upscale from laboratory experiments to field scale and watershed scale for finger flow and preferential flow paths and illustrates the hysteresis behavior at field scale.

Episodic soil succession on basaltic lava fields in a cool, dry environment

USGS Publications Warehouse

Vaughan, K.L.; McDaniel, P.A.; Phillips, W.M.

2011-01-01

Holocene- to late Pleistocene-aged lava flows at Craters of the Moon National Monument and Preserve provide an ideal setting to examine the early stages of soil formation under cool, dry conditions. Transects were used to characterize the amount and nature of soil cover on across basaltic lava flows ranging in age from 2.1 to 18.4 ka. Results indicate that on flows <13 ka, very shallow organic soils (Folists in Soil Taxonomy) are the dominant soil type, providing an areal coverage of up to ∼25%. On flows ≥13.9 ka, deeper mineral soils including Entisols, Aridisols, and Mollisols become dominant and the areal extent increases to ≥95% on flows older than 18.4 ka. These data suggest there are two distinct pedogenic pathways associated with lava flows of the region. The first pathway is illustrated by the younger flows, where Folists dominate. In the absence of a major source of loess, relatively little mineral material accumulates and soils provide only minor coverage of the lava flows. Our results indicate that this pathway of soil development has not changed appreciably over the past ∼10 ka. The second pedogenic pathway is illustrated by the flows older than 13.9 ka. These flows have been subject to deposition of large quantities of loess during and after the last regional glaciation, resulting in almost complete coverage. Subsequent pedogenesis has given rise to Aridisols and Mollisols with calcic and cambic horizons and mollic epipedons. This research highlights the importance of regional climate change on the evolution of Craters of the Moon soilscapes.

Ru–protein–Co biohybrids designed for solar hydrogen production: understanding electron transfer pathways related to photocatalytic function† †Electronic supplementary information (ESI) available: Time traces of photocatalysis, additional EPR spectra and parameters, UV-visible spectroscopy data, and kinetic fits of TA traces. See DOI: 10.1039/c6sc03121h Click here for additional data file.

PubMed Central

Soltau, Sarah R.; Dahlberg, Peter D.; Niklas, Jens; Poluektov, Oleg G.; Mulfort, Karen L.

2016-01-01

A series of Ru–protein–Co biohybrids have been prepared using the electron transfer proteins ferredoxin (Fd) and flavodoxin (Fld) as scaffolds for photocatalytic hydrogen production. The light-generated charge separation within these hybrids has been monitored by transient optical and electron paramagnetic resonance spectroscopies. Two distinct electron transfer pathways are observed. The Ru–Fd–Co biohybrid produces up to 650 turnovers of H2 utilizing an oxidative quenching mechanism for Ru(ii)* and a sequential electron transfer pathway via the native [2Fe–2S] cluster to generate a Ru(iii)–Fd–Co(i) charge separated state that lasts for ∼6 ms. In contrast, a direct electron transfer pathway occurs for the Ru–ApoFld–Co biohybrid, which lacks an internal electron relay, generating Ru(i)–ApoFld–Co(i) charge separated state that persists for ∼800 μs and produces 85 turnovers of H2 by a reductive quenching mechanism for Ru(ii)*. This work demonstrates the utility of protein architectures for linking donor and catalytic function via direct or sequential electron transfer pathways to enable stabilized charge separation which facilitates photocatalysis for solar fuel production. PMID:28451142

Electron Bifurcation: Thermodynamics and Kinetics of Two-Electron Brokering in Biological Redox Chemistry.

PubMed

Zhang, Peng; Yuly, Jonathon L; Lubner, Carolyn E; Mulder, David W; King, Paul W; Peters, John W; Beratan, David N

2017-09-19

How can proteins drive two electrons from a redox active donor onto two acceptors at very different potentials and distances? And how can this transaction be conducted without dissipating very much energy or violating the laws of thermodynamics? Nature appears to have addressed these challenges by coupling thermodynamically uphill and downhill electron transfer reactions, using two-electron donor cofactors that have very different potentials for the removal of the first and second electron. Although electron bifurcation is carried out with near perfection from the standpoint of energy conservation and electron delivery yields, it is a biological energy transduction paradigm that has only come into focus recently. This Account provides an exegesis of the biophysical principles that underpin electron bifurcation. Remarkably, bifurcating electron transfer (ET) proteins typically send one electron uphill and one electron downhill by similar energies, such that the overall reaction is spontaneous, but not profligate. Electron bifurcation in the NADH-dependent reduced ferredoxin: NADP + oxidoreductase I (Nfn) is explored in detail here. Recent experimental progress in understanding the structure and function of Nfn allows us to dissect its workings in the framework of modern ET theory. The first electron that leaves the two-electron donor flavin (L-FAD) executes a positive free energy "uphill" reaction, and the departure of this electron switches on a second thermodynamically spontaneous ET reaction from the flavin along a second pathway that moves electrons in the opposite direction and at a very different potential. The singly reduced ET products formed from the bifurcating flavin are more than two nanometers distant from each other. In Nfn, the second electron to leave the flavin is much more reducing than the first: the potentials are said to be "crossed." The eventually reduced cofactors, NADH and ferredoxin in the case of Nfn, perform crucial downstream redox processes of their own. We dissect the thermodynamics and kinetics of electron bifurcation in Nfn and find that the key features of electron bifurcation are (1) spatially separated transfer pathways that diverge from a two-electron donor, (2) one thermodynamically uphill and one downhill redox pathway, with a large negative shift in the donor's reduction potential after departure of the first electron, and (3) electron tunneling and activation factors that enable bifurcation, producing a 1:1 partitioning of electrons onto the two pathways. Electron bifurcation is found in the CO 2 reducing pathways of methanogenic archaea, in the hydrogen pathways of hydrogenases, in the nitrogen fixing pathway of Fix, and in the mitochondrial charge transfer chain of complex III, cytochrome bc 1 . While crossed potentials may offer the biological advantage of producing tightly regulated high energy reactive species, neither kinetic nor thermodynamic considerations mandate crossed potentials to generate successful electron bifurcation. Taken together, the theoretical framework established here, focusing on the underpinning electron tunneling barriers and activation free energies, explains the logic of electron bifurcation that enables energy conversion and conservation in Nfn, points toward bioinspired schemes to execute multielectron redox chemistry, and establishes a roadmap for examining novel electron bifurcation networks in nature.

Geology, hydrology, and results of tracer testing in the Galena-Platteville aquifer at a waste-disposal site near Byron, Illinois

USGS Publications Warehouse

Kay, Robert T.; Yeskis, Douglas J.; Prinos, Scott T.; Morrow, William S.; Vendl, Mark

1999-01-01

A study was conducted by the U.S. Geological Survey and the U.S. Environmental Protection Agency of the geohydrology of the dolomite bedrock at a waste-disposal site near Byron, Illinois. The study was designed to identify and characterize the flow pathways through the bedrock aquifer beneath the site. The geologic units of concern at the site are the Glenwood Formation of the Ancell Group, and the Platteville and Galena Groups. These deposits compose the Galena-Platteville aquifer and the underlying Harmony Hill Shale semiconfining unit. The Galena-Platteville aquifer is an unconfined aquifer. Geophysical logging, water levels, and aquifer-test data indicate the presence of interconnected, hydraulically active fractures in the middle of the Galena-Platteville aquifer (the upper flow pathway), and a second set of hydraulically active fractures (the lower flow pathway). The lower flow pathway may be present through much of the site. Few hydraulically active fractures are present in the upper part of the aquifer near the center of the site, but appear to be more numerous in the upper part of the aquifer in the western and northeastern parts of the site. Water-level data obtained during the tracer test indicate that pumping effects were present near the pumped wells. Pumping effects may have been present at several wells located along directions of identified fracture orientation from the pumped well. The upper part of the aquifer did not appear to be hydraulically well connected to the flow pathways supplying water to the pumped well. Large background changes in water levels obscured the effects of pumping and prevented calculation of aquifer properties. The velocity of the bromide tracer through the lower flow pathway under the hydraulic gradient resulting from the pumping was about 152 feet per day. Solution of the Darcy velocity equation results in a calculated effective porosity for this interval of 3.5 percent, indicating hydraulic interconnection between the fractures and the aquifer matrix. Ground-water velocity through the lower flow pathway was calculated to be 15.4 feet per day under hydrostatic conditions.

Cooling system for electronic components

DOEpatents

Anderl, William James; Colgan, Evan George; Gerken, James Dorance; Marroquin, Christopher Michael; Tian, Shurong

2015-12-15

Embodiments of the present invention provide for non interruptive fluid cooling of an electronic enclosure. One or more electronic component packages may be removable from a circuit card having a fluid flow system. When installed, the electronic component packages are coincident to and in a thermal relationship with the fluid flow system. If a particular electronic component package becomes non-functional, it may be removed from the electronic enclosure without affecting either the fluid flow system or other neighboring electronic component packages.

Cooling system for electronic components

DOEpatents

Anderl, William James; Colgan, Evan George; Gerken, James Dorance; Marroquin, Christopher Michael; Tian, Shurong

2016-05-17

Embodiments of the present invention provide for non interruptive fluid cooling of an electronic enclosure. One or more electronic component packages may be removable from a circuit card having a fluid flow system. When installed, the electronic component packages are coincident to and in a thermal relationship with the fluid flow system. If a particular electronic component package becomes non-functional, it may be removed from the electronic enclosure without affecting either the fluid flow system or other neighboring electronic component packages.

Pathway enrichment based on text mining and its validation on carotenoid and vitamin A metabolism.

PubMed

Waagmeester, Andra; Pezik, Piotr; Coort, Susan; Tourniaire, Franck; Evelo, Chris; Rebholz-Schuhmann, Dietrich

2009-10-01

Carotenoid metabolism is relevant to the prevention of various diseases. Although the main actors in this metabolic pathway are known, our understanding of the pathway is still incomplete. The information on the carotenoids is scattered in the large and growing body of scientific literature. We designed a text-mining work flow to enrich existing pathways. It has been validated on the vitamin A pathway, which is a well-studied part of the carotenoid metabolism. In this study we used the vitamin A metabolism pathway as it has been described by an expert team on carotenoid metabolism from the European network of excellence in Nutrigenomics (NuGO). This work flow uses an initial set of publications cited in a review paper (1,191 publications), enlarges this corpus with Medline abstracts (13,579 documents), and then extracts the key terminology from all relevant publications. Domain experts validated the intermediate and final results of our text-mining work flow. With our approach we were able to enrich the pathway representing vitamin A metabolism. We found 37 new and relevant terms from a total of 89,086 terms, which have been qualified for inclusion in the analyzed pathway. These 37 terms have been assessed manually and as a result 13 new terms were then added as entities to the pathway. Another 14 entities belonged to other pathways, which could form the link of these pathways with the vitamin A pathway. The remaining 10 terms were classified as biomarkers or nutrients. Automatic literature analysis improves the enrichment of pathways with entities already described in the scientific literature.

The water-water cycle is essential for chloroplast protection in the absence of stress.

PubMed

Rizhsky, Ludmila; Liang, Hongjian; Mittler, Ron

2003-10-03

Maintaining electron flow through the photosynthetic apparatus, even in the absence of a sufficient amount of NADP+ as an electron acceptor, is essential for chloroplast protection from photooxidative stress. At least two different pathways are thought to participate in this process, i.e. cyclic electron flow and the water-water cycle. Although the function of the water-water cycle was inferred from a number of biochemical and physiological studies, genetic evidence for the function of this cycle is very limited. Here we show that knockdown Arabidopsis plants with suppressed expression of the key water-water cycle enzyme, thylakoid-attached copper/zinc superoxide dismutase (KD-SOD), are suppressed in their growth and development. Chloroplast size, chlorophyll content, and photosynthetic activity were also reduced in KD-SOD plants. Microarray analysis of KD-SOD plants, grown under controlled conditions, revealed changes in transcript expression consistent with an acclimation response to light stress. Although a number of transcripts involved in the defense of plants from oxidative stress were induced in KD-SOD plants, and seedlings of KD-SOD plants were more tolerant to oxidative stress, these mechanisms were unable to compensate for the suppression of the water-water cycle in mature leaves. Thus, the localization of copper/zinc superoxide dismutase at the vicinity of photosystem I may be essential for its function. Our studies provide genetic evidence for the importance of the water-water cycle in protecting the photosynthetic apparatus of higher plants from photooxidative damage.

Simulation of patient flow in multiple healthcare units using process and data mining techniques for model identification.

PubMed

Kovalchuk, Sergey V; Funkner, Anastasia A; Metsker, Oleg G; Yakovlev, Aleksey N

2018-06-01

An approach to building a hybrid simulation of patient flow is introduced with a combination of data-driven methods for automation of model identification. The approach is described with a conceptual framework and basic methods for combination of different techniques. The implementation of the proposed approach for simulation of the acute coronary syndrome (ACS) was developed and used in an experimental study. A combination of data, text, process mining techniques, and machine learning approaches for the analysis of electronic health records (EHRs) with discrete-event simulation (DES) and queueing theory for the simulation of patient flow was proposed. The performed analysis of EHRs for ACS patients enabled identification of several classes of clinical pathways (CPs) which were used to implement a more realistic simulation of the patient flow. The developed solution was implemented using Python libraries (SimPy, SciPy, and others). The proposed approach enables more a realistic and detailed simulation of the patient flow within a group of related departments. An experimental study shows an improved simulation of patient length of stay for ACS patient flow obtained from EHRs in Almazov National Medical Research Centre in Saint Petersburg, Russia. The proposed approach, methods, and solutions provide a conceptual, methodological, and programming framework for the implementation of a simulation of complex and diverse scenarios within a flow of patients for different purposes: decision making, training, management optimization, and others. Copyright © 2018 Elsevier Inc. All rights reserved.

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

Investigations of photosynthetic light harvesting by two-dimensional electronic spectroscopy

NASA Astrophysics Data System (ADS)

Read, Elizabeth Louise

Photosynthesis begins with the harvesting of sunlight by antenna pigments, organized in a network of pigment-protein complexes that rapidly funnel energy to photochemical reaction centers. The intricate design of these systems---the widely varying structural motifs of pigment organization within proteins and protein organization within a larger, cooperative network---underlies the remarkable speed and efficiency of light harvesting. Advances in femtosecond laser spectroscopy have enabled researchers to follow light energy on its course through the energetic levels of photosynthetic systems. Now, newly-developed femtosecond two-dimensional electronic spectroscopy reveals deeper insight into the fundamental molecular interactions and dynamics that emerge in these structures. The following chapters present investigations of a number of natural light-harvesting complexes using two-dimensional electronic spectroscopy. These studies demonstrate the various types of information contained in experimental two-dimensional spectra, and they show that the technique makes it possible to probe pigment-protein complexes on the length- and time-scales relevant to their functioning. New methods are described that further extend the capabilities of two-dimensional electronic spectroscopy, for example, by independently controlling the excitation laser pulse polarizations. The experiments, coupled with theoretical simulation, elucidate spatial pathways of energy flow, unravel molecular and electronic structures, and point to potential new quantum mechanical mechanisms of light harvesting.

Emitron: microwave diode

DOEpatents

Craig, G.D.; Pettibone, J.S.; Drobot, A.T.

1982-05-06

The invention comprises a new class of device, driven by electron or other charged particle flow, for producing coherent microwaves by utilizing the interaction of electromagnetic waves with electron flow in diodes not requiring an external magnetic field. Anode and cathode surfaces are electrically charged with respect to one another by electron flow, for example caused by a Marx bank voltage source or by other charged particle flow, for example by a high energy charged particle beam. This produces an electric field which stimulates an emitted electron beam to flow in the anode-cathode region. The emitted electrons are accelerated by the electric field and coherent microwaves are produced by the three dimensional spatial and temporal interaction of the accelerated electrons with geometrically allowed microwave modes which results in the bunching of the electrons and the pumping of at least one dominant microwave mode.

Cyclic electron flow is redox-controlled but independent of state transition.

PubMed

Takahashi, Hiroko; Clowez, Sophie; Wollman, Francis-André; Vallon, Olivier; Rappaport, Fabrice

2013-01-01

Photosynthesis is the biological process that feeds the biosphere with reduced carbon. The assimilation of CO2 requires the fine tuning of two co-existing functional modes: linear electron flow, which provides NADPH and ATP, and cyclic electron flow, which only sustains ATP synthesis. Although the importance of this fine tuning is appreciated, its mechanism remains equivocal. Here we show that cyclic electron flow as well as formation of supercomplexes, thought to contribute to the enhancement of cyclic electron flow, are promoted in reducing conditions with no correlation with the reorganization of the thylakoid membranes associated with the migration of antenna proteins towards Photosystems I or II, a process known as state transition. We show that cyclic electron flow is tuned by the redox power and this provides a mechanistic model applying to the entire green lineage including the vast majority of the cases in which state transition only involves a moderate fraction of the antenna.

Hydroxyacetone production from C 3 Criegee intermediates

DOE PAGES

Taatjes, Craig A.; Liu, Fang; Rotavera, Brandon; ...

2016-12-21

Hydroxyacetone (CH 3C(O)CH 2OH) is observed as a stable end product from reactions of the (CH 3) 2COO Criegee intermediate, acetone oxide, in a flow tube coupled with multiplexed photoionization mass spectrometer detection. In the experiment, the isomers at m/z = 74 are distinguished by their different photoionization spectra and reaction times. Hydroxyacetone is observed as a persistent signal at longer reaction times at a higher photoionization threshold of ca. 9.7 eV than Criegee intermediate and definitively identified by comparison with the known photoionization spectrum. Complementary electronic structure calculations reveal multiple possible reaction pathways for hydroxyacetone formation, including unimolecular isomerizationmore » via hydrogen atom transfer and –OH group migration as well as self-reaction of Criegee intermediates. Varying the concentration of Criegee intermediates suggests contributions from both unimolecular and self-reaction pathways to hydroxyacetone. As a result, the hydroxyacetone end product can provide an effective, stable marker for the production of transient Criegee intermediates in future studies of alkene ozonolysis.« less

Comprehensive Analysis of Migration Pathways (CAMP): Contaminant Migration Pathways at Confined Dredged Material Disposal Facilities

DTIC Science & Technology

1990-09-01

fluctuating flow rates make such approximations relatively inexact. Accuracy of mass loading estimates can be improved by increasing the number of...Engler, Patin, and Theriot 1988; Patin and Baylot 1989). 26. Effluent flow from an upland CDF is highest when large quantities of water are being...dispersion in conjunction with lower flows during placement of mechanical dredged material. Interactions between sediment and water that occur during

Laser-etch patterning of metal oxide coated carbon nanotube 3D architectures.

PubMed

Aksu, Cemile; Ingram, Wade; Bradford, Philip D; Jur, Jesse S

2018-08-17

This paper describes a way to fabricate novel hybrid low density nanostructures containing both carbon nanotubes (CNTs) and ceramic nanotubes. Using atomic layer deposition, a thin film of aluminum oxide was conformally deposited on aligned multiwall CNT foams in which the CNTs make porous, three-dimensional interconnected networks. A CO 2 laser was used to etch pure alumina nanotube structures by burning out the underlying CNT substrate in discrete locations via the printed laser pattern. Structural and morphological transitions during the calcination process of aluminum oxide coated CNTs were investigated through in situ transmission electron microscopy and high-resolution scanning electron microscopy. Laser parameters were optimized to etch the CNT away (i.e. etching speed, power and focal length) while minimizing damage to the alumina nanotubes due to overheating. This study opens a new route for fabricating very low density three dimensionally patterned materials with areas of dissimilar materials and properties. To demonstrate the attributes of these structures, the etched areas were used toward anisotropic microfluidic liquid flow. The demonstration used the full thickness of the material to make complex pathways for the liquid flow in the structure. Through tuning of processing conditions, the alumina nanotube (etched) regions became hydrophilic while the bulk material remained hydrophobic and electrically conductive.

A Method of Accounting for Enzyme Costs in Flux Balance Analysis Reveals Alternative Pathways and Metabolite Stores in an Illuminated Arabidopsis Leaf.

PubMed

Cheung, C Y Maurice; Ratcliffe, R George; Sweetlove, Lee J

2015-11-01

Flux balance analysis of plant metabolism is an established method for predicting metabolic flux phenotypes and for exploring the way in which the plant metabolic network delivers specific outcomes in different cell types, tissues, and temporal phases. A recurring theme is the need to explore the flexibility of the network in meeting its objectives and, in particular, to establish the extent to which alternative pathways can contribute to achieving specific outcomes. Unfortunately, predictions from conventional flux balance analysis minimize the simultaneous operation of alternative pathways, but by introducing flux-weighting factors to allow for the variable intrinsic cost of supporting each flux, it is possible to activate different pathways in individual simulations and, thus, to explore alternative pathways by averaging thousands of simulations. This new method has been applied to a diel genome-scale model of Arabidopsis (Arabidopsis thaliana) leaf metabolism to explore the flexibility of the network in meeting the metabolic requirements of the leaf in the light. This identified alternative flux modes in the Calvin-Benson cycle revealed the potential for alternative transitory carbon stores in leaves and led to predictions about the light-dependent contribution of alternative electron flow pathways and futile cycles in energy rebalancing. Notable features of the analysis include the light-dependent tradeoff between the use of carbohydrates and four-carbon organic acids as transitory storage forms and the way in which multiple pathways for the consumption of ATP and NADPH can contribute to the balancing of the requirements of photosynthetic metabolism with the energy available from photon capture. © 2015 American Society of Plant Biologists. All Rights Reserved.

Electron-Beam Diagnostic Methods for Hypersonic Flow Diagnostics

NASA Technical Reports Server (NTRS)

1994-01-01

The purpose of this work was the evaluation of the use of electron-bean fluorescence for flow measurements during hypersonic flight. Both analytical and numerical models were developed in this investigation to evaluate quantitatively flow field imaging concepts based upon the electron beam fluorescence technique for use in flight research and wind tunnel applications. Specific models were developed for: (1) fluorescence excitation/emission for nitrogen, (2) rotational fluorescence spectrum for nitrogen, (3) single and multiple scattering of electrons in a variable density medium, (4) spatial and spectral distribution of fluorescence, (5) measurement of rotational temperature and density, (6) optical filter design for fluorescence imaging, and (7) temperature accuracy and signal acquisition time requirements. Application of these models to a typical hypersonic wind tunnel flow is presented. In particular, the capability of simulating the fluorescence resulting from electron impact ionization in a variable density nitrogen or air flow provides the capability to evaluate the design of imaging instruments for flow field mapping. The result of this analysis is a recommendation that quantitative measurements of hypersonic flow fields using electron-bean fluorescence is a tractable method with electron beam energies of 100 keV. With lower electron energies, electron scattering increases with significant beam divergence which makes quantitative imaging difficult. The potential application of the analytical and numerical models developed in this work is in the design of a flow field imaging instrument for use in hypersonic wind tunnels or onboard a flight research vehicle.

Redox potential as a master variable controlling pathways of metal reduction by Geobacter sulfurreducens

PubMed Central

Levar, Caleb E; Hoffman, Colleen L; Dunshee, Aubrey J; Toner, Brandy M; Bond, Daniel R

2017-01-01

Geobacter sulfurreducens uses at least two different pathways to transport electrons out of the inner membrane quinone pool before reducing acceptors beyond the outer membrane. When growing on electrodes poised at oxidizing potentials, the CbcL-dependent pathway operates at or below redox potentials of –0.10 V vs the standard hydrogen electrode, whereas the ImcH-dependent pathway operates only above this value. Here, we provide evidence that G. sulfurreducens also requires different electron transfer proteins for reduction of a wide range of Fe(III)- and Mn(IV)-(oxyhydr)oxides, and must transition from a high- to low-potential pathway during reduction of commonly studied soluble and insoluble metal electron acceptors. Freshly precipitated Fe(III)-(oxyhydr)oxides could not be reduced by mutants lacking the high-potential pathway. Aging these minerals by autoclaving did not change their powder X-ray diffraction pattern, but restored reduction by mutants lacking the high-potential pathway. Mutants lacking the low-potential, CbcL-dependent pathway had higher growth yields with both soluble and insoluble Fe(III). Together, these data suggest that the ImcH-dependent pathway exists to harvest additional energy when conditions permit, and CbcL switches on to allow respiration closer to thermodynamic equilibrium conditions. With evidence of multiple pathways within a single organism, the study of extracellular respiration should consider not only the crystal structure or solubility of a mineral electron acceptor, but rather the redox potential, as this variable determines the energetic reward affecting reduction rates, extents, and final microbial growth yields in the environment. PMID:28045456

The Type II NADPH Dehydrogenase Facilitates Cyclic Electron Flow, Energy-Dependent Quenching, and Chlororespiratory Metabolism during Acclimation of Chlamydomonas reinhardtii to Nitrogen Deprivation1[OPEN

PubMed Central

Grossman, Arthur R.

2016-01-01

When photosynthetic organisms are deprived of nitrogen (N), the capacity to grow and assimilate carbon becomes limited, causing a decrease in the productive use of absorbed light energy and likely a rise in the cellular reduction state. Although there is a scarcity of N in many terrestrial and aquatic environments, a mechanistic understanding of how photosynthesis adjusts to low-N conditions and the enzymes/activities integral to these adjustments have not been described. In this work, we use biochemical and biophysical analyses of photoautotrophically grown wild-type and mutant strains of Chlamydomonas reinhardtii to determine the integration of electron transport pathways critical for maintaining active photosynthetic complexes even after exposure of cells to N deprivation for 3 d. Key to acclimation is the type II NADPH dehydrogenase, NDA2, which drives cyclic electron flow (CEF), chlororespiration, and the generation of an H+ gradient across the thylakoid membranes. N deprivation elicited a doubling of the rate of NDA2-dependent CEF, with little contribution from PGR5/PGRL1-dependent CEF. The H+ gradient generated by CEF is essential to sustain nonphotochemical quenching, while an increase in the level of reduced plastoquinone would promote a state transition; both are necessary to down-regulate photosystem II activity. Moreover, stimulation of NDA2-dependent chlororespiration affords additional relief from the elevated reduction state associated with N deprivation through plastid terminal oxidase-dependent water synthesis. Overall, rerouting electrons through the NDA2 catalytic hub in response to photoautotrophic N deprivation sustains cell viability while promoting the dissipation of excess excitation energy through quenching and chlororespiratory processes. PMID:26858365

Imaging electron flow from collimating contacts in graphene

NASA Astrophysics Data System (ADS)

Bhandari, S.; Lee, G. H.; Watanabe, K.; Taniguchi, T.; Kim, P.; Westervelt, R. M.

2018-04-01

The ballistic motion of electrons in graphene opens exciting opportunities for electron-optic devices based on collimated electron beams. We form a collimating contact in a hBN-encapsulated graphene hall bar by adding zigzag contacts on either side of an electron emitter that absorb stray electrons; collimation can be turned off by floating the zig-zag contacts. The electron beam is imaged using a liquid-He cooled scanning gate microscope (SGM). The tip deflects electrons as they pass from the collimating contact to a receiving contact on the opposite side of the channel, and an image of electron flow can be made by displaying the change in transmission as the tip is raster scanned across the sample. The angular half width Δθ of the electron beam is found by applying a perpendicular magnetic field B that bends electron paths into cyclotron orbits. The images reveal that the electron flow from the collimating contact drops quickly at B  =  0.05 T when the electron orbits miss the receiving contact. The flow for the non-collimating case persists longer, up to B  =  0.19 T, due to the broader range of entry angles. Ray-tracing simulations agree well with the experimental images. By fitting the fields B at which the magnitude of electron flow drops in the experimental SGM images, we find Δθ  =  9° for electron flow from the collimating contact, compared with Δθ  =  54° for the non-collimating case.

Design of an FPGA-based electronic flow regulator (EFR) for spacecraft propulsion system

NASA Astrophysics Data System (ADS)

Manikandan, J.; Jayaraman, M.; Jayachandran, M.

2011-02-01

This paper describes a scheme for electronically regulating the flow of propellant to the thruster from a high-pressure storage tank used in spacecraft application. Precise flow delivery of propellant to thrusters ensures propulsion system operation at best efficiency by maximizing the propellant and power utilization for the mission. The proposed field programmable gate array (FPGA) based electronic flow regulator (EFR) is used to ensure precise flow of propellant to the thrusters from a high-pressure storage tank used in spacecraft application. This paper presents hardware and software design of electronic flow regulator and implementation of the regulation logic onto an FPGA.Motivation for proposed FPGA-based electronic flow regulation is on the disadvantages of conventional approach of using analog circuits. Digital flow regulation overcomes the analog equivalent as digital circuits are highly flexible, are not much affected due to noise, accurate performance is repeatable, interface is easier to computers, storing facilities are possible and finally failure rate of digital circuits is less. FPGA has certain advantages over ASIC and microprocessor/micro-controller that motivated us to opt for FPGA-based electronic flow regulator. Also the control algorithm being software, it is well modifiable without changing the hardware. This scheme is simple enough to adopt for a wide range of applications, where the flow is to be regulated for efficient operation.The proposed scheme is based on a space-qualified re-configurable field programmable gate arrays (FPGA) and hybrid micro circuit (HMC). A graphical user interface (GUI) based application software is also developed for debugging, monitoring and controlling the electronic flow regulator from PC COM port.

Fluid flows and forces in development: functions, features and biophysical principles

PubMed Central

Freund, Jonathan B.; Goetz, Jacky G.; Hill, Kent L.; Vermot, Julien

2012-01-01

Throughout morphogenesis, cells experience intracellular tensile and contractile forces on microscopic scales. Cells also experience extracellular forces, such as static forces mediated by the extracellular matrix and forces resulting from microscopic fluid flow. Although the biological ramifications of static forces have received much attention, little is known about the roles of fluid flows and forces during embryogenesis. Here, we focus on the microfluidic forces generated by cilia-driven fluid flow and heart-driven hemodynamics, as well as on the signaling pathways involved in flow sensing. We discuss recent studies that describe the functions and the biomechanical features of these fluid flows. These insights suggest that biological flow determines many aspects of cell behavior and identity through a specific set of physical stimuli and signaling pathways. PMID:22395739

Inhibition of ERK1/2 or AKT Activity Equally Enhances Radiation Sensitization in B16F10 Cells

PubMed Central

Kalal, Bhuvanesh Sukhlal; Fathima, Faraz; Pai, Vinitha Ramanath; Sanjeev, Ganesh; Krishna, Chilakapati Murali; Upadhya, Dinesh

2018-01-01

Background The aim of the study was to evaluate the radiation sensitizing ability of ERK1/2, PI3K-AKT and JNK inhibitors in highly radiation resistant and metastatic B16F10 cells which carry wild-type Ras and Braf. Methods Mouse melanoma cell line B16F10 was exposed to 1.0, 2.0 and 3.0 Gy of electron beam radiation. Phosphorylated ERK1/2, AKT and JNK levels were estimated by ELISA. Cells were exposed to 2.0 and 3.0 Gy of radiation with or without prior pharmacological inhibition of ERK1/2, AKT as well as JNK pathways. Cell death induced by radiation as well as upon inhibition of these pathways was measured by TUNEL assay using flow cytometry. Results Exposure of B16F10 cells to 1.0, 2.0 and 3.0 Gy of electron beam irradiation triggered an increase in all the three phosphorylated proteins compared to sham-treated and control groups. B16F10 cells pre-treated with either ERK1/2 or AKT inhibitors equally enhanced radiation-induced cell death at 2.0 as well as 3.0 Gy (P < 0.001), while inhibition of JNK pathway increased radiation-induced cell death to a lesser extent. Interestingly combined inhibition of ERK1/2 or AKT pathways did not show additional cell death compared to individual ERK1/2 or AKT inhibition. This indicates that ERK1/2 or AKT mediates radiation resistance through common downstream molecules in B16F10 cells. Conclusions Even without activating mutations in Ras or Braf genes, ERK1/2 and AKT play a critical role in B16F10 cell survival upon radiation exposure and possibly act through common downstream effector/s. PMID:29581812

Dexter energy transfer pathways

PubMed Central

Skourtis, Spiros S.; Liu, Chaoren; Antoniou, Panayiotis; Virshup, Aaron M.; Beratan, David N.

2016-01-01

Energy transfer with an associated spin change of the donor and acceptor, Dexter energy transfer, is critically important in solar energy harvesting assemblies, damage protection schemes of photobiology, and organometallic opto-electronic materials. Dexter transfer between chemically linked donors and acceptors is bridge mediated, presenting an enticing analogy with bridge-mediated electron and hole transfer. However, Dexter coupling pathways must convey both an electron and a hole from donor to acceptor, and this adds considerable richness to the mediation process. We dissect the bridge-mediated Dexter coupling mechanisms and formulate a theory for triplet energy transfer coupling pathways. Virtual donor–acceptor charge-transfer exciton intermediates dominate at shorter distances or higher tunneling energy gaps, whereas virtual intermediates with an electron and a hole both on the bridge (virtual bridge excitons) dominate for longer distances or lower energy gaps. The effects of virtual bridge excitons were neglected in earlier treatments. The two-particle pathway framework developed here shows how Dexter energy-transfer rates depend on donor, bridge, and acceptor energetics, as well as on orbital symmetry and quantum interference among pathways. PMID:27382185

Dexter energy transfer pathways.

PubMed

Skourtis, Spiros S; Liu, Chaoren; Antoniou, Panayiotis; Virshup, Aaron M; Beratan, David N

2016-07-19

Energy transfer with an associated spin change of the donor and acceptor, Dexter energy transfer, is critically important in solar energy harvesting assemblies, damage protection schemes of photobiology, and organometallic opto-electronic materials. Dexter transfer between chemically linked donors and acceptors is bridge mediated, presenting an enticing analogy with bridge-mediated electron and hole transfer. However, Dexter coupling pathways must convey both an electron and a hole from donor to acceptor, and this adds considerable richness to the mediation process. We dissect the bridge-mediated Dexter coupling mechanisms and formulate a theory for triplet energy transfer coupling pathways. Virtual donor-acceptor charge-transfer exciton intermediates dominate at shorter distances or higher tunneling energy gaps, whereas virtual intermediates with an electron and a hole both on the bridge (virtual bridge excitons) dominate for longer distances or lower energy gaps. The effects of virtual bridge excitons were neglected in earlier treatments. The two-particle pathway framework developed here shows how Dexter energy-transfer rates depend on donor, bridge, and acceptor energetics, as well as on orbital symmetry and quantum interference among pathways.

Fourier transform infrared difference and time-resolved infrared detection of the electron and proton transfer dynamics in photosynthetic water oxidation.

PubMed

Noguchi, Takumi

2015-01-01

Photosynthetic water oxidation, which provides the electrons necessary for CO₂ reduction and releases O₂ and protons, is performed at the Mn₄CaO₅ cluster in photosystem II (PSII). In this review, studies that assessed the mechanism of water oxidation using infrared spectroscopy are summarized focusing on electron and proton transfer dynamics. Structural changes in proteins and water molecules between intermediates known as Si states (i=0-3) were detected using flash-induced Fourier transform infrared (FTIR) difference spectroscopy. Electron flow in PSII and proton release from substrate water were monitored using the infrared changes in ferricyanide as an exogenous electron acceptor and Mes buffer as a proton acceptor. Time-resolved infrared (TRIR) spectroscopy provided information on the dynamics of proton-coupled electron transfer during the S-state transitions. In particular, a drastic proton movement during the lag phase (~200μs) before electron transfer in the S3→S0 transition was detected directly by monitoring the infrared absorption of a polarizable proton in a hydrogen bond network. Furthermore, the proton release pathways in the PSII proteins were analyzed by FTIR difference measurements in combination with site-directed mutagenesis, isotopic substitutions, and quantum chemical calculations. Therefore, infrared spectroscopy is a powerful tool for understanding the molecular mechanism of photosynthetic water oxidation. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems. Copyright © 2014 Elsevier B.V. All rights reserved.

(Per)Chlorate-Reducing Bacteria Can Utilize Aerobic and Anaerobic Pathways of Aromatic Degradation with (Per)Chlorate as an Electron Acceptor

PubMed Central

Carlström, Charlotte I.; Loutey, Dana; Bauer, Stefan; Clark, Iain C.; Rohde, Robert A.; Iavarone, Anthony T.; Lucas, Lauren

2015-01-01

ABSTRACT The pathways involved in aromatic compound oxidation under perchlorate and chlorate [collectively known as (per)chlorate]-reducing conditions are poorly understood. Previous studies suggest that these are oxygenase-dependent pathways involving O2 biogenically produced during (per)chlorate respiration. Recently, we described Sedimenticola selenatireducens CUZ and Dechloromarinus chlorophilus NSS, which oxidized phenylacetate and benzoate, two key intermediates in aromatic compound catabolism, coupled to the reduction of perchlorate or chlorate, respectively, and nitrate. While strain CUZ also oxidized benzoate and phenylacetate with oxygen as an electron acceptor, strain NSS oxidized only the latter, even at a very low oxygen concentration (1%, vol/vol). Strains CUZ and NSS contain similar genes for both the anaerobic and aerobic-hybrid pathways of benzoate and phenylacetate degradation; however, the key genes (paaABCD) encoding the epoxidase of the aerobic-hybrid phenylacetate pathway were not found in either genome. By using transcriptomics and proteomics, as well as by monitoring metabolic intermediates, we investigated the utilization of the anaerobic and aerobic-hybrid pathways on different electron acceptors. For strain CUZ, the results indicated utilization of the anaerobic pathways with perchlorate and nitrate as electron acceptors and of the aerobic-hybrid pathways in the presence of oxygen. In contrast, proteomic results suggest that strain NSS may use a combination of the anaerobic and aerobic-hybrid pathways when growing on phenylacetate with chlorate. Though microbial (per)chlorate reduction produces molecular oxygen through the dismutation of chlorite (ClO2−), this study demonstrates that anaerobic pathways for the degradation of aromatics can still be utilized by these novel organisms. PMID:25805732

4D XMT of Reaction in Carbonates: Reactive Transport Dynamics at Multiples Scales

NASA Astrophysics Data System (ADS)

Menke, H. P.; Reynolds, C. A.; Andrew, M. G.; Nunes, J. P. P.; Bijeljic, B.; Blunt, M. J.

2016-12-01

Upscaling pore scale rock-fluid interaction processes for predictive modelling poses a challenge to underground carbon storage. We have completed experiments and flow modelling to investigate the impact of pore-space heterogeneity and scale on the dissolution of two limestones at both the mm and cm scales. Two samples were reacted with reservoir condition CO2-saturated brine at both scales and scanned dynamically as dissolution took place. First, 1-cm long 4-mm diameter micro cores were scanned during reactive flow at a 4-μm resolution between 4 and 40 times using 4D X-ray micro-tomography over the course of 1.5 hours using a laboratory μ-CT. Second, 3.8-cm diameter, 8-cm long macro cores were reacted at the same conditions inside a reservoir condition flow rig and imaged using a medical CT scanner. Each sample was imaged 10 times over the course of 1.5 hours at a 250 x 250 x 500-μm resolution. The reacted macro cores were then scanned inside a μ-CT at a 27-μm resolution to assess the alteration in pore-scale reaction-induced heterogeneity. It was found that both limestones showed channel formation at the pore-scale and progressive high porosity pathway dissolution at the core-scale with the more heterogeneous rock having dissolution progressing along direction of flow more quickly. Additionally, upon analysis of the high-resolution macro core images it was found that the dissolution pathways contained a distinct microstructure that was not visible at the resolution of the medical CT, where the reactive fluid had not completely dissolved the internal pore-structure. Flow was modelled in connected pathways, the flow streamlines were traced and streamline density for each voxel was calculated. It was found that the streamline density was highest in the most well-connected pathways and that density increased with increasing heterogeneity as the number of connected pathways decreased and flow was consolidated along fewer pathways. This work represents the first study of scale dependency using reservoir condition 4D X-ray tomography and provides insight into the mechanisms that control local reaction rates at multiple scales.

Osm1 facilitates the transfer of electrons from Erv1 to fumarate in the redox-regulated import pathway in the mitochondrial intermembrane space

PubMed Central

Neal, Sonya E.; Dabir, Deepa V.; Wijaya, Juwina; Boon, Cennyana; Koehler, Carla M.

2017-01-01

Prokaryotes have aerobic and anaerobic electron acceptors for oxidative folding of periplasmic proteins. The mitochondrial intermembrane space has an analogous pathway with the oxidoreductase Mia40 and sulfhydryl oxidase Erv1, termed the mitochondrial intermembrane space assembly (MIA) pathway. The aerobic electron acceptors include oxygen and cytochrome c, but an acceptor that can function under anaerobic conditions has not been identified. Here we show that the fumarate reductase Osm1, which facilitates electron transfer from fumarate to succinate, fills this gap as a new electron acceptor. In addition to microsomes, Osm1 localizes to the mitochondrial intermembrane space and assembles with Erv1 in a complex. In reconstitution studies with reduced Tim13, Mia40, and Erv1, the addition of Osm1 and fumarate completes the disulfide exchange pathway that results in Tim13 oxidation. From in vitro import assays, mitochondria lacking Osm1 display decreased import of MIA substrates, Cmc1 and Tim10. Comparative reconstitution assays support that the Osm1/fumarate couple accepts electrons with similar efficiency to cytochrome c and that the cell has strategies to coordinate expression of the terminal electron acceptors. Thus Osm1/fumarate is a new electron acceptor couple in the mitochondrial intermembrane space that seems to function in both aerobic and anaerobic conditions. PMID:28814504

Regulation of electron temperature gradient turbulence by zonal flows driven by trapped electron modes

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

Asahi, Y., E-mail: y.asahi@nr.titech.ac.jp; Tsutsui, H.; Tsuji-Iio, S.

2014-05-15

Turbulent transport caused by electron temperature gradient (ETG) modes was investigated by means of gyrokinetic simulations. It was found that the ETG turbulence can be regulated by meso-scale zonal flows driven by trapped electron modes (TEMs), which are excited with much smaller growth rates than those of ETG modes. The zonal flows of which radial wavelengths are in between the ion and the electron banana widths are not shielded by trapped ions nor electrons, and hence they are effectively driven by the TEMs. It was also shown that an E × B shearing rate of the TEM-driven zonal flows is larger thanmore » or comparable to the growth rates of long-wavelength ETG modes and TEMs, which make a main contribution to the turbulent transport before excitation of the zonal flows.« less

Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language.

PubMed

Elmarakeby, Haitham; Arefiyan, Mostafa; Myers, Elijah; Li, Song; Grene, Ruth; Heath, Lenwood S

2017-12-01

The Beacon Editor is a cross-platform desktop application for the creation and modification of signal transduction pathways using the Systems Biology Graphical Notation Activity Flow (SBGN-AF) language. Prompted by biologists' requests for enhancements, the Beacon Editor includes numerous powerful features for the benefit of creation and presentation.

Low-energy electron-induced dissociation in gas-phase nicotine, pyridine, and methyl-pyrrolidine

NASA Astrophysics Data System (ADS)

Ryszka, Michal; Alizadeh, Elahe; Li, Zhou; Ptasińska, Sylwia

2017-09-01

Dissociative electron attachment to nicotine, pyridine, and N-methyl-pyrrolidine was studied in the gas phase in order to assess their stability with respect to low-energy electron interactions. Anion yield curves for different products at electron energies ranging from zero to 15 eV were measured, and the molecular fragmentation pathways were proposed. Nicotine does not form a stable parent anion or a dehydrogenated anion, contrary to other biological systems. However, we have observed complex dissociation pathways involving fragmentation at the pyrrolidine side accompanied by isomerization mechanisms. Combining structure optimization and enthalpy calculations, performed with the Gaussian09 package, with the comparison with a deuterium-labeled N-methyl-d3-pyrrolidine allowed for the determination of the fragmentation pathways. In contrast to nicotine and N-methylpyrrolidine, the dominant pathway in dissociative electron attachment to pyridine is the loss of hydrogen, leading to the formation of an [M—H]- anion. The presented results provide important new information about the stability of nicotine and its constituent parts and contribute to a better understanding of the fragmentation mechanisms and their effects on the biological environment.

Novel organic-inorganic hybrid mesoporous materials and nanocomposites

NASA Astrophysics Data System (ADS)

Feng, Qiuwei

Organic-inorganic hybrid mesoporous materials have been prepared successfully via the nonsurfactant templated sol-gel pathway using dibenzoyl-L-tartaric acid (DBTA) as the templating compound. Styrene and methyl methacrylate polymers have been incorporated into the mesoporous silica matrix on the molecular level. The synthetic conditions have been systematically studied and optimized. Titania based mesoporous materials have also been made using nonionic polyethylene glycol surfactant as the pore forming or structure-directing agent. In all of the above mesoporous materials, pore structures have been studied in detail by Transmission Electron Microscopy (TEM), X-ray diffraction and Brunauer-Emmett-Teller (BET) characterizations. The relationship between the template concentration and the pore parameters has been established. This nonsurfactant templated pathway possesses many advantages over the known surfactant approaches such as low cost, environment friendly and biocompatability. To overcome the drawback of nonsurfactant templated mesoporous materials that lack a well ordered pore structure, a flow induced synthesis has been attempted to orientate the sol-gel solution in order to obtain aligned pore structures. The versatility of this nonsurfactant templated pathway can even be extended to the making of organic-inorganic hybrid nanocomposite materials. On the basis of this approach, polymer-silica nanocomposite materials have been prepared using a polymerizable template. It is shown that the organic monomer such as hydroxyethyl methacrylate can act as a template in making nanoporous silica materials and then be further polymerized through a post synthesis technique. The properties and morphology of this new material have been studied by Differential Scanning Calorimetry (DSC), Scanning Electron Microscopy (SEM) and Infrared Absorption Spectroscopy (FTIR). Electroactive organic-inorganic hybrid materials have also been synthesized via the sol-gel process. A coupling agent was used to covalently bond the organic and inorganic species. The morphology and conductivity of the products have been investigated.

Oxidation mode of pyranose 2-oxidase is controlled by pH.

PubMed

Prongjit, Methinee; Sucharitakul, Jeerus; Palfey, Bruce A; Chaiyen, Pimchai

2013-02-26

Pyranose 2-oxidase (P2O) from Trametes multicolor is a flavoenzyme that catalyzes the oxidation of d-glucose and other aldopyranose sugars at the C2 position by using O₂ as an electron acceptor to form the corresponding 2-keto-sugars and H₂O₂. In this study, the effects of pH on the oxidative half-reaction of P2O were investigated using stopped-flow spectrophotometry. The results showed that flavin oxidation occurred via different pathways depending on the pH of the environment. At pH values lower than 8.0, reduced P2O reacts with O₂ to form a C4a-hydroperoxyflavin intermediate, leading to elimination of H₂O₂. At pH 8.0 and higher, the majority of the reduced P2O reacts with O₂ via a pathway that does not allow detection of the C4a-hydroperoxyflavin, and flavin oxidation occurs with decreased rate constants upon the rise in pH. The switching between the two modes of P2O oxidation is controlled by protonation of a group which has a pK(a) of 7.6 ± 0.1. Oxidation reactions of reduced P2O under rapid pH change as performed by stopped-flow mixing were different from the same reactions performed with enzyme pre-equilibrated at the same specified pH values, implying that the protonation of the group which controls the mode of flavin oxidation cannot be rapidly equilibrated with outside solvent. Using a double-mixing stopped-flow experiment, a rate constant for proton dissociation from the reaction site was determined to be 21.0 ± 0.4 s⁻¹.

The oxidation mode of pyranose 2-oxidase is controlled by pH

PubMed Central

Prongjit, Methinee; Sucharitakul, Jeerus; Palfey, Bruce A.; Chaiyen, Pimchai

2013-01-01

Pyranose 2-oxidase (P2O) from Trametes multicolor is a flavoenzyme that catalyzes the oxidation of D-glucose and other aldopyranose sugars at the C2 position by using O2 as an electron acceptor to form the corresponding 2-keto-sugars and H2O2. In this study, the effects of pH on the oxidative half-reaction of P2O were investigated using stopped-flow spectrophotometry. The results showed that flavin oxidation occurred via different pathways depending on the pH of the environment. At pH values lower than 8.0, reduced P2O reacts with O2 to form a C4a-hydroperoxy-flavin intermediate, leading to elimination of H2O2. At pH 8.0 and higher, the majority of the reduced P2O reacts with O2 via a pathway which does not allow detection of the C4a-hydroperoxy-flavin, and flavin oxidation occurs with decreased rate constants upon the rise in pH. The switching between the two modes of P2O oxidation is controlled by protonation of a group which has a pKa of 7.6 ± 0.1. Oxidation reactions of reduced P2O under rapid pH change as performed by stopped-flow mixing were different from the same reactions performed with enzyme pre-equilibrated at the same specified pH values, implying that the protonation of the group which controls the mode of flavin oxidation cannot be rapidly equilibrated with outside solvent. Using a double-mixing stopped-flow experiment, a rate constant for proton dissociation from the reaction site was determined to be 21.0 ± 0.4 s-1. PMID:23356577

The effects of protein crowding in bacterial photosynthetic membranes on the flow of quinone redox species between the photochemical reaction center and the ubiquinol-cytochrome c2 oxidoreductase.

PubMed

Woronowicz, Kamil; Sha, Daniel; Frese, Raoul N; Sturgis, James N; Nanda, Vikas; Niederman, Robert A

2011-08-01

Atomic force microscopy (AFM) of the native architecture of the intracytoplasmic membrane (ICM) of a variety of species of purple photosynthetic bacteria, obtained at submolecular resolution, shows a tightly packed arrangement of light harvesting (LH) and reaction center (RC) complexes. Since there are no unattributed structures or gaps with space sufficient for the cytochrome bc(1) or ATPase complexes, they are localized in membrane domains distinct from the flat regions imaged by AFM. This has generated a renewed interest in possible long-range pathways for lateral diffusion of UQ redox species that functionally link the RC and the bc(1) complexes. Recent proposals to account for UQ flow in the membrane bilayer are reviewed, along with new experimental evidence provided from an analysis of intrinsic near-IR fluorescence emission that has served to test these hypotheses. The results suggest that different mechanism of UQ flow exist between species such as Rhodobacter sphaeroides, with a highly organized arrangement of LH and RC complexes and fast RC electron transfer turnover, and Phaeospirillum molischianum with a more random organization and slower RC turnover. It is concluded that packing density of the peripheral LH2 antenna in the Rba. sphaeroides ICM imposes constraints that significantly slow the diffusion of UQ redox species between the RC and cytochrome bc(1) complex, while in Phs. molischianum, the crowding of the ICM with LH3 has little effect upon UQ diffusion. This supports the proposal that in this type of ICM, a network of RC-LH1 core complexes observed in AFM provides a pathway for long-range quinone diffusion that is unaffected by differences in LH complex composition or organization.

Anisotropic Covalency Contributions to Superexchange Pathways in Type One Copper Active Sites

PubMed Central

2015-01-01

Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu–S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (HDA) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu–S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites. PMID:25310460

Directing the path of light-induced electron transfer at a molecular fork using vibrational excitation

NASA Astrophysics Data System (ADS)

Delor, Milan; Archer, Stuart A.; Keane, Theo; Meijer, Anthony J. H. M.; Sazanovich, Igor V.; Greetham, Gregory M.; Towrie, Michael; Weinstein, Julia A.

2017-11-01

Ultrafast electron transfer in condensed-phase molecular systems is often strongly coupled to intramolecular vibrations that can promote, suppress and direct electronic processes. Recent experiments exploring this phenomenon proved that light-induced electron transfer can be strongly modulated by vibrational excitation, suggesting a new avenue for active control over molecular function. Here, we achieve the first example of such explicit vibrational control through judicious design of a Pt(II)-acetylide charge-transfer donor-bridge-acceptor-bridge-donor 'fork' system: asymmetric 13C isotopic labelling of one of the two -C≡C- bridges makes the two parallel and otherwise identical donor→acceptor electron-transfer pathways structurally distinct, enabling independent vibrational perturbation of either. Applying an ultrafast UVpump(excitation)-IRpump(perturbation)-IRprobe(monitoring) pulse sequence, we show that the pathway that is vibrationally perturbed during UV-induced electron transfer is dramatically slowed down compared to its unperturbed counterpart. One can thus choose the dominant electron transfer pathway. The findings deliver a new opportunity for precise perturbative control of electronic energy propagation in molecular devices.

The synthesis method for design of electron flow sources

NASA Astrophysics Data System (ADS)

Alexahin, Yu I.; Molodozhenzev, A. Yu

1997-01-01

The synthesis method to design a relativistic magnetically - focused beam source is described in this paper. It allows to find a shape of electrodes necessary to produce laminar space charge flows. Electron guns with shielded cathodes designed with this method were analyzed using the EGUN code. The obtained results have shown the coincidence of the synthesis and analysis calculations [1]. This method of electron gun calculation may be applied for immersed electron flows - of interest for the EBIS electron gun design.

Dynamic fluid connectivity during steady-state multiphase flow in a sandstone.

PubMed

Reynolds, Catriona A; Menke, Hannah; Andrew, Matthew; Blunt, Martin J; Krevor, Samuel

2017-08-01

The current conceptual picture of steady-state multiphase Darcy flow in porous media is that the fluid phases organize into separate flow pathways with stable interfaces. Here we demonstrate a previously unobserved type of steady-state flow behavior, which we term "dynamic connectivity," using fast pore-scale X-ray imaging. We image the flow of N 2 and brine through a permeable sandstone at subsurface reservoir conditions, and low capillary numbers, and at constant fluid saturation. At any instant, the network of pores filled with the nonwetting phase is not necessarily connected. Flow occurs along pathways that periodically reconnect, like cars controlled by traffic lights. This behavior is consistent with an energy balance, where some of the energy of the injected fluids is sporadically converted to create new interfaces.

Insulation of a synthetic hydrogen metabolism circuit in bacteria

PubMed Central

2010-01-01

Background The engineering of metabolism holds tremendous promise for the production of desirable metabolites, particularly alternative fuels and other highly reduced molecules. Engineering approaches must redirect the transfer of chemical reducing equivalents, preventing these electrons from being lost to general cellular metabolism. This is especially the case for high energy electrons stored in iron-sulfur clusters within proteins, which are readily transferred when two such clusters are brought in close proximity. Iron sulfur proteins therefore require mechanisms to ensure interaction between proper partners, analogous to many signal transduction proteins. While there has been progress in the isolation of engineered metabolic pathways in recent years, the design of insulated electron metabolism circuits in vivo has not been pursued. Results Here we show that a synthetic hydrogen-producing electron transfer circuit in Escherichia coli can be insulated from existing cellular metabolism via multiple approaches, in many cases improving the function of the pathway. Our circuit is composed of heterologously expressed [Fe-Fe]-hydrogenase, ferredoxin, and pyruvate-ferredoxin oxidoreductase (PFOR), allowing the production of hydrogen gas to be coupled to the breakdown of glucose. We show that this synthetic pathway can be insulated through the deletion of competing reactions, rational engineering of protein interaction surfaces, direct protein fusion of interacting partners, and co-localization of pathway components on heterologous protein scaffolds. Conclusions Through the construction and characterization of a synthetic metabolic circuit in vivo, we demonstrate a novel system that allows for predictable engineering of an insulated electron transfer pathway. The development of this system demonstrates working principles for the optimization of engineered pathways for alternative energy production, as well as for understanding how electron transfer between proteins is controlled. PMID:20184755

Highly flexible electronics from scalable vertical thin film transistors.

PubMed

Liu, Yuan; Zhou, Hailong; Cheng, Rui; Yu, Woojong; Huang, Yu; Duan, Xiangfeng

2014-03-12

Flexible thin-film transistors (TFTs) are of central importance for diverse electronic and particularly macroelectronic applications. The current TFTs using organic or inorganic thin film semiconductors are usually limited by either poor electrical performance or insufficient mechanical flexibility. Here, we report a new design of highly flexible vertical TFTs (VTFTs) with superior electrical performance and mechanical robustness. By using the graphene as a work-function tunable contact for amorphous indium gallium zinc oxide (IGZO) thin film, the vertical current flow across the graphene-IGZO junction can be effectively modulated by an external gate potential to enable VTFTs with a highest on-off ratio exceeding 10(5). The unique vertical transistor architecture can readily enable ultrashort channel devices with very high delivering current and exceptional mechanical flexibility. With large area graphene and IGZO thin film available, our strategy is intrinsically scalable for large scale integration of VTFT arrays and logic circuits, opening up a new pathway to highly flexible macroelectronics.

Hybrid integration of III-V semiconductor lasers on silicon waveguides using optofluidic microbubble manipulation

PubMed Central

Jung, Youngho; Shim, Jaeho; Kwon, Kyungmook; You, Jong-Bum; Choi, Kyunghan; Yu, Kyoungsik

2016-01-01

Optofluidic manipulation mechanisms have been successfully applied to micro/nano-scale assembly and handling applications in biophysics, electronics, and photonics. Here, we extend the laser-based optofluidic microbubble manipulation technique to achieve hybrid integration of compound semiconductor microdisk lasers on the silicon photonic circuit platform. The microscale compound semiconductor block trapped on the microbubble surface can be precisely assembled on a desired position using photothermocapillary convective flows induced by focused laser beam illumination. Strong light absorption within the micro-scale compound semiconductor object allows real-time and on-demand microbubble generation. After the assembly process, we verify that electromagnetic radiation from the optically-pumped InGaAsP microdisk laser can be efficiently coupled to the single-mode silicon waveguide through vertical evanescent coupling. Our simple and accurate microbubble-based manipulation technique may provide a new pathway for realizing high precision fluidic assembly schemes for heterogeneously integrated photonic/electronic platforms as well as microelectromechanical systems. PMID:27431769

Clinical information transfer and data capture in the acute myocardial infarction pathway: an observational study.

PubMed

Kesavan, Sujatha; Kelay, Tanika; Collins, Ruth E; Cox, Benita; Bello, Fernando; Kneebone, Roger L; Sevdalis, Nick

2013-10-01

Acute myocardial infarctions (MIs) or heart attacks are the result of a complete or an incomplete occlusion of the lumen of the coronary artery with a thrombus. Prompt diagnosis and early coronary intervention results in maximum myocardial salvage, hence time to treat is of the essence. Adequate, accurate and complete information is vital during the early stages of admission of an MI patient and can impact significantly on the quality and safety of patient care. This study aimed to record how clinical information between different clinical teams during the journey of a patient in the MI care pathway is captured and to review the flow of information within this care pathway. A prospective, descriptive, structured observational study to assess (i) current clinical information systems (CIS) utilization and (ii) real-time information availability within an acute cardiac care setting was carried out. Completeness and availability of patient information capture across four key stages of the MI care pathway were assessed prospectively. Thirteen separate information systems were utilized during the four phases of the MI pathway. Observations revealed fragmented CIS utilization, with users accessing an average of six systems to gain a complete set of patient information. Data capture was found to vary between each pathway stage and in both patient cohort risk groupings. The highest level of information completeness (100%) was observed only in the discharge stage of the MI care pathway. The lowest level of information completeness (58%) was observed in the admission stage. The study highlights fragmentation, CIS duplication, and discrepancies in the current clinical information capture and data transfer across the MI care pathway in an acute cardiac care setting. The development of an integrated and user-friendly electronic data capture and transfer system would reduce duplication and would facilitate efficient and complete information provision at the point of care. © 2012 John Wiley & Sons Ltd.

Flow pathways and sediment trapping in a field-scale vegetative filter

Treesearch

M. J. Helmers; D. E. Eisenhauer; Mike G. Dosskey; T. G. Franti; J. M. Brothers; M. C. McCullough

2005-01-01

Vegetative filters (VF) are a best management practive installed in many areas to control sediment movement to water bodies. It is commonly assumed that runoff proceeds perpendicularly across a VF as sheet flow. However, there is little research information on natural pathways of water movement and performance of field-scale VF. The objectives of this study were: (1)...

Quantum control via a genetic algorithm of the field ionization pathway of a Rydberg electron

NASA Astrophysics Data System (ADS)

Gregoric, Vincent C.; Kang, Xinyue; Liu, Zhimin Cheryl; Rowley, Zoe A.; Carroll, Thomas J.; Noel, Michael W.

2017-08-01

Quantum control of the pathway along which a Rydberg electron field ionizes is experimentally and computationally demonstrated. Selective field ionization is typically done with a slowly rising electric field pulse. The (1/n*)4 scaling of the classical ionization threshold leads to a rough mapping between arrival time of the electron signal and principal quantum number of the Rydberg electron. This is complicated by the many avoided level crossings that the electron must traverse on the way to ionization, which in general leads to broadening of the time-resolved field ionization signal. In order to control the ionization pathway, thus directing the signal to the desired arrival time, a perturbing electric field produced by an arbitrary wave-form generator is added to a slowly rising electric field. A genetic algorithm evolves the perturbing field in an effort to achieve the target time-resolved field ionization signal.

Photosynthesis and Photosynthetic Electron Flow in the Alpine Evergreen Species Quercus guyavifolia in Winter

PubMed Central

Huang, Wei; Hu, Hong; Zhang, Shi-Bao

2016-01-01

Alpine evergreen broadleaf tree species must regularly cope with low night temperatures in winter. However, the effects of low night temperatures on photosynthesis in alpine evergreen broadleaf tree species are unclear. We measured the diurnal photosynthetic parameters before and after cold snap for leaves of Quercus guyavifolia growing in its native habitat at 3290 m. On 11 and 12 December 2013 (before cold snap), stomatal and mesophyll conductances (gs and gm), CO2 assimilation rate (An), and total electron flow through PSII (JPSII) at daytime were maintained at high levels. The major action of alternative electron flow was to provide extra ATP for primary metabolisms. On 20 December 2013 (after cold snap), the diurnal values of gs, gm, An, and JPSII at daytime largely decreased, mainly due to the large decrease in night air temperature. Meanwhile, the ratio of photorespiration and alternative electron flow to JPSII largely increased on 20 December. Furthermore, the high levels of alternative electron flow were accompanied with low rates of extra ATP production. A quantitative limitation analysis reveals that the gm limitation increased on 20 December with decreased night air temperature. Therefore, the night air temperature was an important determinant of stomatal/mesophyll conductance and photosynthesis. When photosynthesis is inhibited following freezing night temperatures, photorespiration and alternative electron flow are important electron sinks, which support the role of photorespiration and alternative electron flow in photoportection for alpine plants under low temperatures. PMID:27812359

[Shunt and short circuit].

PubMed

Rangel-Abundis, Alberto

2006-01-01

Shunt and short circuit are antonyms. In French, the term shunt has been adopted to denote the alternative pathway of blood flow. However, in French, as well as in Spanish, the word short circuit (court-circuit and cortocircuito) is synonymous with shunt, giving rise to a linguistic and scientific inconsistency. Scientific because shunt and short circuit made reference to a phenomenon that occurs in the field of the physics. Because shunt and short circuit are antonyms, it is necessary to clarify that shunt is an alternative pathway of flow from a net of high resistance to a net of low resistance, maintaining the stream. Short circuit is the interruption of the flow, because a high resistance impeaches the flood. This concept is applied to electrical and cardiovascular physiology, as well as to the metabolic pathways.

Apoptosis Governs the Elimination of Schistosoma japonicum from the Non-Permissive Host Microtus fortis

PubMed Central

Peng, Jinbiao; Gobert, Geoffrey N.; Hong, Yang; Jiang, Weibin; Han, Hongxiao; McManus, Donald P.; Wang, Xinzhi; Liu, Jinming; Fu, Zhiqiang; Shi, Yaojun; Lin, Jiaojiao

2011-01-01

The reed vole, Microtus fortis, is the only known mammalian host in which schistosomes of Schistosoma japonicum are unable to mature and cause significant pathogenesis. However, little is known about how Schistosoma japonicum maturation (and, therefore, the development of schistosomiasis) is prevented in M. fortis. In the present study, the ultrastructure of 10 days post infection schistosomula from BALB/c mice and M. fortis were first compared using scanning electron microscopy and transmission electron microscopy. Electron microscopic investigations showed growth retardation and ultrastructural differences in the tegument and sub-tegumental tissues as well as in the parenchymal cells of schistosomula from M. fortis compared with those in BALB/c mice. Then, microarray analysis revealed significant differential expression between the schistosomula from the two rodents, with 3,293 down-regulated (by ≥2-fold) and 71 up-regulated (≥2 fold) genes in schistosomula from the former. The up-regulated genes included a proliferation-related gene encoding granulin (Grn) and tropomyosin. Genes that were down-regulated in schistosomula from M. fortis included apoptosis-inhibited genes encoding a baculoviral IAP repeat-containing protein (SjIAP) and cytokine-induced apoptosis inhibitor (SjCIAP), genes encoding molecules involved in insulin metabolism, long-chain fatty acid metabolism, signal transduction, the transforming growth factor (TGF) pathway, the Wnt pathway and in development. TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labeling) and PI/Annexin V-FITC assays, caspase 3/7 activity analysis, and flow cytometry revealed that the percentages of early apoptotic and late apoptotic and/or necrotic cells, as well as the level of caspase activity, in schistosomula from M. fortis were all significantly higher than in those from BALB/c mice. PMID:21731652

Activation of cyclic electron flow by hydrogen peroxide in vivo

DOE PAGES

Strand, Deserah D.; Livingston, Aaron K.; Satoh-Cruz, Mio; ...

2015-04-13

Cyclic electron flow (CEF) around photosystem I is thought to balance the ATP/NADPH energy budget of photosynthesis, requiring that its rate be finely regulated. The mechanisms of this regulation are not well understood. We observed that mutants that exhibited constitutively high rates of CEF also showed elevated production of H 2O 2. We thus tested the hypothesis that CEF can be activated by H 2O 2 in vivo. CEF was strongly increased by H 2O 2 both by infiltration or in situ production by chloroplast-localized glycolate oxidase, implying that H 2O 2 can activate CEF either directly by redox modulationmore » of key enzymes, or indirectly by affecting other photosynthetic processes. CEF appeared with a half time of about 20 min after exposure to H 2O 2, suggesting activation of previously expressed CEF-related machinery. H 2O 2-dependent CEF was not sensitive to antimycin A or loss of PGR5, indicating that increased CEF probably does not involve the PGR5-PGRL1 associated pathway. In contrast, the rise in CEF was not observed in a mutant deficient in the chloroplast NADPH:PQ reductase (NDH), supporting the involvement of this complex in CEF activated by H 2O 2. In conclusion, we propose that H 2O 2 is a missing link between environmental stress, metabolism, and redox regulation of CEF in higher plants.« less

Anti-tumor effects and apoptosis induction by Realgar bioleaching solution in Sarcoma-180 cells in vitro and transplanted tumors in mice in vivo.

PubMed

Xie, Qin-Jian; Cao, Xin-Li; Bai, Lu; Wu, Zheng-Rong; Ma, Ying-Ping; Li, Hong-Yu

2014-01-01

Realgar which contains arsenic components has been used in traditional Chinese medicine (TCM) as an anticancer drug. However, neither Realgar nor its formula are soluble in water. As a result, high dose of Realgar has to be administered to achieve an effective blood medicine concentration, and this is associated with adverse side effects. The objective of the present study was to increase the solubility of a formula using hydrometallurgy technology as well as investigating its effects on in vitro and in vivo cell proliferation and apoptosis in Sarcoma-180 cell line. Antiproliferative activity of Realgar Bioleaching Solution (RBS) was evaluated by MTT assay. Further, effects of RBS on cell proliferation and apoptosis were studied using flow cytometry and transmission electron microscopy. Kunming mice were administered RBS in vivo, where arsenic specifically targeted solid tumors. The results indicated that RBS extract potently inhibited the tumor growth of Sarcoma-180 cell line in a dose-dependent manner. Flow cytometry and transmission electron microscopy further indicated that RBS significantly induced cell apoptosis through the inhibition of cell cycle pathway in a dose-dependent manner. Further, on RBS administration to mice, arsenic was specifically targeted to solid tumors RBS could substitute for traditional Realgar or its formula to work as a potent tool in cancer treatment.

Chloroplast evolution, structure and functions

PubMed Central

Jensen, Poul Erik

2014-01-01

In this review, we consider a selection of recent advances in chloroplast biology. These include new findings concerning chloroplast evolution, such as the identification of Chlamydiae as a third partner in primary endosymbiosis, a second instance of primary endosymbiosis represented by the chromatophores found in amoebae of the genus Paulinella, and a new explanation for the longevity of captured chloroplasts (kleptoplasts) in sacoglossan sea slugs. The controversy surrounding the three-dimensional structure of grana, its recent resolution by tomographic analyses, and the role of the CURVATURE THYLAKOID1 (CURT1) proteins in supporting grana formation are also discussed. We also present an updated inventory of photosynthetic proteins and the factors involved in the assembly of thylakoid multiprotein complexes, and evaluate findings that reveal that cyclic electron flow involves NADPH dehydrogenase (NDH)- and PGRL1/PGR5-dependent pathways, both of which receive electrons from ferredoxin. Other topics covered in this review include new protein components of nucleoids, an updated inventory of the chloroplast proteome, new enzymes in chlorophyll biosynthesis and new candidate messengers in retrograde signaling. Finally, we discuss the first successful synthetic biology approaches that resulted in chloroplasts in which electrons from the photosynthetic light reactions are fed to enzymes derived from secondary metabolism. PMID:24991417

PATHWAYS - ELECTRON TUNNELING PATHWAYS IN PROTEINS

NASA Technical Reports Server (NTRS)

Beratan, D. N.

1994-01-01

The key to understanding the mechanisms of many important biological processes such as photosynthesis and respiration is a better understanding of the electron transfer processes which take place between metal atoms (and other groups) fixed within large protein molecules. Research is currently focused on the rate of electron transfer and the factors that influence it, such as protein composition and the distance between metal atoms. Current models explain the swift transfer of electrons over considerable distances by postulating bridge-mediated tunneling, or physical tunneling pathways, made up of interacting bonds in the medium around and between donor and acceptor sites. The program PATHWAYS is designed to predict the route along which electrons travel in the transfer processes. The basic strategy of PATHWAYS is to begin by recording each possible path element on a connectivity list, including in each entry which two atoms are connected and what contribution the connection would make to the overall rate if it were included in a pathway. The list begins with the bonded molecular structure (including the backbone sequence and side chain connectivity), and then adds probable hydrogen bond links and through-space contacts. Once this list is completed, the program runs a tree search from the donor to the acceptor site to find the dominant pathways. The speed and efficiency of the computer search offers an improvement over manual techniques. PATHWAYS is written in FORTRAN 77 for execution on DEC VAX series computers running VMS. The program inputs data from four data sets and one structure file. The software was written to input BIOGRAF (old format) structure files based on x-ray crystal structures and outputs ASCII files listing the best pathways and BIOGRAF vector files containing the paths. Relatively minor changes could be made in the input format statements for compatibility with other graphics software. The executable and source code are included with the distribution. The main memory requirement for execution is 2.6 Mb. This program is available in DEC VAX BACKUP format on a 9-track 1600 BPI magnetic tape (standard distribution) or on a TK50 tape cartridge. PATHWAYS was developed in 1988. PATHWAYS is a copyrighted work with all copyright vested in NASA. DEC, VAX, VMS, and TK50 are trademarks of Digital Equipment Corporation. BIOGRAF is a trademark of Molecular Simulations, Inc., Sunnyvale, CA.

Characterization of vanadium ion uptake in sulfonated diels alder poly(phenylene) membranes

DOE PAGES

Lawton, Jamie; Jones, Amanda; Tang, Zhijiang; ...

2015-11-28

Sulfonated diels alder poly(phenylene) (SDAPP), alternative aromatic hydrocarbon membranes for vanadium redox flow batteries (VRFBs) are characterized using electron paramagnetic resonance (EPR). Membranes soaked in sulfuric acid and vanadyl sulfate are analyzed to determine the membrane environment in which the vanadyl ion (VO 2+) diffuses in the membranes. These results are compared to Nafion 117 membranes. In contrast to Nafion, the VO 2+ in SDAPP membranes exists in two different environments. The results of analysis of rotational diffusion determined from fits the EPR spectral lineshapes in comparison with previously reported permeation studies and measurements of partitioning functions reported here suggestmore » that the diffusion pathways in SDAPP are very different than in Nafion.« less

Molecular dynamics simulations give insight into the conformational change, complex formation, and electron transfer pathway for cytochrome P450 reductase

PubMed Central

Sündermann, Axel; Oostenbrink, Chris

2013-01-01

Cytochrome P450 reductase (CYPOR) undergoes a large conformational change to allow for an electron transfer to a redox partner to take place. After an internal electron transfer over its cofactors, it opens up to facilitate the interaction and electron transfer with a cytochrome P450. The open conformation appears difficult to crystallize. Therefore, a model of a human CYPOR in the open conformation was constructed to be able to investigate the stability and conformational change of this protein by means of molecular dynamics simulations. Since the role of the protein is to provide electrons to a redox partner, the interactions with cytochrome P450 2D6 (2D6) were investigated and a possible complex structure is suggested. Additionally, electron pathway calculations with a newly written program were performed to investigate which amino acids relay the electrons from the FMN cofactor of CYPOR to the HEME of 2D6. Several possible interacting amino acids in the complex, as well as a possible electron transfer pathway were identified and open the way for further investigation by site directed mutagenesis studies. PMID:23832577

Theory of the electron sheath and presheath

DOE PAGES

Scheiner, Brett; Baalrud, Scott D.; Yee, Benjamin T.; ...

2015-12-30

Here, electron sheaths are commonly found near Langmuir probes collecting the electron saturation current. The common assumption is that the probe collects the random flux of electrons incident on the sheath, which tacitly implies that there is no electron presheath and that the flux collected is due to a velocity space truncation of the electron velocity distribution function (EVDF). This work provides a dedicated theory of electron sheaths, which suggests that they are not so simple. Motivated by EVDFs observed in particle-in-cell(PIC) simulations, a 1D model for the electron sheath and presheath is developed. In the model, under low temperaturemore » plasma conditions (T e >> T i), an electron pressure gradient accelerates electrons in the presheath to a flow velocity that exceeds the electron thermal speed at the sheath edge. This pressure gradient generates large flow velocities compared to what would be generated by ballistic motion in response to the electric field. It is found that in many situations, under common plasma conditions, the electron presheath extends much further into the plasma than an analogous ion presheath. PIC simulations reveal that the ion density in the electron presheath is determined by a flow around the electron sheath and that this flow is due to 2D aspects of the sheath geometry. Simulations also indicate the presence of ion acoustic instabilities excited by the differential flow between electrons and ions in the presheath, which result in sheath edge fluctuations. The 1D model and time averaged PIC simulations are compared and it is shown that the model provides a good description of the electron sheath and presheath.« less

Electronic connection between the quinone and cytochrome C redox pools and its role in regulation of mitochondrial electron transport and redox signaling.

PubMed

Sarewicz, Marcin; Osyczka, Artur

2015-01-01

Mitochondrial respiration, an important bioenergetic process, relies on operation of four membranous enzymatic complexes linked functionally by mobile, freely diffusible elements: quinone molecules in the membrane and water-soluble cytochromes c in the intermembrane space. One of the mitochondrial complexes, complex III (cytochrome bc1 or ubiquinol:cytochrome c oxidoreductase), provides an electronic connection between these two diffusible redox pools linking in a fully reversible manner two-electron quinone oxidation/reduction with one-electron cytochrome c reduction/oxidation. Several features of this homodimeric enzyme implicate that in addition to its well-defined function of contributing to generation of proton-motive force, cytochrome bc1 may be a physiologically important point of regulation of electron flow acting as a sensor of the redox state of mitochondria that actively responds to changes in bioenergetic conditions. These features include the following: the opposing redox reactions at quinone catalytic sites located on the opposite sides of the membrane, the inter-monomer electronic connection that functionally links four quinone binding sites of a dimer into an H-shaped electron transfer system, as well as the potential to generate superoxide and release it to the intermembrane space where it can be engaged in redox signaling pathways. Here we highlight recent advances in understanding how cytochrome bc1 may accomplish this regulatory physiological function, what is known and remains unknown about catalytic and side reactions within the quinone binding sites and electron transfers through the cofactor chains connecting those sites with the substrate redox pools. We also discuss the developed molecular mechanisms in the context of physiology of mitochondria. Copyright © 2015 the American Physiological Society.

Electronic Connection Between the Quinone and Cytochrome c Redox Pools and Its Role in Regulation of Mitochondrial Electron Transport and Redox Signaling

PubMed Central

Sarewicz, Marcin; Osyczka, Artur

2015-01-01

Mitochondrial respiration, an important bioenergetic process, relies on operation of four membranous enzymatic complexes linked functionally by mobile, freely diffusible elements: quinone molecules in the membrane and water-soluble cytochromes c in the intermembrane space. One of the mitochondrial complexes, complex III (cytochrome bc1 or ubiquinol:cytochrome c oxidoreductase), provides an electronic connection between these two diffusible redox pools linking in a fully reversible manner two-electron quinone oxidation/reduction with one-electron cytochrome c reduction/oxidation. Several features of this homodimeric enzyme implicate that in addition to its well-defined function of contributing to generation of proton-motive force, cytochrome bc1 may be a physiologically important point of regulation of electron flow acting as a sensor of the redox state of mitochondria that actively responds to changes in bioenergetic conditions. These features include the following: the opposing redox reactions at quinone catalytic sites located on the opposite sides of the membrane, the inter-monomer electronic connection that functionally links four quinone binding sites of a dimer into an H-shaped electron transfer system, as well as the potential to generate superoxide and release it to the intermembrane space where it can be engaged in redox signaling pathways. Here we highlight recent advances in understanding how cytochrome bc1 may accomplish this regulatory physiological function, what is known and remains unknown about catalytic and side reactions within the quinone binding sites and electron transfers through the cofactor chains connecting those sites with the substrate redox pools. We also discuss the developed molecular mechanisms in the context of physiology of mitochondria. PMID:25540143

Deleterious Thermal Effects Due To Randomized Flow Paths in Pebble Bed, and Particle Bed Style Reactors

NASA Technical Reports Server (NTRS)

Moran, Robert P.

2013-01-01

A review of literature associated with Pebble Bed and Particle Bed reactor core research has revealed a systemic problem inherent to reactor core concepts which utilize randomized rather than structured coolant channel flow paths. For both the Pebble Bed and Particle Bed Reactor designs; case studies reveal that for indeterminate reasons, regions within the core would suffer from excessive heating leading to thermal runaway and localized fuel melting. A thermal Computational Fluid Dynamics model was utilized to verify that In both the Pebble Bed and Particle Bed Reactor concepts randomized coolant channel pathways combined with localized high temperature regions would work together to resist the flow of coolant diverting it away from where it is needed the most to cooler less resistive pathways where it is needed the least. In other words given the choice via randomized coolant pathways the reactor coolant will take the path of least resistance, and hot zones offer the highest resistance. Having identified the relationship between randomized coolant channel pathways and localized fuel melting it is now safe to assume that other reactor concepts that utilize randomized coolant pathways such as the foam core reactor are also susceptible to this phenomenon.

Clathrin-mediated Endocytosis and Subsequent Endo-Lysosomal Trafficking of Adeno-associated Virus/Phage*

PubMed Central

Stoneham, Charlotte A.; Hollinshead, Michael; Hajitou, Amin

2012-01-01

Adeno-associated virus/phage (AAVP) is a gene delivery vector constructed as a hybrid between adeno-associated virus and filamentous phage. Tumor targeting following systemic administration has previously been demonstrated in several in vivo cancer models, with tumor specificity achieved through display of an αv integrin-targeting ligand on the capsid. However, high titers of AAVP are required for transduction of large numbers of mammalian cells. This study is the first to investigate the mechanisms involved in entry and intracellular trafficking of AAVP. Using a combination of flow cytometry, confocal, and electron microscopy techniques, together with pharmacological agents, RNAi and dominant negative mutants, we have demonstrated that targeted AAVP endocytosis is both dynamin and clathrin-dependent. Following entry, the majority of AAVP particles are sequestered by the endosomal-lysosomal degradative pathway. Finally, we have demonstrated that disruption of this pathway leads to improved transgene expression by AAVP, thus demonstrating that escape from the late endosomes/lysosomes is a critical step for improving gene delivery by AAVP. These findings have important implications for the rational design of improved AAVP and RGD-targeted vectors. PMID:22915587

Writing with ring currents: selectively hydrogenated polycyclic aromatics as finite models of graphene and graphane

PubMed Central

Fowler, Patrick W.; Gibson, Christopher M.; Bean, David E.

2014-01-01

Alternating partial hydrogenation of the interior region of a polycyclic aromatic hydrocarbon gives a finite model system representing systems on the pathway from graphene to the graphane modification of the graphene sheet. Calculations at the DFT and coupled Hartree–Fock levels confirm that sp2 cycles of bare carbon centres isolated by selective hydrogenation retain the essentially planar geometry and electron delocalization of the annulene that they mimic. Delocalization is diagnosed by the presence of ring currents, as detected by ipsocentric calculation and visualization of the current density induced in the π system by a perpendicular external magnetic field. These induced ‘ring’ currents have essentially the same sense, strength and orbital origin as in the free hydrocarbon. Subjected to the important experimental proviso of the need for atomic-scale control of hydrogenation, this finding predicts the possibility of writing single, multiple and concentric diatropic and/or paratropic ring currents on the graphene/graphane sheet. The implication is that pathways for free flow of ballistic current can be modelled in the same way. PMID:24611026

Reactivity of seventeen- and nineteen-valence electron complexes in organometallic chemistry

NASA Technical Reports Server (NTRS)

Stiegman, Albert E.; Tyler, David R.

1986-01-01

A guideline to the reactivity of 17- and 19-valence electron species in organometallic chemistry is proposed which the authors believe will supersede all others. The thesis holds that the reactions of 17-electron metal radicals are associatively activated with reactions proceeding through a 19-valence electron species. The disparate reaction chemistry of the 17-electron metal radicals are unified in terms of this associative reaction pathway, and the intermediacy of 19-valence electron complexes in producing the observed products is discussed. It is suggested that related associatively activated pathways need to be considered in some reactions that are thought to occur by more conventional routes involving 16- and 18-electron intermediates. The basic reaction chemistry and electronic structures of these species are briefly discussed.

An integrated groundwater and surface water approach to quantifying the contribution of hydrological pathways to streamflow

NASA Astrophysics Data System (ADS)

O'Brien, R. J.; Deakin, J.; Misstear, B.; Gill, L.; Flynn, R. M.

2012-12-01

An appreciation of the quantity of streamflow derived from the main hydrological groundwater and surface water pathways transporting diffuse pollutants is critical when addressing a wide range of water resource management issues. The Pathways Project, funded by the Irish EPA, is developing a Catchment Management Tool (CMT) as an aid to water resource decision makers. The pollutants investigated by the CMT include phosphorus, nitrogen, sediments, pesticides and pathogens. An important first step in this process is to provide reliable estimates of the slower responding groundwater pathways in conjunction with the quicker overland and interflow pathways. Four watersheds are being investigated, with continuous rainfall, discharge, temperature and conductivity data being collected at gauging points within each of the watersheds. These datasets are being used to populate the semi-distributed, lumped flow model, NAM and also the distributed, finite difference model, MODFLOW. One of the main challenges is to achieve credible separations of the hydrograph into the main pathways in relatively small catchments (sometimes less than 5km2) with short response times. To assist the numerical modelling, physical separation techniques have been used to constrain the separations within probable limits. Physical techniques include: Master Recession Analysis; a modified Lyne and Hollick one-parameter digital separation; an approach developed in Ireland involving the application of recharge coefficients to hydrologically effective rainfall estimates; and finally using the NAM and MODFLOW models themselves as means of investigating separations. The contribution from each of the pathways, combined with an understanding of the attenuation of the contaminants along those pathways, will inform the CMT. This understanding will lay the foundation for linking the parameters of the NAM model to watershed descriptors such as slope, drainage density, watershed area, soil type, etc., in order to predict the response of a watershed to rainfall. This is an important deliverable of this research and will be fundamental for initial investigations in ungauged watersheds. This approach to quantifying hydrological pathways will therefore have wider applicability across Ireland and in hydrological settings elsewhere internationally. The research is being carried out for the Environmental Protection Agency by a consortium involving Queen's University Belfast, University College Dublin and Trinity College Dublin. Pathway separations in a karst watershed. Observed discharge (Black) with separated pathways: quick diffuse flow (Blue); slow diffuse flow (Green); interflow (Light Blue) and overland flow (Red).

Analytic model of a magnetically insulated transmission line with collisional flow electrons

NASA Astrophysics Data System (ADS)

Stygar, W. A.; Wagoner, T. C.; Ives, H. C.; Corcoran, P. A.; Cuneo, M. E.; Douglas, J. W.; Gilliland, T. L.; Mazarakis, M. G.; Ramirez, J. J.; Seamen, J. F.; Seidel, D. B.; Spielman, R. B.

2006-09-01

We have developed a relativistic-fluid model of the flow-electron plasma in a steady-state one-dimensional magnetically insulated transmission line (MITL). The model assumes that the electrons are collisional and, as a result, drift toward the anode. The model predicts that in the limit of fully developed collisional flow, the relation between the voltage Va, anode current Ia, cathode current Ik, and geometric impedance Z0 of a 1D planar MITL can be expressed as Va=IaZ0h(χ), where h(χ)≡[(χ+1)/4(χ-1)]1/2-ln⁡⌊χ+(χ2-1)1/2⌋/2χ(χ-1) and χ≡Ia/Ik. The relation is valid when Va≳1MV. In the minimally insulated limit, the anode current Ia,min⁡=1.78Va/Z0, the electron-flow current If,min⁡=1.25Va/Z0, and the flow impedance Zf,min⁡=0.588Z0. {The electron-flow current If≡Ia-Ik. Following Mendel and Rosenthal [Phys. Plasmas 2, 1332 (1995)PHPAEN1070-664X10.1063/1.871345], we define the flow impedance Zf as Va/(Ia2-Ik2)1/2.} In the well-insulated limit (i.e., when Ia≫Ia,min⁡), the electron-flow current If=9Va2/8IaZ02 and the flow impedance Zf=2Z0/3. Similar results are obtained for a 1D collisional MITL with coaxial cylindrical electrodes, when the inner conductor is at a negative potential with respect to the outer, and Z0≲40Ω. We compare the predictions of the collisional model to those of several MITL models that assume the flow electrons are collisionless. We find that at given values of Va and Z0, collisions can significantly increase both Ia,min⁡ and If,min⁡ above the values predicted by the collisionless models, and decrease Zf,min⁡. When Ia≫Ia,min⁡, we find that, at given values of Va, Z0, and Ia, collisions can significantly increase If and decrease Zf. Since the steady-state collisional model is valid only when the drift of electrons toward the anode has had sufficient time to establish fully developed collisional flow, and collisionless models assume there is no net electron drift toward the anode, we expect these two types of models to provide theoretical bounds on Ia, If, and Zf.

Using all energy in a battery

DOE PAGES

Dudney, Nancy J.; Li, Juchuan

2015-01-09

It is not simple to pull all the energy from a battery. For a battery to discharge, electrons and ions have to reach the same place in the active electrode material at the same moment. To reach the entire volume of the battery and maximize energy use, internal pathways for both electrons and ions must be low-resistance and continuous, connecting all regions of the battery electrode. Traditional batteries consist of a randomly distributed mixture of conductive phases within the active battery material. In these materials, bottlenecks and poor contacts may impede effective access to parts of the battery. On pagemore » 149 of this issue, Kirshenbaum et al. (1) explore a different approach, in which silver electronic pathways form on internal surfaces as the battery is discharged. Finally, the electronic pathways are well distributed throughout the electrode, improving battery performance.« less

Computer simulation of electron flow in linear-beam microwave tubes

NASA Astrophysics Data System (ADS)

Kumar, Lalit

1990-12-01

The computer simulation of electron flow in linear-beam microwave tubes, such as a travelling-wave tube (TWT) and klystron, is used for designing and optimising the electron gun and collector and for analysing the large-signal beam-wave interaction phenomenon. Major aspects of simulation of electron flow in static and rf fields present in such tubes are discussed. Some advancements made in this respect and results obtained from computer programs developed by the research group at CEERI for a gridded electron gun, depressed collector, and large-signal analysis of TWT and klystron are presented.

Enhanced hip fracture management: use of statistical methods and dataset to evaluate a fractured neck of femur fast track pathway-pilot study.

PubMed

Gilchrist, Nigel; Dalzell, Kristian; Pearson, Scott; Hooper, Gary; Hoeben, Kit; Hickling, Jeremy; McKie, John; Yi, Ma; Chamberlain, Sandra; McCullough, Caroline; Gutenstein, Marc

2017-05-12

The increasing elderly population and subsequent rise in total hip fracture(s) in this group means more effective management strategies are necessary to improve efficiency. We have changed our patient care strategy from the emergency department (ED), acute orthopaedic wards, operating theatre, post-operation and rehabilitation, and called it Fracture Neck of Femur Fast Track Pathway. All clinical data and actions were captured, integrated and displayed on a weekly basis using 'signalfromnoise' (SFN) software. The initial four months analysis of this project showed significant improvement in patient flow within the hospitals. The overall length of stay was reduced by four days. Time in ED was reduced by 30 minutes, and the wait for rehabilitation reduced by three days. Overall time in rehabilitation reduced by 3-7 days depending on facility. On average, fast track patients spent 95 less hours in hospital, resulting in 631 bed days saved in this period, with projected savings of NZD700,000. No adverse effects were seen in mortality, readmission and functional improvement status. Fractured neck of femur has increasing clinical demand in a busy tertiary hospital. Length of stay, co-morbidities and waiting time for theatres are seen as major barriers to treatment for these conditions. Wait for rehabilitation can significantly lengthen hospital stay; also poor communication between the individual hospital management facets of this condition has been an ongoing issue. Lack of instant and available electronic information on this patient group has also been seen as a major barrier to improvement. This paper demonstrates how integration of service components that are involved in fractured neck of femur can be achieved. It also shows how the use of electronic data capture and analysis can give a very quick and easily interpretable data trend that will enable change in practice. This paper indicates that cooperation between health professionals and practitioners can significantly improve the length of stay and the time in which patients can be returned home. Full interdisciplinary involvement was the key to this approach. The use of electronic data capture and analysis can be used in many other health pathways within the health system.

Investigating low flow process controls, through complex modelling, in a UK chalk catchment

NASA Astrophysics Data System (ADS)

Lubega Musuuza, Jude; Wagener, Thorsten; Coxon, Gemma; Freer, Jim; Woods, Ross; Howden, Nicholas

2017-04-01

The typical streamflow response of Chalk catchments is dominated by groundwater contributions due the high degree of groundwater recharge through preferential flow pathways. The groundwater store attenuates the precipitation signal, which causes a delay between the corresponding high and low extremes in the precipitation and the stream flow signals. Streamflow responses can therefore be quite out of phase with the precipitation input to a Chalk catchment. Therefore characterising such catchment systems, including modelling approaches, clearly need to reproduce these percolation and groundwater dominated pathways to capture these dominant flow pathways. The simulation of low flow conditions for chalk catchments in numerical models is especially difficult due to the complex interactions between various processes that may not be adequately represented or resolved in the models. Periods of low stream flows are particularly important due to competing water uses in the summer, including agriculture and water supply. In this study we apply and evaluate the physically-based Pennstate Integrated Hydrologic Model (PIHM) to the River Kennet, a sub-catchment of the Thames Basin, to demonstrate how the simulations of a chalk catchment are improved by a physically-based system representation. We also use an ensemble of simulations to investigate the sensitivity of various hydrologic signatures (relevant to low flows and droughts) to the different parameters in the model, thereby inferring the levels of control exerted by the processes that the parameters represent.

Electronic coupling through natural amino acids.

PubMed

Berstis, Laura; Beckham, Gregg T; Crowley, Michael F

2015-12-14

Myriad scientific domains concern themselves with biological electron transfer (ET) events that span across vast scales of rate and efficiency through a remarkably fine-tuned integration of amino acid (AA) sequences, electronic structure, dynamics, and environment interactions. Within this intricate scheme, many questions persist as to how proteins modulate electron-tunneling properties. To help elucidate these principles, we develop a model set of peptides representing the common α-helix and β-strand motifs including all natural AAs within implicit protein-environment solvation. Using an effective Hamiltonian strategy with density functional theory, we characterize the electronic coupling through these peptides, furthermore considering side-chain dynamics. For both motifs, predictions consistently show that backbone-mediated electronic coupling is distinctly sensitive to AA type (aliphatic, polar, aromatic, negatively charged and positively charged), and to side-chain orientation. The unique properties of these residues may be employed to design activated, deactivated, or switch-like superexchange pathways. Electronic structure calculations and Green's function analyses indicate that localized shifts in the electron density along the peptide play a role in modulating these pathways, and further substantiate the experimentally observed behavior of proline residues as superbridges. The distinct sensitivities of tunneling pathways to sequence and conformation revealed in this electronic coupling database help improve our fundamental understanding of the broad diversity of ET reactivity and provide guiding principles for peptide design.

Impacts of Cropland Changes on Water Balance, Sediment and Nutrient Transport in Eden River, UK

NASA Astrophysics Data System (ADS)

Huang, Yumei; Quinn, Paul; Liang, Qiuhua; Adams, Russell

2017-04-01

Water is the key to food and human life. Farming is the main part of economic and society in Eden, with approximately 2000 farms which covers 95% of under crops. However, with the growth of farming practice and global climate changes, Eden has presented great challenges and bringing uncertainty in the water quality caused by the agricultural diffuse pollution. This expected to reduce negative impacts of the water diffuse pollution from agriculture in Eden. Therefore, there is a high need to ensure effective water resource management to enhance water quality, to address the flow pathways and sediment transport in different farming practice and cropland changes. Hence we need to understand nutrient and the hydrological flow pathways from soil to Hillslope to channel. The aim of this research is to evaluate the impacts of different cropland changes on water balance, sediment and nutrient transport. By using the hydrological models Soil and Water Assessment Tool (SWAT) and the Catchment Runoff Attenuation Flux Tool (CRAFT), it can show the sediment and nutrient export from the load for each flow pathways (overland flow, soil water flow and ground water flow). We will show results from a small research catchment (10km2) area to the whole of Eden (800km2) at a daily time step.

Hydrochemical and isotopic effects associated with petroleum fuel biodegradation pathways in a chalk aquifer.

PubMed

Spence, Michael J; Bottrell, Simon H; Thornton, Steven F; Richnow, Hans H; Spence, Keith H

2005-09-01

Hydrochemical data, compound specific carbon isotope analysis and isotopic enrichment trends in dissolved hydrocarbons and residual electron acceptors have been used to deduce BTEX and MTBE degradation pathways in a fractured chalk aquifer. BTEX compounds are mineralised sequentially within specific redox environments, with changes in electron acceptor utilisation being defined by the exhaustion of specific BTEX components. A zone of oxygen and nitrate exhaustion extends approximately 100 m downstream from the plume source, with residual sulphate, toluene, ethylbenzene and xylene. Within this zone complete removal of the TEX components occurs by bacterial sulphate reduction, with sulphur and oxygen isotopic enrichment of residual sulphate (epsilon(s) = -14.4 per thousand to -16.0 per thousand). Towards the plume margins and at greater distance along the plume flow path nitrate concentrations increase with delta15N values of up to +40 per thousand indicating extensive denitrification. Benzene and MTBE persist into the denitrification zone, with carbon isotope enrichment of benzene indicating biodegradation along the flow path. A Rayleigh kinetic isotope enrichment model for 13C-enrichment of residual benzene gives an apparent epsilon value of -0.66 per thousand. MTBE shows no significant isotopic enrichment (delta13C = -29.3 per thousand to -30.7 per thousand) and is isotopically similar to a refinery sample (delta13C = -30.1 per thousand). No significant isotopic variation in dissolved MTBE implies that either the magnitude of any biodegradation-induced isotopic fractionation is small, or that relatively little degradation has taken place in the presence of BTEX hydrocarbons. It is possible, however, that MTBE degradation occurs under aerobic conditions in the absence of BTEX since no groundwater samples were taken with co-existing MTBE and oxygen. Low benzene delta13C values are correlated with high sulphate delta34S, indicating that little benzene degradation has occurred in the sulphate reduction zone. Benzene degradation may be associated with denitrification since increased benzene delta13C is associated with increased delta15N in residual nitrate. Re-supply of electron acceptors by diffusion from the matrix into fractures and dispersive mixing is an important constraint on degradation rates and natural attenuation capacity in this dual-porosity aquifer.

Open-channel integrating-type flow meter

USGS Publications Warehouse

Koopman, K.C.

1971-01-01

A relatively inexpensive meter for measuring cumulative flow in open channels with a rated control,. called a "totalizer", was developed. It translates the nonlinear function of gage height to flow by use of a cam and a float. A variable resistance element in an electronic circuit is controlled by the float so that the electron flow in the circuit corresponds to the flow of water. The flow of electricity causes electroplating of an electrode with silver. The amount of silver deposited is proportionate to the flow of water. The total flow of water is determined by removing the silver from the electrode at a fixed rate with ·an electronic device and recording the time for removal with a counter. The circuit is designed so that the ,resultant reading on the counter is in acre-feet of water.

Electronic Implementation of Integrated End-of-life Care: A Local Approach

PubMed Central

Schlieper, Daniel; Altreuther, Christiane; Schallenburger, Manuela; Neukirchen, Martin; Schmitz, Andrea

2017-01-01

Introduction: The Liverpool Care Pathway for the Dying Patient is an instrument to deliver integrated care for patients in their last hours of life. Originally a paper-based system, this study investigates the feasibility of an electronic version. Methods: An electronic Liverpool Care Pathway was implemented in a specialized palliative care unit of a German university hospital. Its use is exemplified by means of auditing and analysis of the proportion of recorded items. Results: In the years 2013 and 2014 the electronic Liverpool Care Pathway was used for the care of 159 patients. The uptake of the instrument was high (67%). Most items were recorded. Apart from a high usability, the fast data retrieval allows fast analysis for auditing and research. Conclusions and discussion: The electronic instrument is feasible in a computerized ward and has strong advantages for retrospective analysis. Trial registration: Internal Clinical Trial Register of the Medical Faculty, Heinrich Heine University Düsseldorf, No. 2015124683 (7 December 2015). PMID:28970746

Electrochemistry in Organisms: Electron Flow and Power Output

ERIC Educational Resources Information Center

Chirpich, Thomas P.

1975-01-01

Presents a series of calculations, appropriate for the freshman level, to determine the flow of electrons to oxygen along the electron transport chain. States that living organisms resemble fuel cells and develops calculations for determining power output. (GS)

The water-water cycle is a major electron sink in Camellia species when CO2 assimilation is restricted.

PubMed

Cai, Yan-Fei; Yang, Qiu-Yun; Li, Shu-Fa; Wang, Ji-Hua; Huang, Wei

2017-03-01

The water-water cycle (WWC) is thought to dissipate excess excitation energy and balance the ATP/NADPH energy budget under some conditions. However, the importance of the WWC in photosynthetic regulation remains controversy. We observed that three Camellia cultivars exhibited high rates of photosynthetic electron flow under high light when photosynthesis was restricted. We thus tested the hypothesis that the WWC is a major electron sink in the three Camellia cultivars when CO 2 assimilation is restricted. Light response curves indicated that the WWC was strongly increased with photorespiration and was positively correlated with extra ATP supplied from other flexible mechanisms excluding linear electron flow, implying that the WWC is an important alternative electron sink to balance ATP/NADPH energy demand for sustaining photorespiration in Camellia cultivars. Interestingly, when photosynthesis was depressed by the decreases in stomatal and mesophyll conductance, the rates of photosynthetic electron flow through photosystem II declined slightly and the rates of WWC was enhanced. Furthermore, the increased electron flow of WWC was positively correlated with the ratio of Rubisco oxygenation to carboxylation, supporting the involvement of alternative electron flow in balancing the ATP/NADPH energy budget. We propose that the WWC is a crucial electron sink to regulate ATP/NADPH energy budget and dissipate excess energy excitation in Camellia species when CO 2 assimilation is restricted. Copyright © 2017. Published by Elsevier B.V.

Soil pipe flow tracer experiments: 2. Application of a transient storage zone model

USDA-ARS?s Scientific Manuscript database

Soil pipes, defined here as discrete preferential flow paths generally parallel to the slope, are important subsurface flow pathways that play a role in many soil erosion phenomena. However, limited research has been performed on quantifying and characterizing their flow and transport characteristic...

Numerical simulation of inducing characteristics of high energy electron beam plasma for aerodynamics applications

NASA Astrophysics Data System (ADS)

Deng, Yongfeng; Jiang, Jian; Han, Xianwei; Tan, Chang; Wei, Jianguo

2017-04-01

The problem of flow active control by low temperature plasma is considered to be one of the most flourishing fields of aerodynamics due to its practical advantages. Compared with other means, the electron beam plasma is a potential flow control method for large scale flow. In this paper, a computational fluid dynamics model coupled with a multi-fluid plasma model is established to investigate the aerodynamic characteristics induced by electron beam plasma. The results demonstrate that the electron beam strongly influences the flow properties, not only in the boundary layers, but also in the main flow. A weak shockwave is induced at the electron beam injection position and develops to the other side of the wind tunnel behind the beam. It brings additional energy into air, and the inducing characteristics are closely related to the beam power and increase nonlinearly with it. The injection angles also influence the flow properties to some extent. Based on this research, we demonstrate that the high energy electron beam air plasma has three attractive advantages in aerodynamic applications, i.e. the high energy density, wide action range and excellent action effect. Due to the rapid development of near space hypersonic vehicles and atmospheric fighters, by optimizing the parameters, the electron beam can be used as an alternative means in aerodynamic steering in these applications.

Observations of reduced electron Gyroscale fluctuations in national spherical torus experiment H-mode plasmas with large ExB flow shear.

PubMed

Smith, D R; Kaye, S M; Lee, W; Mazzucato, E; Park, H K; Bell, R E; Domier, C W; Leblanc, B P; Levinton, F M; Luhmann, N C; Menard, J E; Yuh, H

2009-06-05

Electron gyroscale fluctuation measurements in National Spherical Torus Experiment H-mode plasmas with large toroidal rotation reveal fluctuations consistent with electron temperature gradient (ETG) turbulence. Large toroidal rotation in National Spherical Torus Experiment plasmas with neutral beam injection generates ExB flow shear rates comparable to ETG linear growth rates. Enhanced fluctuations occur when the electron temperature gradient is marginally stable with respect to the ETG linear critical gradient. Fluctuation amplitudes decrease when the ExB flow shear rate exceeds ETG linear growth rates. The observations indicate that ExB flow shear can be an effective suppression mechanism for ETG turbulence.

Electron-beam generated porous dextran gels: experimental and quantum chemical studies.

PubMed

Naumov, Sergej; Knolle, Wolfgang; Becher, Jana; Schnabelrauch, Matthias; Reichelt, Senta

2014-06-01

The aim of this work was to investigate the reaction mechanism of electron-beam generated macroporous dextran cryogels by quantum chemical calculation and electron paramagnetic resonance measurements. Electron-beam radiation was used to initiate the cross-linking reaction of methacrylated dextran in semifrozen aqueous solutions. The pore morphology of the resulting cryogels was visualized by scanning electron microscopy. Quantum chemical calculations and electron paramagnetic resonance studies provided information on the most probable reaction pathway and the chain growth radicals. The most probable reaction pathway was a ring opening reaction and the addition of a C-atom to the double-bond of the methacrylated dextran molecule. First detailed quantum chemical calculation on the reaction mechanism of electron-beam initiated cross-linking reaction of methacrylated dextran are presented.

Integrated turbomachine oxygen plant

DOEpatents

Anand, Ashok Kumar; DePuy, Richard Anthony; Muthaiah, Veerappan

2014-06-17

An integrated turbomachine oxygen plant includes a turbomachine and an air separation unit. One or more compressor pathways flow compressed air from a compressor through one or more of a combustor and a turbine expander to cool the combustor and/or the turbine expander. An air separation unit is operably connected to the one or more compressor pathways and is configured to separate the compressed air into oxygen and oxygen-depleted air. A method of air separation in an integrated turbomachine oxygen plant includes compressing a flow of air in a compressor of a turbomachine. The compressed flow of air is flowed through one or more of a combustor and a turbine expander of the turbomachine to cool the combustor and/or the turbine expander. The compressed flow of air is directed to an air separation unit and is separated into oxygen and oxygen-depleted air.

Hot-electron-mediated surface chemistry: toward electronic control of catalytic activity.

PubMed

Park, Jeong Young; Kim, Sun Mi; Lee, Hyosun; Nedrygailov, Ievgen I

2015-08-18

Energy dissipation at surfaces and interfaces is mediated by excitation of elementary processes, including phonons and electronic excitation, once external energy is deposited to the surface during exothermic chemical processes. Nonadiabatic electronic excitation in exothermic catalytic reactions results in the flow of energetic electrons with an energy of 1-3 eV when chemical energy is converted to electron flow on a short (femtosecond) time scale before atomic vibration adiabatically dissipates the energy (in picoseconds). These energetic electrons that are not in thermal equilibrium with the metal atoms are called "hot electrons". The detection of hot electron flow under atomic or molecular processes and understanding its role in chemical reactions have been major topics in surface chemistry. Recent studies have demonstrated electronic excitation produced during atomic or molecular processes on surfaces, and the influence of hot electrons on atomic and molecular processes. We outline research efforts aimed at identification of the intrinsic relation between the flow of hot electrons and catalytic reactions. We show various strategies for detection and use of hot electrons generated by the energy dissipation processes in surface chemical reactions and photon absorption. A Schottky barrier localized at the metal-oxide interface of either catalytic nanodiodes or hybrid nanocatalysts allows hot electrons to irreversibly transport through the interface. We show that the chemicurrent, composed of hot electrons excited by the surface reaction of CO oxidation or hydrogen oxidation, correlates well with the turnover rate measured separately by gas chromatography. Furthermore, we show that hot electron flows generated on a gold thin film by photon absorption (or internal photoemission) can be amplified by localized surface plasmon resonance. The influence of hot charge carriers on the chemistry at the metal-oxide interface are discussed for the cases of Au, Ag, and Pt nanoparticles on oxide supports and Pt-CdSe-Pt nanodumbbells. We show that the accumulation or depletion of hot electrons on metal nanoparticles, in turn, can also influence catalytic reactions. Mechanisms suggested for hot-electron-induced chemical reactions on a photoexcited plasmonic metal are discussed. We propose that the manipulation of the flow of hot electrons by changing the electrical characteristics of metal-oxide and metal-semiconductor interfaces can give rise to the intriguing capability of tuning the catalytic activity of hybrid nanocatalysts.

Low volume flow meter

DOEpatents

Meixler, Lewis D.

1993-01-01

The low flow monitor provides a means for determining if a fluid flow meets a minimum threshold level of flow. The low flow monitor operates with a minimum of intrusion by the flow detection device into the flow. The electrical portion of the monitor is externally located with respect to the fluid stream which allows for repairs to the monitor without disrupting the flow. The electronics provide for the adjustment of the threshold level to meet the required conditions. The apparatus can be modified to provide an upper limit to the flow monitor by providing for a parallel electronic circuit which provides for a bracketing of the desired flow rate.

Secondary mineral formation associated with respiration of nontronite, NAu-1 by iron reducing bacteria

PubMed Central

O'Reilly, S Erin; Watkins, Janet; Furukawa, Yoko

2005-01-01

Experimental batch and miscible-flow cultures were studied in order to determine the mechanistic pathways of microbial Fe(III) respiration in ferruginous smectite clay, NAu-1. The primary purpose was to resolve if alteration of smectite and release of Fe precedes microbial respiration. Alteration of NAu-1, represented by the morphological and mineralogical changes, occurred regardless of the extent of microbial Fe(III) reduction in all of our experimental systems, including those that contained heat-killed bacteria and those in which O2, rather than Fe(III), was the primary terminal electron acceptor. The solid alteration products observed under transmission electron microscopy included poorly crystalline smectite with diffuse electron diffraction signals, discrete grains of Fe-free amorphous aluminosilicate with increased Al/Si ratio, Fe-rich grains, and amorphous Si globules in the immediate vicinity of bacterial cells and extracellular polymeric substances. In reducing systems, Fe was also found as siderite. The small amount of Fe partitioned to the aqueous phase was primarily in the form of dissolved Fe(III) species even in the systems in which Fe(III) was the primary terminal electron acceptor for microbial respiration. From these observations, we conclude that microbial respiration of Fe(III) in our laboratory systems proceeded through the following: (1) alteration of NAu-1 and concurrent release of Fe(III) from the octahedral sheets of NAu-1; and (2) subsequent microbial respiration of Fe(III).

Imaging Electron Motion in a Few Layer MoS2 Device

NASA Astrophysics Data System (ADS)

Bhandari, S.; Wang, K.; Watanabe, K.; Taniguchi, T.; Kim, P.; Westervelt, R. M.

2017-06-01

Ultrathin sheets of MoS2 are a newly discovered 2D semiconductor that holds great promise for nanoelectronics. Understanding the pattern of current flow will be crucial for developing devices. In this talk, we present images of current flow in MoS2 obtained with a Scanned Probe Microscope (SPM) cooled to 4 K. We previously used this technique to image electron trajectories in GaAs/AlGaAs heterostructures and graphene. The charged SPM tip is held just above the sample surface, creating an image charge inside the device that scatters electrons. By measuring the change in resistance ΔR while the tip is raster scanned above the sample, an image of electron flow is obtained. We present images of electron flow in an MoS2 device patterned into a hall bar geometry. A three-layer MoS2 sheet is encased by two hBN layers, top and bottom, and patterned into a hall-bar with multilayer graphene contacts. An SPM image shows the current flow pattern from the wide contact at the end of the device for a Hall density n = 1.3×1012 cm-2. The SPM tip tends to block flow, increasing the resistance R. The pattern of flow was also imaged for a narrow side contact on the sample. At density n = 5.4×1011 cm-2; the pattern seen in the SPM image is similar to the wide contact. The ability to image electron flow promises to be very useful for the development of ultrathin devices from new 2D materials.

The influence of ZnO-SnO2 nanoparticles and activated carbon on the photocatalytic degradation of toluene using continuous flow mode.

PubMed

Rangkooy, Hossein Ali; Tanha, Fatemeh; Jaafarzadeh, Neamat; Mohammadbeigi, Abolfazl

2017-01-01

The present study examined the gas-phase photocatalytic degradation of toluene using ZnO-SnO 2 nanocomposite supported on activated carbon in a photocatalytic reactor. Toluene was selected as a model pollutant from volatile organic compounds to determine the pathway of photocatalytic degradation and the factors influencing this degradation. The ZnO-SnO 2 nanocomposite was synthesized through co-precipitation method in a ratio of 2:1 and then supported on activated carbon. The immobilization of ZnO-SnO 2 nanocomposite on activated carbon was determined by the surface area and scanning electron micrograph technique proposed by Brunauer, Emmett, and Teller. The laboratory findings showed that the highest efficiency was 40% for photocatalytic degradation of toluene. The results also indicated that ZnO-SnO 2 nano-oxides immobilization on activated carbon had a synergic effect on photocatalytic degradation of toluene. Use of a hybrid photocatalytic system (ZnO/SnO 2 nano coupled oxide) and application of absorbent (activated carbon) may be efficient and effective technique for refinement of toluene from air flow.

Generation of zonal flows by electrostatic drift waves in electron-positron-ion plasmas

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

Kaladze, T. D.; I. Vekua Institute of Applied Mathematics, Tbilisi State University, 2 University Str., 0186 Tbilisi; Shad, M.

2010-02-15

Generation of large-scale zonal flows by comparatively small-scale electrostatic drift waves in electron-positron-ion plasmas is considered. The generation mechanism is based on the parametric excitation of convective cells by finite amplitude drift waves having arbitrary wavelengths (as compared with the ion Larmor radius of plasma ions at the plasma electron temperature). Temperature inhomogeneity of electrons and positrons is taken into account assuming ions to be cold. To describe the generation of zonal flow generalized Hasegawa-Mima equation containing both vector and two scalar (of different nature) nonlinearities is used. A set of coupled equations describing the nonlinear interaction of drift wavesmore » and zonal flows is deduced. Explicit expressions for the maximum growth rate as well as for the optimal spatial dimensions of the zonal flows are obtained. Enriched possibilities of zonal flow generation with different growth rates are revealed. The present theory can be used for interpretations of drift wave observations in laboratory and astrophysical plasmas.« less

[Anaerobic reduction of humus/Fe (III) and electron transport mechanism of Fontibacter sp. SgZ-2].

PubMed

Ma, Chen; Yang, Gui-qin; Lu, Qin; Zhou, Shun-gui

2014-09-01

Humus and Fe(III) respiration are important extracellular respiration metabolism. Electron transport pathway is the key issue of extracellular respiration. To understand the electron transport properties and the environmental behavior of a novel Fe(III)- reducing bacterium, Fontibacter sp. SgZ-2, capacities of anaerobic humus/Fe(III) reduction and electron transport mechanisms with four electron acceptors were investigated in this study. The results of anaerobic batch experiments indicated that strain SgZ-2 had the ability to reduce humus analog [ 9,10-anthraquinone-2,6-disulfonic acid (AQDS) and 9,10-anthraquinone-2-sulfonic acid (AQS)], humic acids (HA), soluble Fe(III) (Fe-EDTA and Fe-citrate) and Fe(III) oxides [hydrous ferric oxide (HFO)]. Fermentative sugars (glucose and sucrose) were the most effective electron donors in the humus/Fe(III) reduction by strain SgZ-2. Additionally, differences of electron carrier participating in the process of electron transport with different electron acceptors (i. e. , oxygen, AQS, Fe-EDTA and HFO) were investigated using respiratory inhibitors. The results suggested that similar respiratory chain components were involved in the reducing process of oxygen and Fe-EDTA, including dehydrogenase, quinones and cytochromes b-c. In comparison, only dehydrogenase was found to participate in the reduction of AQS and HFO. In conclusion, different electron transport pathways may be employed by strain SgZ-2 between insoluble and soluble electron acceptors or among soluble electron acceptors. Preliminary models of electron transport pathway with four electron acceptors were proposed for strain SgZ-2, and the study of electron transport mechanism was explored to the genus Fontibacter. All the results from this study are expected to help understand the electron transport properties and the environmental behavior of the genus Fontibacter.

Vibrational and Electronic Energy Transfer and Dissociation of Diatomic Molecules by Electron Collisions

NASA Technical Reports Server (NTRS)

Huo, Winifred M.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

At high altitudes and velocities equal to or greater than the geosynchronous return velocity (10 kilometers per second), the shock layer of a hypersonic flight will be in thermochemical nonequilibrium and partially ionized. The amount of ionization is determined by the velocity. For a trans atmospheric flight of 10 kilometers per second and at an altitude of 80 kilometers, a maximum of 1% ionization is expected. At a velocity of 12 - 17 kilometer per second, such as a Mars return mission, up to 30% of the atoms and molecules in the flow field will be ionized. Under those circumstances, electrons play an important role in determining the internal states of atoms and molecules in the flow field and hence the amount of radiative heat load and the distance it takes for the flow field to re-establish equilibrium. Electron collisions provide an effective means of transferring energy even when the electron number density is as low as 1%. Because the mass of an electron is 12,760 times smaller than the reduced mass of N2, its average speed, and hence its average collision frequency, is more than 100 times larger. Even in the slightly ionized regime with only 1% electrons, the frequency of electron-molecule collisions is equal to or larger than that of molecule-molecule collisions, an important consideration in the low density part of the atmosphere. Three electron-molecule collision processes relevant to hypersonic flows will be considered: (1) vibrational excitation/de-excitation of a diatomic molecule by electron impact, (2) electronic excitation/de-excitation, and (3) dissociative recombination in electron-diatomic ion collisions. A review of available data, both theory and experiment, will be given. Particular attention will be paid to tailoring the molecular physics to the condition of hypersonic flows. For example, the high rotational temperatures in a hypersonic flow field means that most experimental data carried out under room temperatures are not applicable. Also, the average electron temperature is expected to be between 10,000 and 20,000 K. Thus only data for low energy electrons are relevant to the model.

Osm1 facilitates the transfer of electrons from Erv1 to fumarate in the redox-regulated import pathway in the mitochondrial intermembrane space.

PubMed

Neal, Sonya E; Dabir, Deepa V; Wijaya, Juwina; Boon, Cennyana; Koehler, Carla M

2017-10-15

Prokaryotes have aerobic and anaerobic electron acceptors for oxidative folding of periplasmic proteins. The mitochondrial intermembrane space has an analogous pathway with the oxidoreductase Mia40 and sulfhydryl oxidase Erv1, termed the mitochondrial intermembrane space assembly (MIA) pathway. The aerobic electron acceptors include oxygen and cytochrome c , but an acceptor that can function under anaerobic conditions has not been identified. Here we show that the fumarate reductase Osm1, which facilitates electron transfer from fumarate to succinate, fills this gap as a new electron acceptor. In addition to microsomes, Osm1 localizes to the mitochondrial intermembrane space and assembles with Erv1 in a complex. In reconstitution studies with reduced Tim13, Mia40, and Erv1, the addition of Osm1 and fumarate completes the disulfide exchange pathway that results in Tim13 oxidation. From in vitro import assays, mitochondria lacking Osm1 display decreased import of MIA substrates, Cmc1 and Tim10. Comparative reconstitution assays support that the Osm1/fumarate couple accepts electrons with similar efficiency to cytochrome c and that the cell has strategies to coordinate expression of the terminal electron acceptors. Thus Osm1/fumarate is a new electron acceptor couple in the mitochondrial intermembrane space that seems to function in both aerobic and anaerobic conditions. © 2017 Neal et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Electronic coupling through natural amino acids

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

Berstis, Laura; Beckham, Gregg T., E-mail: michael.crowley@nrel.gov, E-mail: gregg.beckham@nrel.gov; Crowley, Michael F., E-mail: michael.crowley@nrel.gov, E-mail: gregg.beckham@nrel.gov

2015-12-14

Myriad scientific domains concern themselves with biological electron transfer (ET) events that span across vast scales of rate and efficiency through a remarkably fine-tuned integration of amino acid (AA) sequences, electronic structure, dynamics, and environment interactions. Within this intricate scheme, many questions persist as to how proteins modulate electron-tunneling properties. To help elucidate these principles, we develop a model set of peptides representing the common α-helix and β-strand motifs including all natural AAs within implicit protein-environment solvation. Using an effective Hamiltonian strategy with density functional theory, we characterize the electronic coupling through these peptides, furthermore considering side-chain dynamics. For bothmore » motifs, predictions consistently show that backbone-mediated electronic coupling is distinctly sensitive to AA type (aliphatic, polar, aromatic, negatively charged and positively charged), and to side-chain orientation. The unique properties of these residues may be employed to design activated, deactivated, or switch-like superexchange pathways. Electronic structure calculations and Green’s function analyses indicate that localized shifts in the electron density along the peptide play a role in modulating these pathways, and further substantiate the experimentally observed behavior of proline residues as superbridges. The distinct sensitivities of tunneling pathways to sequence and conformation revealed in this electronic coupling database help improve our fundamental understanding of the broad diversity of ET reactivity and provide guiding principles for peptide design.« less

On the nature of organic and inorganic centers that bifurcate electrons, coupling exergonic and endergonic oxidation-reduction reactions.

PubMed

Peters, John W; Beratan, David N; Schut, Gerrit J; Adams, Michael W W

2018-04-19

Bifurcating electrons to couple endergonic and exergonic electron-transfer reactions has been shown to have a key role in energy conserving redox enzymes. Bifurcating enzymes require a redox center that is capable of directing electron transport along two spatially separate pathways. Research into the nature of electron bifurcating sites indicates that one of the keys is the formation of a low potential oxidation state to satisfy the energetics required of the endergonic half reaction, indicating that any redox center (organic or inorganic) that can exist in multiple oxidation states with sufficiently separated redox potentials should be capable of electron bifurcation. In this Feature Article, we explore a paradigm for bifurcating electrons down independent high and low potential pathways, and describe redox cofactors that have been demonstrated or implicated in driving this unique biochemistry.

Unfolding pathway of CotA-laccase and the role of copper on the prevention of refolding through aggregation of the unfolded state

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

Fernandes, Andre T.; Lopes, Carlos; Martins, Ligia O.

2012-06-08

Highlights: Black-Right-Pointing-Pointer CotA-laccase unfolds with an intermediate state. Black-Right-Pointing-Pointer Copper stabilizes the native and the intermediate state. Black-Right-Pointing-Pointer Copper binding to the unfolded state prevents refolding through protein aggregation. Black-Right-Pointing-Pointer Copper incorporation in CotA-laccase occurs as a later step during folding. -- Abstract: Copper is a redox-active metal and the main player in electron transfer reactions occurring in multicopper oxidases. The role of copper in the unfolding pathway and refolding of the multicopper oxidase CotA laccase in vitro was solved using double-jump stopped-flow experiments. Unfolding of apo- and holo-CotA was described as a three-state process with accumulation of an intermediatemore » in between the native and unfolded state. Copper stabilizes the native holo-CotA but also the intermediate state showing that copper is still bound to this state. Also, copper binds to unfolded holo-CotA in a non-native coordination promoting CotA aggregation and preventing refolding to the native structure. These results gather information on unfolding/folding pathways of multicopper oxidases and show that copper incorporation in vivo should be a tight controlled process as copper binding to the unfolded state under native conditions promotes protein aggregation.« less

An electronic flow control system for a variable-rate tree sprayer

USDA-ARS?s Scientific Manuscript database

Precise modulation of nozzle flow rates is a critical measure to achieve variable-rate spray applications. An electronic flow rate control system accommodating with microprocessors and pulse width modulation (PWM) controlled solenoid valves was designed to manipulate the output of spray nozzles inde...

Effect of flow on endothelial endocytosis of nanocarriers targeted to ICAM-1

PubMed Central

Bhowmick, Tridib; Berk, Erik; Cui, Xiumin; Muzykantov, Vladimir R.; Muro, Silvia

2011-01-01

Delivery of drugs into the endothelium by nanocarriers targeted to endothelial determinants may improve treatment of vascular maladies. This is the case for intercellular adhesion molecule 1 (ICAM-1), a glycoprotein overexpressed on endothelial cells (ECs) in many pathologies. ICAM-1-targeted nanocarriers bind to and are internalized by ECs via a non-classical pathway, CAM-mediated endocytosis. In this work we studied the effects of endothelial adaptation to physiological flow on the endocytosis of model polymer nanocarriers targeted to ICAM-1 (anti-ICAM/NCs, ~180-nm diameter). Culturing established endothelial-like cells (EAhy926 cells) and primary human umbilical vein ECs (HUVECs) under 4 dyn/cm2 laminar shear stress for 24 h resulted in flow adaptation: cell elongation and formation of actin stress fibers aligned to the flow direction. Fluorescence microscopy showed that flow-adapted cells internalized anti-ICAM/NCs under flow, although at slower rate versus non flow-adapted cells under static incubation (~35% reduction). Uptake was inhibited by amiloride, whereas marginally affected by filipin and cadaverine, implicating that CAM-endocytosis accounts for anti-ICAM/NC uptake under flow. Internalization under flow was more modestly affected by inhibiting protein kinase C, which regulates actin remodeling during CAM-endocytosis. Actin recruitment to stress fibers that maintain the cell shape under flow may delay uptake of anti-ICAM/NCs under this condition by interfering with actin reorganization needed for CAM-endocytosis. Electron microscopy revealed somewhat slow, yet effective endocytosis of anti-ICAM/NCs by pulmonary endothelium after i.v. injection in mice, similar to that of flow-adapted cell cultures: ~40% (30 min) and 80% (3 h) internalization. Similar to cell culture data, uptake was slightly faster in capillaries with lower shear stress. Further, LPS treatment accelerated internalization of anti-ICAM/NCs in mice. Therefore, regulation of endocytosis of ICAM-1-targeted nanocarriers by flow and endothelial status may modulate drug delivery into ECs exposed to different physiological (capillaries vs. arterioles/venules) or pathological (ischemia, inflammation) levels and patterns of blood flow. PMID:21951807

Effect of flow on endothelial endocytosis of nanocarriers targeted to ICAM-1.

PubMed

Bhowmick, Tridib; Berk, Erik; Cui, Xiumin; Muzykantov, Vladimir R; Muro, Silvia

2012-02-10

Delivery of drugs into the endothelium by nanocarriers targeted to endothelial determinants may improve treatment of vascular maladies. This is the case for intercellular adhesion molecule 1 (ICAM-1), a glycoprotein overexpressed on endothelial cells (ECs) in many pathologies. ICAM-1-targeted nanocarriers bind to and are internalized by ECs via a non-classical pathway, CAM-mediated endocytosis. In this work we studied the effects of endothelial adaptation to physiological flow on the endocytosis of model polymer nanocarriers targeted to ICAM-1 (anti-ICAM/NCs, ~180 nm diameter). Culturing established endothelial-like cells (EAhy926 cells) and primary human umbilical vein ECs (HUVECs) under 4 dyn/cm(2) laminar shear stress for 24 h resulted in flow adaptation: cell elongation and formation of actin stress fibers aligned to the flow direction. Fluorescence microscopy showed that flow-adapted cells internalized anti-ICAM/NCs under flow, although at slower rate versus non flow-adapted cells under static incubation (~35% reduction). Uptake was inhibited by amiloride, whereas marginally affected by filipin and cadaverine, implicating that CAM-endocytosis accounts for anti-ICAM/NC uptake under flow. Internalization under flow was more modestly affected by inhibiting protein kinase C, which regulates actin remodeling during CAM-endocytosis. Actin recruitment to stress fibers that maintain the cell shape under flow may delay uptake of anti-ICAM/NCs under this condition by interfering with actin reorganization needed for CAM-endocytosis. Electron microscopy revealed somewhat slow, yet effective endocytosis of anti-ICAM/NCs by pulmonary endothelium after i.v. injection in mice, similar to that of flow-adapted cell cultures: ~40% (30 min) and 80% (3 h) internalization. Similar to cell culture data, uptake was slightly faster in capillaries with lower shear stress. Further, LPS treatment accelerated internalization of anti-ICAM/NCs in mice. Therefore, regulation of endocytosis of ICAM-1-targeted nanocarriers by flow and endothelial status may modulate drug delivery into ECs exposed to different physiological (capillaries vs. arterioles/venules) or pathological (ischemia, inflammation) levels and patterns of blood flow. Copyright © 2011 Elsevier B.V. All rights reserved.

Ion flow experiments in a multipole discharge chamber

NASA Technical Reports Server (NTRS)

Kaufman, H. R.; Robinson, R. S.; Frisa, L. E.

1982-01-01

It has been customary to assume that ions flow nearly equally in all directions from the ion production region within an electron-bombardment discharge chamber. Ion flow measurements in a multipole discharge chamber have shown that this assumption is not true. In general, the electron current through a magnetic field can alter the electron density, and hence the ion density, in such a way that ions tend to be directed away from the region bounded by the magnetic field. When this mechanism is understood, it becomes evident that many past discharge chamber designs have operated with a preferentially directed flow of ions.

Microscale Digital Vacuum Electronic Gates

NASA Technical Reports Server (NTRS)

Manohara, Harish (Inventor); Mojarradi, Mohammed M. (Inventor)

2014-01-01

Systems and methods in accordance with embodiments of the invention implement microscale digital vacuum electronic gates. In one embodiment, a microscale digital vacuum electronic gate includes: a microscale field emitter that can emit electrons and that is a microscale cathode; and a microscale anode; where the microscale field emitter and the microscale anode are disposed within at least a partial vacuum; where the microscale field emitter and the microscale anode are separated by a gap; and where the potential difference between the microscale field emitter and the microscale anode is controllable such that the flow of electrons between the microscale field emitter and the microscale anode is thereby controllable; where when the microscale anode receives a flow of electrons, a first logic state is defined; and where when the microscale anode does not receive a flow of electrons, a second logic state is defined.

Impact of dissolution and carbonate precipitation on carbon storage in basalt

NASA Astrophysics Data System (ADS)

Wells, R. K.; Xiong, W.; Tadeoye, J.; Menefee, A.; Ellis, B. R.; Skemer, P. A.; Giammar, D.

2016-12-01

The spatial evolution of silicate mineral dissolution, carbonate precipitation, and the transport of fluids influence the viability of carbon storage in basalt reservoirs. Dissolution of natural basalt and subsequent carbonate precipitation in systems with different transport processes operating were characterized using static and flow-through (5 mL/hr) experiments at 50, 100, and 150 °C, and 100 bar CO2. Intact samples and cores with milled pathways that simulate fractures were tested. Spatial and mineralogical patterns in dissolution and precipitation were analyzed using optical and electron microscopy, microCT scanning, and surface roughness data. Precipitates and fluid chemistry were analyzed using Raman spectroscopy, SEM-EDS, and ICP-MS. Analysis of the bulk solution and surface topography suggests dissolution of olivine and pyroxene grains begins within hours of the start of the experiments. In flow-through experiments, total effluent cation concentrations reach a peak concentration within a few hours then drop towards a steady state within a few days. In static experiments, the initial rate of cation release is faster than it is after several weeks. In both cases Ca2+, Mg2+, and Fe2+ are the dominant cations in solution in the initial stages of reaction. Lower concentrations of Na2+, K+, and Al3+, and the preservation of feldspar and matrix grains after several weeks of reaction indicate the slow reactivity of these minerals. As the reaction progresses, the surface roughness increases steadily with cavities developing at the sites of olivine and pyroxene grains. Post-reaction analysis of basalt samples reacted at static conditions with milled pathways reveals that both siderite and amorphous silica precipitated within diffusion-limited zones as early as 4-6 weeks. Siderite abundance varies with distance along the pathway with the highest concentration of carbonates 1-2 cm below the fracture opening. Siderite precipitates are large enough to fill fracture opening 100 μm wide within 4-6 weeks.

Quantification and Control of Wall Effects in Porous Media Experiments

NASA Astrophysics Data System (ADS)

Roth, E. J.; Mays, D. C.; Neupauer, R.; Crimaldi, J. P.

2017-12-01

Fluid flow dynamics in porous media are dominated by media heterogeneity. This heterogeneity can create preferential pathways in which local seepage velocities dwarf system seepage velocities, further complicating an already incomplete understanding of dispersive processes. In physical models of porous media flows, apparatus walls introduce preferential flow paths (i.e., wall effects) that may overwhelm other naturally occurring preferential pathways within the apparatus, leading to deceptive results. We used planar laser-induced fluorescence (PLIF) in conjunction with refractive index matched (RIM) porous media and pore fluid to observe fluid dynamics in the porous media, with particular attention to the region near the apparatus walls in a 17 cm x 8 cm x 7 cm uniform flow cell. Hexagonal close packed spheres were used to create an isotropic, homogenous porous media field in the interior of the apparatus. Visualization of the movement of a fluorescent dye revealed the influence of the wall in creating higher permeability preferential flow paths in an otherwise homogenous media packing. These preferential flow paths extended approximately one half of one sphere diameter from the wall for homogenously packed regions, with a quickly diminishing effect on flow dynamics for homogenous media adjacent to the preferential pathway, but with major influence on flow dynamics for adjoining heterogeneous regions. Multiple approaches to mitigate wall effects were investigated, and a modified wall was created such that the fluid dynamics near the wall mimics the fluid dynamics within the homogenous porous media. This research supports the design of a two-dimensional experimental apparatus that will simulate engineered pumping schemes for use in contaminant remediation. However, this research could benefit the design of fixed bed reactors or other engineering challenges in which vessel walls contribute to unwanted preferential flow.

Visualization of three pathways for macromolecule transport across cultured endothelium and their modification by flow.

PubMed

Ghim, Mean; Alpresa, Paola; Yang, Sung-Wook; Braakman, Sietse T; Gray, Stephen G; Sherwin, Spencer J; van Reeuwijk, Maarten; Weinberg, Peter D

2017-11-01

Transport of macromolecules across vascular endothelium and its modification by fluid mechanical forces are important for normal tissue function and in the development of atherosclerosis. However, the routes by which macromolecules cross endothelium, the hemodynamic stresses that maintain endothelial physiology or trigger disease, and the dependence of transendothelial transport on hemodynamic stresses are controversial. We visualized pathways for macromolecule transport and determined the effect on these pathways of different types of flow. Endothelial monolayers were cultured under static conditions or on an orbital shaker producing different flow profiles in different parts of the wells. Fluorescent tracers that bound to the substrate after crossing the endothelium were used to identify transport pathways. Maps of tracer distribution were compared with numerical simulations of flow to determine effects of different shear stress metrics on permeability. Albumin-sized tracers dominantly crossed the cultured endothelium via junctions between neighboring cells, high-density lipoprotein-sized tracers crossed at tricellular junctions, and low-density lipoprotein-sized tracers crossed through cells. Cells aligned close to the angle that minimized shear stresses across their long axis. The rate of paracellular transport under flow correlated with the magnitude of these minimized transverse stresses, whereas transport across cells was uniformly reduced by all types of flow. These results contradict the long-standing two-pore theory of solute transport across microvessel walls and the consensus view that endothelial cells align with the mean shear vector. They suggest that endothelial cells minimize transverse shear, supporting its postulated proatherogenic role. Preliminary data show that similar tracer techniques are practicable in vivo. NEW & NOTEWORTHY Solutes of increasing size crossed cultured endothelium through intercellular junctions, through tricellular junctions, or transcellularly. Cells aligned to minimize the shear stress acting across their long axis. Paracellular transport correlated with the level of this minimized shear, but transcellular transport was reduced uniformly by flow regardless of the shear profile. Copyright © 2017 the American Physiological Society.

Investigating dysregulated pathways in Staphylococcus aureus (SA) exposed macrophages based on pathway interaction network.

PubMed

Zhou, Wei; Zhang, Yan; Li, Yue-Hua; Wang, Shuang; Zhang, Jing-Jing; Zhang, Cui-Xia; Zhang, Zhi-Sheng

2017-02-01

This work aimed to identify dysregulated pathways for Staphylococcus aureus (SA) exposed macrophages based on pathway interaction network (PIN). The inference of dysregulated pathways was comprised of four steps: preparing gene expression data, protein-protein interaction (PPI) data and pathway data; constructing a PIN dependent on the data and Pearson correlation coefficient (PCC); selecting seed pathway from PIN by computing activity score for each pathway according to principal component analysis (PCA) method; and investigating dysregulated pathways in a minimum set of pathways (MSP) utilizing seed pathway and the area under the receiver operating characteristics curve (AUC) index implemented in support vector machines (SVM) model. A total of 20,545 genes, 449,833 interactions and 1189 pathways were obtained in the gene expression data, PPI data and pathway data, respectively. The PIN was consisted of 8388 interactions and 1189 nodes, and Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins was identified as the seed pathway. Finally, 15 dysregulated pathways in MSP (AUC=0.999) were obtained for SA infected samples, such as Respiratory electron transport and DNA Replication. We have identified 15 dysregulated pathways for SA infected macrophages based on PIN. The findings might provide potential biomarkers for early detection and therapy of SA infection, and give insights to reveal the molecular mechanism underlying SA infections. However, how these dysregulated pathways worked together still needs to be studied. Copyright © 2016 Elsevier Ltd. All rights reserved.

Arbuscular mycorrhizal symbiosis increases relative apoplastic water flow in roots of the host plant under both well-watered and drought stress conditions.

PubMed

Bárzana, Gloria; Aroca, Ricardo; Paz, José Antonio; Chaumont, François; Martinez-Ballesta, Mari Carmen; Carvajal, Micaela; Ruiz-Lozano, Juan Manuel

2012-04-01

The movement of water through mycorrhizal fungal tissues and between the fungus and roots is little understood. It has been demonstrated that arbuscular mycorrhizal (AM) symbiosis regulates root hydraulic properties, including root hydraulic conductivity. However, it is not clear whether this effect is due to a regulation of root aquaporins (cell-to-cell pathway) or to enhanced apoplastic water flow. Here we measured the relative contributions of the apoplastic versus the cell-to-cell pathway for water movement in roots of AM and non-AM plants. We used a combination of two experiments using the apoplastic tracer dye light green SF yellowish and sodium azide as an inhibitor of aquaporin activity. Plant water and physiological status, root hydraulic conductivity and apoplastic water flow were measured. Roots of AM plants enhanced significantly relative apoplastic water flow as compared with non-AM plants and this increase was evident under both well-watered and drought stress conditions. The presence of the AM fungus in the roots of the host plants was able to modulate the switching between apoplastic and cell-to-cell water transport pathways. The ability of AM plants to switch between water transport pathways could allow a higher flexibility in the response of these plants to water shortage according to the demand from the shoot.

Arbuscular mycorrhizal symbiosis increases relative apoplastic water flow in roots of the host plant under both well-watered and drought stress conditions

PubMed Central

Bárzana, Gloria; Aroca, Ricardo; Paz, José Antonio; Chaumont, François; Martinez-Ballesta, Mari Carmen; Carvajal, Micaela; Ruiz-Lozano, Juan Manuel

2012-01-01

Background and Aims The movement of water through mycorrhizal fungal tissues and between the fungus and roots is little understood. It has been demonstrated that arbuscular mycorrhizal (AM) symbiosis regulates root hydraulic properties, including root hydraulic conductivity. However, it is not clear whether this effect is due to a regulation of root aquaporins (cell-to-cell pathway) or to enhanced apoplastic water flow. Here we measured the relative contributions of the apoplastic versus the cell-to-cell pathway for water movement in roots of AM and non-AM plants. Methods We used a combination of two experiments using the apoplastic tracer dye light green SF yellowish and sodium azide as an inhibitor of aquaporin activity. Plant water and physiological status, root hydraulic conductivity and apoplastic water flow were measured. Key Results Roots of AM plants enhanced significantly relative apoplastic water flow as compared with non-AM plants and this increase was evident under both well-watered and drought stress conditions. The presence of the AM fungus in the roots of the host plants was able to modulate the switching between apoplastic and cell-to-cell water transport pathways. Conclusions The ability of AM plants to switch between water transport pathways could allow a higher flexibility in the response of these plants to water shortage according to the demand from the shoot. PMID:22294476

Lack of a peroxiredoxin suppresses the lethality of cells devoid of electron donors by channelling electrons to oxidized ribonucleotide reductase.

PubMed

Boronat, Susanna; Domènech, Alba; Carmona, Mercè; García-Santamarina, Sarela; Bañó, M Carmen; Ayté, José; Hidalgo, Elena

2017-06-01

The thioredoxin and glutaredoxin pathways are responsible of recycling several enzymes which undergo intramolecular disulfide bond formation as part of their catalytic cycles such as the peroxide scavengers peroxiredoxins or the enzyme ribonucleotide reductase (RNR). RNR, the rate-limiting enzyme of deoxyribonucleotide synthesis, is an essential enzyme relying on these electron flow cascades for recycling. RNR is tightly regulated in a cell cycle-dependent manner at different levels, but little is known about the participation of electron donors in such regulation. Here, we show that cytosolic thioredoxins Trx1 and Trx3 are the primary electron donors for RNR in fission yeast. Unexpectedly, trx1 transcript and Trx1 protein levels are up-regulated in a G1-to-S phase-dependent manner, indicating that the supply of electron donors is also cell cycle-regulated. Indeed, genetic depletion of thioredoxins triggers a DNA replication checkpoint ruled by Rad3 and Cds1, with the final goal of up-regulating transcription of S phase genes and constitutive RNR synthesis. Regarding the thioredoxin and glutaredoxin cascades, one combination of gene deletions is synthetic lethal in fission yeast: cells lacking both thioredoxin reductase and cytosolic dithiol glutaredoxin. We have isolated a suppressor of this lethal phenotype: a mutation at the Tpx1-coding gene, leading to a frame shift and a loss-of-function of Tpx1, the main client of electron donors. We propose that in a mutant strain compromised in reducing equivalents, the absence of an abundant and competitive substrate such as the peroxiredoxin Tpx1 has been selected as a lethality suppressor to favor RNR function at the expense of the non-essential peroxide scavenging function, to allow DNA synthesis and cell growth.

Hydrogen-bond Specific Materials Modification in Group IV Semiconductors

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

Tolk, Norman H.; Feldman, L. C.; Luepke, G.

Executive summary Semiconductor dielectric crystals consist of two fundamental components: lattice atoms and electrons. The former component provides a crystalline structure that can be disrupted by various defects or the presence of an interface, or by transient oscillations known as phonons. The latter component produces an energetic structure that is responsible for the optical and electronic properties of the material, and can be perturbed by lattice defects or by photo-excitation. Over the period of this project, August 15, 1999 to March 31, 2015, a persistent theme has been the elucidation of the fundamental role of defects arising from the presencemore » of radiation damage, impurities (in particular, hydrogen), localized strain or some combination of all three. As our research effort developed and evolved, we have experienced a few title changes, which reflected this evolution. Throughout the project, ultrafast lasers usually in a pump-probe configuration provided the ideal means to perturb and study semiconductor crystals by both forms of excitation, vibrational (phonon) and electronic (photon). Moreover, we have found in the course of this research that there are many interesting and relevant scientific questions that may be explored when phonon and photon excitations are controlled separately. Our early goals were to explore the dynamics of bond-selective vibrational excitation of hydrogen from point defects and impurities in crystalline and amorphous solids, initiating an investigation into the behavior of hydrogen isotopes utilizing a variety of ultrafast characterization techniques, principally transient bleaching spectroscopy to experimentally obtain vibrational lifetimes. The initiative could be divided into three related areas: (a) investigation of the change in electronic structure of solids due to the presence of hydrogen defect centers, (b) dynamical studies of hydrogen in materials and (c) characterization and stability of metastable hydrogen impurity states under transient compression. This research focused on the characterization of photon and ion stimulated hydrogen related defect and impurity reactions and migration in solid state matter, which requires a detailed understanding of the rates and pathways of vibrational energy flow, of the transfer channels and of the coupling mechanisms between local vibrational modes (LVMs) and phonon bath as well as the electronic system of the host material. It should be stressed that researchers at Vanderbilt and William and Mary represented a unique group with a research focus and capabilities for low temperature creation and investigation of such material systems. Later in the program, we carried out a vigorous research effort addressing the roles of defects, interfaces, and dopants on the optical and electronic characteristics of semiconductor crystals, using phonon generation by means of ultrafast coherent acoustic phonon (CAP) spectroscopy, nonlinear characterization using second harmonic generation (SHG), and ultrafast pump-and-probe reflectivity and absorption measurements. This program featured research efforts from hydrogen defects in silicon alone to other forms of defects such as interfaces and dopant layers, as well as other important semiconducting systems. Even so, the emphasis remains on phenomena and processes far from equilibrium, such as hot electron effects and travelling localized phonon waves. This program relates directly to the mission of the Department of Energy. Knowledge of the rates and pathways of vibrational energy flow in condensed matter is critical for understanding dynamical processes in solids including electronically, optically and thermally stimulated defect and impurity reactions and migration. The ability to directly probe these pathways and rates allows tests of theory and scaling laws at new levels of precision. Hydrogen embedded in model crystalline semiconductors and metal oxides is of particular interest, since the associated local mode can be excited cleanly, and is usually well-separated in energy from the phonon bath. These basic dynamical studies have provided new insights for example into the fundamental mechanisms that control proton diffusion in these oxides. This area of materials science has largely fulfilled its promise to identify degradation mechanisms in electronic and optoelectronic devices, and to advance solid oxide proton conductors for fuel cells, gas sensors and proton-exchange membrane applications. It also provides the basis for innovations in materials synthesis involving atomic-selective diffusion and desorption.« less

The Expression of Dectin-1, Irak1 and Rip2 During the Host Response to Aspergillus fumigatus.

PubMed

Liu, Jinguo; Yu, Lin; Chen, Cuicui; Zhou, Jian; Gong, Xin; Li, Dandan; Hou, Dongni; Song, Yuanlin; Shao, Changzhou

2018-04-01

C-type lectin receptors (CLRs), Toll-like receptors (TLRs), and Nod-like receptors (NLRs) have the ability to recognize Aspergillus fumigatus (A. fumigates) and induce innate immune response. Dectin-1 is a well-described CLR, while interleukin-1 receptor-associated kinase 1 (Irak1) and receptor-interacting protein 2 (Rip2) are pivotal adaptor proteins of TLRs and NLRs signaling pathways, respectively. Our primary aim is to elucidate whether Dectin-1 regulates the expression of Irak1 and Rip2, and confirm that CLRs, TLRs, and NLRs pathways act synergistically in response to A. fumigatus infection. Pulmonary infection mouse models were established. Myeloid cells were differentiated in cell culture and examined by inverted microscopy, flow cytometry, and scanning electron microscopy. The relative mRNA levels were determined by qRT-PCR. The protein expression levels were determined by immunohistochemistry and Western blot. The expression of Dectin-1, Irak1, Rip2, and phosphorylation level of nuclear factor (NF)-κB p65 were induced by conidia in immunocompetent mice, while their expression and phosphorylation level were inhibited in immunocompromised mice after the administration of conidia. Conidia increased the expression of Dectin-1, Irak1, and Rip2 in myeloid cells, while Dectin-1 silencing significantly reduced their expression. Our findings demonstrate that Dectin-1, Irak1, and Rip2 are involved in response to A. fumigatus infection. Dectin-1 modulates the expression of Irak1 and Rip2. Additionally, these three signaling pathways are interconnected, and CLRs pathway plays a dominant role against A. fumigatus invasion.

miR-34a mediates oxaliplatin resistance of colorectal cancer cells by inhibiting macroautophagy via transforming growth factor-β/Smad4 pathway.

PubMed

Sun, Chen; Wang, Fu-Jing; Zhang, Hao-Gang; Xu, Xun-Zheng; Jia, Rui-Chun; Yao, Lei; Qiao, Peng-Fei

2017-03-14

To investigate whether microRNA (miR)-34a mediates oxaliplatin (OXA) resistance of colorectal cancer (CRC) cells by inhibiting macroautophagy via the transforming growth factor (TGF)-β/Smad4 pathway. miR-34a expression levels were detected in CRC tissues and CRC cell lines by quantitative real-time polymerase chain reaction. Computational search, functional luciferase assay and western blotting were used to demonstrate the downstream target of miR-34a in CRC cells. Cell viability was measured with Cell Counting Kit-8. Apoptosis and macroautophagy of CRC cells were analyzed by flow cytometry and transmission electron microscopy, and expression of beclin I and LC3-II was detected by western blotting. Expression of miR-34a was significantly reduced while expression of TGF-β and Smad4 was increased in CRC patients treated with OXA-based chemotherapy. OXA treatment also resulted in decreased miR-34a levels and increased TGF-β and Smad4 levels in both parental cells and the OXA-resistant CRC cells. Activation of macroautophagy contributed to OXA resistance in CRC cells. Expression levels of Smad4 and miR-34a in CRC patients had a significant inverse correlation and overexpressing miR-34a inhibited macroautophagy activation by directly targeting Smad4 through the TGF-β/Smad4 pathway. OXA-induced downregulation of miR-34a and increased drug resistance by activating macroautophagy in CRC cells. miR-34a mediates OXA resistance of CRC by inhibiting macroautophagy via the TGF-β/Smad4 pathway.

One hundred fold increase in current carrying capacity in a carbon nanotube–copper composite

PubMed Central

Subramaniam, Chandramouli; Yamada, Takeo; Kobashi, Kazufumi; Sekiguchi, Atsuko; Futaba, Don N.; Yumura, Motoo; Hata, Kenji

2013-01-01

Increased portability, versatility and ubiquity of electronics devices are a result of their progressive miniaturization, requiring current flow through narrow channels. Present-day devices operate close to the maximum current-carrying-capacity (that is, ampacity) of conductors (such as copper and gold), leading to decreased lifetime and performance, creating demand for new conductors with higher ampacity. Ampacity represents the maximum current-carrying capacity of the object that depends both on the structure and material. Here we report a carbon nanotube–copper composite exhibiting similar conductivity (2.3–4.7 × 105 S cm−1) as copper (5.8 × 105 S cm−1), but with a 100-times higher ampacity (6 × 108 A cm−2). Vacuum experiments demonstrate that carbon nanotubes suppress the primary failure pathways in copper as observed by the increased copper diffusion activation energy (∼2.0 eV) in carbon nanotube–copper composite, explaining its higher ampacity. This is the only material with both high conductivity and high ampacity, making it uniquely suited for applications in microscale electronics and inverters. PMID:23877359

Electronic waste leachate-mediated DNA fragmentation and cell death by apoptosis in mouse fibroblast (NIH/3T3) cell line.

PubMed

Alabi, Okunola A; Bakare, Adekunle A; Filippin-Monteiro, Fabíola B; Sierra, Jelver A; Creczynski-Pasa, Tânia B

2013-08-01

This study investigated the apoptotic effect of electronic waste on fibroblast cell line. Cells were treated with different concentrations of the leachate for 24h. Cell viability was detected by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) test, nuclear morphology of cells was explored by acridine orange (AO)/ethidium bromide (EB) double staining, mitochondrial membrane potential was evaluated using JC-1 probe while cell cycle analysis was conducted using flow cytometry. The oxidative status was detected using DCFH-DA (dichlorofluorescin diacetate) probe and the relationship between cell death and ROS (reactive oxygen species) was investigated using N-acetylcysteine. Results showed an increased cell death as detected by MTT assay and AO/EB staining. Cell cycle analysis indicated an induction of sub/G1 events while JC-1 probe showed significant disruption of mitochondrial membrane potential. There was significant induction of ROS, while N-acetylcysteine protected the cells from DNA damage. These suggest apoptotic pathway as a possible mechanism of e-waste induced cyto-genotoxicity. Copyright © 2013 Elsevier Inc. All rights reserved.

Diagnostic value and cost-effectiveness of good quality digital images accompanying electronic referrals for suspected skin malignancies.

PubMed

Ng, Michael F Y; Stevenson, J Howard

2011-04-01

The aim of this study was to investigate the outcome and cost-effectiveness of good and poor quality photographs accompanying the electronic referrals for suspected skin malignancies. A retrospective study of 100 patients, divided into 2 groups, 50 with good quality photographs and 50 with poor quality photographs. Patients with no digital images, or who failed to attend, or patients with incomplete notes were excluded from the study. The treatment pathway, waiting times, and estimated cost between the 2 groups were compared. Good photographs were more likely to be treated at the 1-Stop Clinic (P = 0.05). Good images had a better positive predictive value than poor quality images (62.55% vs. 42.86%). Good quality images are more accurate than poor quality images in triaging of patients, and thus more effective in facilitating the treatment of malignant lesions timely. Good quality photographs allow a delayed appropriate treatment of benign lesions. This increases the safety for patients in a queue in a rationed health care system, and improves patient flow.

One hundred fold increase in current carrying capacity in a carbon nanotube-copper composite

NASA Astrophysics Data System (ADS)

Subramaniam, Chandramouli; Yamada, Takeo; Kobashi, Kazufumi; Sekiguchi, Atsuko; Futaba, Don N.; Yumura, Motoo; Hata, Kenji

2013-07-01

Increased portability, versatility and ubiquity of electronics devices are a result of their progressive miniaturization, requiring current flow through narrow channels. Present-day devices operate close to the maximum current-carrying-capacity (that is, ampacity) of conductors (such as copper and gold), leading to decreased lifetime and performance, creating demand for new conductors with higher ampacity. Ampacity represents the maximum current-carrying capacity of the object that depends both on the structure and material. Here we report a carbon nanotube-copper composite exhibiting similar conductivity (2.3-4.7 × 105Scm-1) as copper (5.8 × 105Scm-1), but with a 100-times higher ampacity (6 × 108Acm-2). Vacuum experiments demonstrate that carbon nanotubes suppress the primary failure pathways in copper as observed by the increased copper diffusion activation energy (~2.0eV) in carbon nanotube-copper composite, explaining its higher ampacity. This is the only material with both high conductivity and high ampacity, making it uniquely suited for applications in microscale electronics and inverters.

CymA and Exogenous Flavins Improve Extracellular Electron Transfer and Couple It to Cell Growth in Mtr-Expressing Escherichia coli

DOE PAGES

Jensen, Heather M.; TerAvest, Michaela A.; Kokish, Mark G.; ...

2016-03-22

Introducing extracellular electron transfer pathways into heterologous organisms offers the opportunity to explore fundamental biogeochemical processes and to biologically alter redox states of exogenous metals for various applications. While expression of the MtrCAB electron nanoconduit from Shewanella oneidensis MR-1 permits extracellular electron transfer in Escherichia coli, the low electron flux and absence of growth in these cells limits their practicality for such applications. In this paper, we investigate how the rate of electron transfer to extracellular Fe(III) and cell survival in engineered E. coli are affected by mimicking different features of the S. oneidensis pathway: the number of electron nanoconduits,more » the link between the quinol pool and MtrA, and the presence of flavin-dependent electron transfer. While increasing the number of pathways does not significantly improve the extracellular electron transfer rate or cell survival, using the native inner membrane component, CymA, significantly improves the reduction rate of extracellular acceptors and increases cell viability. Strikingly, introducing both CymA and riboflavin to Mtr-expressing E. coli also allowed these cells to couple metal reduction to growth, which is the first time an increase in biomass of an engineered E. coli has been observed under Fe 2O 3 (s) reducing conditions. Overall and finally, this work provides engineered E. coli strains for modulating extracellular metal reduction and elucidates critical factors for engineering extracellular electron transfer in heterologous organisms.« less

CymA and Exogenous Flavins Improve Extracellular Electron Transfer and Couple It to Cell Growth in Mtr-Expressing Escherichia coli

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

Jensen, Heather M.; TerAvest, Michaela A.; Kokish, Mark G.

Introducing extracellular electron transfer pathways into heterologous organisms offers the opportunity to explore fundamental biogeochemical processes and to biologically alter redox states of exogenous metals for various applications. While expression of the MtrCAB electron nanoconduit from Shewanella oneidensis MR-1 permits extracellular electron transfer in Escherichia coli, the low electron flux and absence of growth in these cells limits their practicality for such applications. In this paper, we investigate how the rate of electron transfer to extracellular Fe(III) and cell survival in engineered E. coli are affected by mimicking different features of the S. oneidensis pathway: the number of electron nanoconduits,more » the link between the quinol pool and MtrA, and the presence of flavin-dependent electron transfer. While increasing the number of pathways does not significantly improve the extracellular electron transfer rate or cell survival, using the native inner membrane component, CymA, significantly improves the reduction rate of extracellular acceptors and increases cell viability. Strikingly, introducing both CymA and riboflavin to Mtr-expressing E. coli also allowed these cells to couple metal reduction to growth, which is the first time an increase in biomass of an engineered E. coli has been observed under Fe 2O 3 (s) reducing conditions. Overall and finally, this work provides engineered E. coli strains for modulating extracellular metal reduction and elucidates critical factors for engineering extracellular electron transfer in heterologous organisms.« less

FAST TRACK COMMUNICATION: Attosecond correlation dynamics during electron tunnelling from molecules

NASA Astrophysics Data System (ADS)

Walters, Zachary B.; Smirnova, Olga

2010-08-01

In this communication, we present an analytical theory of strong-field ionization of molecules, which takes into account the rearrangement of multiple interacting electrons during the ionization process. We show that such rearrangement offers an alternative pathway to the ionization of orbitals more deeply bound than the highest occupied molecular orbital. This pathway is not subject to the full exponential suppression characteristic of direct tunnel ionization from the deeper orbitals. The departing electron produces an 'attosecond correlation pulse' which controls the rearrangement during the tunnelling process. The shape and duration of this pulse are determined by the electronic structure of the relevant states, molecular orientation and laser parameters.

On/off switching of capillary vessel flow controls mitochondrial and glycolysis pathways for energy production.

PubMed

Abo, Toru; Watanabe, Mayumi; Tomiyama, Chikako; Kanda, Yasuhiro

2014-07-01

Capillary vessel flow in the base of the fingernail can be observed by microscopy. This flow is switched off under some conditions, such as coldness, surprise, and anger and is switched on again under other conditions, such as warming, relaxation, and mild exercise. In other words, capillary vessels perform two functions: switching flow on and off. It is speculated that the switch-off function is necessary to direct energy production to the glycolysis pathway, while the switch-on function is necessary for the mitochondrial pathway. This is because glycolysis takes place under anaerobic conditions, while oxidative phosphorylation in the mitochondria proceeds under aerobic conditions in the body. To switch off circulation, the negative electric charges on the surface of erythrocytes and the capillary wall may be decreased by stimulation of the sympathetic nerves and secretion of steroid hormones. Negative charge usually acts as repulsive force between erythrocytes and between erythrocytes and the capillary wall. By decreasing the negative charge, erythrocytes can aggregate and also adhere to the capillary wall. These behaviors may be related to the capillary flow switch-off function. Here, it is emphasized that the capillary vessels possess not only a switch-on function but also a switch-off function for circulation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Structural aspects of denitrifying enzymes.

PubMed

Moura, I; Moura, J J

2001-04-01

The reduction of nitrate to nitrogen gas via nitrite, nitric oxide and nitrous oxide is the metabolic pathway usually known as denitrification, a key step in the nitrogen cycle. As observed for other elemental cycles, a battery of enzymes are utilized, namely the reductases for nitrate, nitrite, nitric oxide and nitrous oxide, as well as multiple electron donors that interact with these enzymes, in order to carry out the stepwise reactions that involve key intermediates. Because of the importance of this pathway (of parallel importance to the nitrogen-fixation pathway), efforts are underway to understand the structures of the participating enzymes and to uncover mechanistic aspects. Three-dimensional structures have been solved for the majority of these enzymes in the past few years, revealing the architecture of the active metal sites as well as global structural aspects, and possible mechanistic aspects. In addition, the recognition of specific electron-transfer partners raises important questions regarding specific electron-transfer pathways, partner recognition and control of metabolism.

Coherent control of the formation of cold heteronuclear molecules by photoassociation

NASA Astrophysics Data System (ADS)

de Lima, Emanuel F.

2017-01-01

We consider the formation of cold diatomic molecules in the electronic ground state by photoassociation of atoms of dissimilar species. A combination of two transition pathways from the free colliding pair of atoms to a bound vibrational level of the electronic molecular ground state is envisioned. The first pathway consists of a pump-dump scheme with two time-delayed laser pulses in the near-infrared frequency domain. The pump pulse drives the transition to a bound vibrational level of an excited electronic state, while the dump pulse transfers the population to a bound vibrational level of the electronic ground state. The second pathway takes advantage of the existing permanent dipole moment and employs a single pulse in the far-infrared domain to drive the transition from the unbound atoms directly to a bound vibrational level in the electronic ground state. We show that this scheme offers the possibility to coherently control the photoassociation yield by manipulating the relative phase and timing of the pulses. The photoassociation mechanism is illustrated for the formation of cold LiCs molecules.

Role of zonal flows in trapped electron mode turbulence through nonlinear gyrokinetic particle and continuum simulationa)

NASA Astrophysics Data System (ADS)

Ernst, D. R.; Lang, J.; Nevins, W. M.; Hoffman, M.; Chen, Y.; Dorland, W.; Parker, S.

2009-05-01

Trapped electron mode (TEM) turbulence exhibits a rich variety of collisional and zonal flow physics. This work explores the parametric variation of zonal flows and underlying mechanisms through a series of linear and nonlinear gyrokinetic simulations, using both particle-in-cell and continuum methods. A new stability diagram for electron modes is presented, identifying a critical boundary at ηe=1, separating long and short wavelength TEMs. A novel parity test is used to separate TEMs from electron temperature gradient driven modes. A nonlinear scan of ηe reveals fine scale structure for ηe≳1, consistent with linear expectation. For ηe<1, zonal flows are the dominant saturation mechanism, and TEM transport is insensitive to ηe. For ηe>1, zonal flows are weak, and TEM transport falls inversely with a power law in ηe. The role of zonal flows appears to be connected to linear stability properties. Particle and continuum methods are compared in detail over a range of ηe=d ln Te/d ln ne values from zero to five. Linear growth rate spectra, transport fluxes, fluctuation wavelength spectra, zonal flow shearing spectra, and correlation lengths and times are in close agreement. In addition to identifying the critical parameter ηe for TEM zonal flows, this paper takes a challenging step in code verification, directly comparing very different methods of simulating simultaneous kinetic electron and ion dynamics in TEM turbulence.

Automated electronic monitoring of circuit pressures during continuous renal replacement therapy: a technical report.

PubMed

Zhang, Ling; Baldwin, Ian; Zhu, Guijun; Tanaka, Aiko; Bellomo, Rinaldo

2015-03-01

Automated electronic monitoring and analysis of circuit pressures during continuous renal replacement therapy (CRRT) has the potential to predict failure and allow intervention to optimise function. Current CRRT machines can measure and store pressure readings for downloading into databases and for analysis. We developed a procedure to obtain such data at intervals of 1 minute and analyse them using the Prismaflex CRRT machine, and we present an example of such analysis. We obtained data on pressures obtained at intervals of 1 minute in a patient with acute kidney injury and sepsis treated with continuous haemofiltration at 2 L/hour of ultrafiltration and a blood flow of 200 mL/minute. Data analysis identified progressive increases in transmembrane pressure (TMP) and prefilter pressure (PFP) from time 0 until 33 hours or clotting. TMP increased from 104 mmHg to 313 mmHg and PFP increased from from 131 mmHg to 185 mmHg. Effluent pressure showed a progressive increase in the negative pressure applied to achieve ultrafiltration from 0 mmHg to -168 mmHg. The inflection point for such changes was also identified. Blood pathway pressures for access and return remained unchanged throughout. Automated electronic monitoring of circuit pressure during CRRT is possible and provides useful information on the evolution of circuit clotting.

Transport coefficients and heat fluxes in non-equilibrium high-temperature flows with electronic excitation

NASA Astrophysics Data System (ADS)

Istomin, V. A.; Kustova, E. V.

2017-02-01

The influence of electronic excitation on transport processes in non-equilibrium high-temperature ionized mixture flows is studied. Two five-component mixtures, N 2 / N2 + / N / N + / e - and O 2 / O2 + / O / O + / e - , are considered taking into account the electronic degrees of freedom for atomic species as well as the rotational-vibrational-electronic degrees of freedom for molecular species, both neutral and ionized. Using the modified Chapman-Enskog method, the transport coefficients (thermal conductivity, shear viscosity and bulk viscosity, diffusion and thermal diffusion) are calculated in the temperature range 500-50 000 K. Thermal conductivity and bulk viscosity coefficients are strongly affected by electronic states, especially for neutral atomic species. Shear viscosity, diffusion, and thermal diffusion coefficients are not sensible to electronic excitation if the size of excited states is assumed to be constant. The limits of applicability for the Stokes relation are discussed; at high temperatures, this relation is violated not only for molecular species but also for electronically excited atomic gases. Two test cases of strongly non-equilibrium flows behind plane shock waves corresponding to the spacecraft re-entry (Hermes and Fire II) are simulated numerically. Fluid-dynamic variables and heat fluxes are evaluated in gases with electronic excitation. In inviscid flows without chemical-radiative coupling, the flow-field is weakly affected by electronic states; however, in viscous flows, their influence can be more important, in particular, on the convective heat flux. The contribution of different dissipative processes to the heat transfer is evaluated as well as the effect of reaction rate coefficients. The competition of diffusion and heat conduction processes reduces the overall effect of electronic excitation on the convective heating, especially for the Fire II test case. It is shown that reliable models of chemical reaction rates are of great importance for accurate predictions of the fluid dynamic variables and heat fluxes.

Relativistic thermal electron scale instabilities in sheared flow plasma

NASA Astrophysics Data System (ADS)

Miller, Evan D.; Rogers, Barrett N.

2016-04-01

> The linear dispersion relation obeyed by finite-temperature, non-magnetized, relativistic two-fluid plasmas is presented, in the special case of a discontinuous bulk velocity profile and parallel wave vectors. It is found that such flows become universally unstable at the collisionless electron skin-depth scale. Further analyses are performed in the limits of either free-streaming ions or ultra-hot plasmas. In these limits, the system is highly unstable in the parameter regimes associated with either the electron scale Kelvin-Helmholtz instability (ESKHI) or the relativistic electron scale sheared flow instability (RESI) recently highlighted by Gruzinov. Coupling between these modes provides further instability throughout the remaining parameter space, provided both shear flow and temperature are finite. An explicit parameter space bound on the highly unstable region is found.

Pathways of nitrobenzene degradation in horizontal subsurface flow constructed wetlands: Effect of intermittent aeration and glucose addition.

PubMed

Kirui, Wesley K; Wu, Shubiao; Kizito, Simon; Carvalho, Pedro N; Dong, Renjie

2016-01-15

Intermittent aeration and addition of glucose were applied to horizontal subsurface flow constructed wetlands in order to investigate the effect on pathways of nitrobenzene (NB) degradation and interactions with microbial nitrogen and sulphur transformations. The experiment was carried out in three phases A, B and C consisting of different NB loading and glucose dosing. For each phase, the effect of aeration was assessed by intermittently aerating one wetland and leaving one unaerated. Regardless of whether or not the wetland was aerated, at an influent NB concentration of 140 mg/L, both wetlands significantly reduced NB to less than 2 mg/L, a reduction efficiency of 98%. However, once the influent NB concentration was increased to 280 mg/L, the aerated wetland had a higher removal performance 82% compared to that of the unaerated wetland 71%. Addition of glucose further intensified the NB removal to 95% in the aerated wetlands and 92% in the unaerated. Aeration of wetlands enhanced NB degradation, but also resulted in higher NB volatilization of 6 mg m(-2) d(-1). The detected high concentration of sulphide 20-60 mg/L in the unaerated wetland gave a strong indication that NB may act as an electron donor to sulphate-reducing bacteria, but this should be further investigated. Aeration positively improved NB removal in constructed wetlands, but resulted in higher NB volatilization. Glucose addition induced co-metabolism to enhance NB degradation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Reverse Methanogenesis and Respiration in Methanotrophic Archaea

PubMed Central

Koehorst, Jasper J.; Jetten, Mike S. M.; Stams, Alfons J. M.

2017-01-01

Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., “trace methane oxidation”). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). Net AOM is exergonic when coupled to an external electron acceptor such as sulfate (ANME-1, ANME-2abc, and ANME-3), nitrate (ANME-2d), or metal (oxides). In this review, the reversibility of the methanogenesis pathway and essential differences between ANME and methanogens are described by combining published information with domain based (meta)genome comparison of archaeal methanotrophs and selected archaea. These differences include abundances and special structure of methyl coenzyme M reductase and of multiheme cytochromes and the presence of menaquinones or methanophenazines. ANME-2a and ANME-2d can use electron acceptors other than sulfate or nitrate for AOM, respectively. Environmental studies suggest that ANME-2d are also involved in sulfate-dependent AOM. ANME-1 seem to use a different mechanism for disposal of electrons and possibly are less versatile in electron acceptors use than ANME-2. Future research will shed light on the molecular basis of reversal of the methanogenic pathway and electron transfer in different ANME types. PMID:28154498

Sinks for photosynthetic electron flow in green petioles and pedicels of Zantedeschia aethiopica: evidence for innately high photorespiration and cyclic electron flow rates.

PubMed

Yiotis, Charilaos; Manetas, Yiannis

2010-07-01

A combination of gas exchange and various chlorophyll fluorescence measurements under varying O(2) and CO(2) partial pressures were used to characterize photosynthesis in green, stomata-bearing petioles of Zantedeschia aethiopica (calla lily) while corresponding leaves served as controls. Compared to leaves, petioles displayed considerably lower CO(2) assimilation rates, limited by both stomatal and mesophyll components. Further analysis of mesophyll limitations indicated lower carboxylating efficiencies and insufficient RuBP regeneration but almost similar rates of linear electron transport. Accordingly, higher oxygenation/carboxylation ratios were assumed for petioles and confirmed by experiments under non-photorespiratory conditions. Higher photorespiration rates in petioles were accompanied by higher cyclic electron flow around PSI, the latter being possibly linked to limitations in electron transport from intermediate electron carriers to end acceptors and low contents of PSI. Based on chlorophyll fluorescence methods, similar conclusions can be drawn for green pedicels, although gas exchange in these organs could not be applied due to their bulky size. Since our test plants were not subjected to stress we argue that higher photorespiration and cyclic electron flow rates are innate attributes of photosynthesis in stalks of calla lily. Active nitrogen metabolism may be inferred, while increased cyclic electron flow may provide the additional ATP required for the enhanced photorespiratory activity in petiole and pedicel chloroplasts and/or the decarboxylation of malate ascending from roots.

First principles studies of electron tunneling in proteins

PubMed Central

Hayashi, Tomoyuki; Stuchebrukhov, Alexei A.

2014-01-01

A first principles study of electronic tunneling along the chain of seven Fe/S clusters in respiratory complex I, a key enzyme in the respiratory electron transport chain, is described. The broken-symmetry states of the Fe/S metal clusters calculated at both DFT and semi-empirical ZINDO levels were utilized to examine both the extremely weak electronic couplings between Fe/S clusters and the tunneling pathways, which provide a detailed atomistic-level description of the charge transfer process in the protein. One-electron tunneling approximation was found to hold within a reasonable accuracy, with only a moderate induced polarization of the core electrons. The method is demonstrated to be able to calculate accurately the coupling matrix elements as small as 10−4 cm−1. A distinct signature of the wave properties of electrons is observed as quantum interferences of multiple tunneling pathways. PMID:25383312

Multiple paths of electron flow to current in microbial electrolysis cells fed with low and high concentrations of propionate.

PubMed

Hari, Ananda Rao; Katuri, Krishna P; Gorron, Eduardo; Logan, Bruce E; Saikaly, Pascal E

2016-07-01

Microbial electrolysis cells (MECs) provide a viable approach for bioenergy generation from fermentable substrates such as propionate. However, the paths of electron flow during propionate oxidation in the anode of MECs are unknown. Here, the paths of electron flow involved in propionate oxidation in the anode of two-chambered MECs were examined at low (4.5 mM) and high (36 mM) propionate concentrations. Electron mass balances and microbial community analysis revealed that multiple paths of electron flow (via acetate/H2 or acetate/formate) to current could occur simultaneously during propionate oxidation regardless of the concentration tested. Current (57-96 %) was the largest electron sink and methane (0-2.3 %) production was relatively unimportant at both concentrations based on electron balances. At a low propionate concentration, reactors supplemented with 2-bromoethanesulfonate had slightly higher coulombic efficiencies than reactors lacking this methanogenesis inhibitor. However, an opposite trend was observed at high propionate concentration, where reactors supplemented with 2-bromoethanesulfonate had a lower coulombic efficiency and there was a greater percentage of electron loss (23.5 %) to undefined sinks compared to reactors without 2-bromoethanesulfonate (11.2 %). Propionate removal efficiencies were 98 % (low propionate concentration) and 78 % (high propionate concentration). Analysis of 16S rRNA gene pyrosequencing revealed the dominance of sequences most similar to Geobacter sulfurreducens PCA and G. sulfurreducens subsp. ethanolicus. Collectively, these results provide new insights on the paths of electron flow during propionate oxidation in the anode of MECs fed with low and high propionate concentrations.

Regulation of energy partitioning and alternative electron transport pathways during cold acclimation of lodgepole pine is oxygen dependent.

PubMed

Savitch, Leonid V; Ivanov, Alexander G; Krol, Marianna; Sprott, David P; Oquist, Gunnar; Huner, Norman P A

2010-09-01

Second year needles of Lodgepole pine (Pinus contorta L.) were exposed for 6 weeks to either simulated control summer ['summer'; 25 °C/250 photon flux denisty (PFD)], autumn ('autumn'; 15°C/250 PFD) or winter conditions ('winter'; 5 °C/250 PFD). We report that the proportion of linear electron transport utilized in carbon assimilation (ETR(CO2)) was 40% lower in both 'autumn' and 'winter' pine when compared with the 'summer' pine. In contrast, the proportion of excess photosynthetic linear electron transport (ETR(excess)) not used for carbon assimilation within the total ETR(Jf) increased by 30% in both 'autumn' and 'winter' pine. In 'autumn' pine acclimated to 15°C, the increased amounts of 'excess' electrons were directed equally to 21  kPa O2-dependent and 2  kPa O2-dependent alternative electron transport pathways and the fractions of excitation light energy utilized by PSII photochemistry (Φ(PSII)), thermally dissipated through Φ(NPQ) and dissipated by additional quenching mechanism(s) (Φ(f,D)) were similar to those in 'summer' pine. In contrast, in 'winter' needles acclimated to 5 °C, 60% of photosynthetically generated 'excess' electrons were utilized through the 2  kPa O2-dependent electron sink and only 15% by the photorespiratory (21  kPa O2) electron pathway. Needles exposed to 'winter' conditions led to a 3-fold lower Φ(PSII), only a marginal increase in Φ(NPQ) and a 2-fold higher Φ(f,D), which was O2 dependent compared with the 'summer' and 'autumn' pine. Our results demonstrate that the employment of a variety of alternative pathways for utilization of photosynthetically generated electrons by Lodgepole pine depends on the acclimation temperature. Furthermore, dissipation of excess light energy through constitutive non-photochemical quenching mechanisms is O2 dependent.

The Gulf Stream Pathway and the Impacts of the Eddy-Driven Abyssal Circulation and the Deep Western Boundary Current

DTIC Science & Technology

2008-07-06

bathymetry, wind forcing, and a meridional overturning circulation (MOC), the latter specified via ports in the northern and southern boundaries. The...small values below the sill depth in all of the simulations. e The upper ocean northward flow of the meridional overturning circulation (MOC) is...plus the northward upper ocean flow (14 Sv) of the meridional overturning circulation (MOC). The mean Gulf Stream IR northwall pathway ±lrr from

40 CFR 90.421 - Dilute gaseous exhaust sampling and analytical system description.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Volume Sampler (PDP-CVS) system with a heat exchanger, or a Critical Flow Venturi—Constant Volume Sampler (CFV-CVS) system with CFV sample probes and/or a heat exchanger or electronic flow compensation. Figure... sampling point. (ii) For the CFV-CVS, either a heat exchanger or electronic flow compensation is required...

40 CFR 91.421 - Dilute gaseous exhaust sampling and analytical system description.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Pump—Constant Volume Sampler (PDP-CVS) system with a heat exchanger, or a Critical Flow Venturi—Constant Volume Sampler (CFV-CVS) system with CVS sample probes and/or a heat exchanger or electronic flow... sampling point. (ii) For the CFV-CVS, either a heat exchanger or electronic flow compensation is required...

40 CFR 91.421 - Dilute gaseous exhaust sampling and analytical system description.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Pump—Constant Volume Sampler (PDP-CVS) system with a heat exchanger, or a Critical Flow Venturi—Constant Volume Sampler (CFV-CVS) system with CVS sample probes and/or a heat exchanger or electronic flow... sampling point. (ii) For the CFV-CVS, either a heat exchanger or electronic flow compensation is required...

40 CFR 90.421 - Dilute gaseous exhaust sampling and analytical system description.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Volume Sampler (PDP-CVS) system with a heat exchanger, or a Critical Flow Venturi—Constant Volume Sampler (CFV-CVS) system with CFV sample probes and/or a heat exchanger or electronic flow compensation. Figure... sampling point. (ii) For the CFV-CVS, either a heat exchanger or electronic flow compensation is required...

40 CFR 91.421 - Dilute gaseous exhaust sampling and analytical system description.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Pump—Constant Volume Sampler (PDP-CVS) system with a heat exchanger, or a Critical Flow Venturi—Constant Volume Sampler (CFV-CVS) system with CVS sample probes and/or a heat exchanger or electronic flow... sampling point. (ii) For the CFV-CVS, either a heat exchanger or electronic flow compensation is required...

40 CFR 90.421 - Dilute gaseous exhaust sampling and analytical system description.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Volume Sampler (PDP-CVS) system with a heat exchanger, or a Critical Flow Venturi—Constant Volume Sampler (CFV-CVS) system with CFV sample probes and/or a heat exchanger or electronic flow compensation. Figure... sampling point. (ii) For the CFV-CVS, either a heat exchanger or electronic flow compensation is required...

Electron Transfer Pathways Facilitating U(VI) Reduction by Fe(II) on Al- vs Fe-Oxides

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

Taylor, S. D.; Becker, U.; Rosso, K. M.

This study continues mechanistic development of heterogeneous electron transfer (ET) pathways at mineral surfaces in aquatic environments that enable the reduction U(VI) by surface-associated Fe(II). Using computational molecular simulation within the framework of Marcus Theory, our findings highlight the importance of the configurations and interaction of the electron donor and acceptor species with the substrate, with respect to influencing its electronic structure and thereby the ability of semiconducting minerals to facilitate ET. U(VI) reduction by surface-associated Fe(II) (adsorbed or structurally incorporated into the lattice) on an insulating, corundum (001) surface (α-Al2O3) occurs when proximal inner-sphere (IS) surface complexes are formed,more » such that ET occurs through a combination of direct exchange (i.e., Fe d- and U f-orbitals overlap through space) and superexchange via intervening surface oxygen atoms. U(VI) reduction by coadsorbed Fe(II) on the isostructural semiconducting hematite (α-Fe2O3) basal surface requires either their direct electronic interaction (e.g., IS complexation) or mediation of this interaction indirectly through the surface via an intrasurface pathway. Conceptually possible longer-range ET by charge-hopping through surface Fe atoms was investigated to determine whether this indirect pathway is competitive with direct ET. The calculations show that energy barriers are large for this conduction-based pathway; interfacial ET into the hematite surface is endothermic (+80.1 kJ/mol) and comprises the rate-limiting step (10–6 s–1). The presence of the IS adsorbates appears to weaken the electronic coupling between underlying Fe ions within the surface, resulting in slower intra-surface ET (10–5 s–1) than expected in the bulk basal plane. Our findings lay out first insights into donor-acceptor communication via a charge-hopping pathway through the surface for heterogeneous reduction of U(VI) by Fe(II) and help provide a basis for experimental interrogation of this important process at mineral-water interfaces.« less

A Critical Role for the cccA Gene Product, Cytochrome c2, in Diverting Electrons from Aerobic Respiration to Denitrification in Neisseria gonorrhoeae

PubMed Central

Hopper, Amanda C.; Li, Ying

2013-01-01

Neisseria gonorrhoeae is a microaerophile that, when oxygen availability is limited, supplements aerobic respiration with a truncated denitrification pathway, nitrite reduction to nitrous oxide. We demonstrate that the cccA gene of Neisseria gonorrhoeae strain F62 (accession number NG0292) is expressed, but the product, cytochrome c2, accumulates to only low levels. Nevertheless, a cccA mutant reduced nitrite at about half the rate of the parent strain. We previously reported that cytochromes c4 and c5 transfer electrons to cytochrome oxidase cbb3 by two independent pathways and that the CcoP subunit of cytochrome oxidase cbb3 transfers electrons to nitrite. We show that mutants defective in either cytochrome c4 or c5 also reduce nitrite more slowly than the parent. By combining mutations in cccA (Δc2), cycA (Δc4), cycB (Δc5), and ccoP (ccoP-C368A), we demonstrate that cytochrome c2 is required for electron transfer from cytochrome c4 via the third heme group of CcoP to the nitrite reductase, AniA, and that cytochrome c5 transfers electrons to nitrite reductase by an independent pathway. We propose that cytochrome c2 forms a complex with cytochrome oxidase. If so, the redox state of cytochrome c2 might regulate electron transfer to nitrite or oxygen. However, our data are more consistent with a mechanism in which cytochrome c2 and the CcoQ subunit of cytochrome oxidase form alternative complexes that preferentially catalyze nitrite and oxygen reduction, respectively. Comparison with the much simpler electron transfer pathway for nitrite reduction in the meningococcus provides fascinating insights into niche adaptation within the pathogenic neisseriae. PMID:23543713

Quantum optimal control pathways of ozone isomerization dynamics subject to competing dissociation: A two-state one-dimensional model

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

Kurosaki, Yuzuru, E-mail: kurosaki.yuzuru@jaea.go.jp; Ho, Tak-San, E-mail: tsho@Princeton.EDU; Rabitz, Herschel, E-mail: hrabitz@Princeton.EDU

We construct a two-state one-dimensional reaction-path model for ozone open → cyclic isomerization dynamics. The model is based on the intrinsic reaction coordinate connecting the cyclic and open isomers with the O{sub 2} + O asymptote on the ground-state {sup 1}A{sup ′} potential energy surface obtained with the high-level ab initio method. Using this two-state model time-dependent wave packet optimal control simulations are carried out. Two possible pathways are identified along with their respective band-limited optimal control fields; for pathway 1 the wave packet initially associated with the open isomer is first pumped into a shallow well on the excitedmore » electronic state potential curve and then driven back to the ground electronic state to form the cyclic isomer, whereas for pathway 2 the corresponding wave packet is excited directly to the primary well of the excited state potential curve. The simulations reveal that the optimal field for pathway 1 produces a final yield of nearly 100% with substantially smaller intensity than that obtained in a previous study [Y. Kurosaki, M. Artamonov, T.-S. Ho, and H. Rabitz, J. Chem. Phys. 131, 044306 (2009)] using a single-state one-dimensional model. Pathway 2, due to its strong coupling to the dissociation channel, is less effective than pathway 1. The simulations also show that nonlinear field effects due to molecular polarizability and hyperpolarizability are small for pathway 1 but could become significant for pathway 2 because much higher field intensity is involved in the latter. The results suggest that a practical control may be feasible with the aid of a few lowly excited electronic states for ozone isomerization.« less

The nitric-oxide reductase from Paracoccus denitrificans uses a single specific proton pathway.

PubMed

ter Beek, Josy; Krause, Nils; Reimann, Joachim; Lachmann, Peter; Ädelroth, Pia

2013-10-18

The NO reductase from Paracoccus denitrificans reduces NO to N2O (2NO + 2H(+) + 2e(-) → N2O + H2O) with electrons donated by periplasmic cytochrome c (cytochrome c-dependent NO reductase; cNOR). cNORs are members of the heme-copper oxidase superfamily of integral membrane proteins, comprising the O2-reducing, proton-pumping respiratory enzymes. In contrast, although NO reduction is as exergonic as O2 reduction, there are no protons pumped in cNOR, and in addition, protons needed for NO reduction are derived from the periplasmic solution (no contribution to the electrochemical gradient is made). cNOR thus only needs to transport protons from the periplasm into the active site without the requirement to control the timing of opening and closing (gating) of proton pathways as is needed in a proton pump. Based on the crystal structure of a closely related cNOR and molecular dynamics simulations, several proton transfer pathways were suggested, and in principle, these could all be functional. In this work, we show that residues in one of the suggested pathways (denoted pathway 1) are sensitive to site-directed mutation, whereas residues in the other proposed pathways (pathways 2 and 3) could be exchanged without severe effects on turnover activity with either NO or O2. We further show that electron transfer during single-turnover reduction of O2 is limited by proton transfer and can thus be used to study alterations in proton transfer rates. The exchange of residues along pathway 1 showed specific slowing of this proton-coupled electron transfer as well as changes in its pH dependence. Our results indicate that only pathway 1 is used to transfer protons in cNOR.

Routes to formation of highly excited neutral atoms in the break-up of strongly driven hydrogen molecule

NASA Astrophysics Data System (ADS)

Emmanouilidou, Agapi

2012-06-01

We present a theoretical quasiclassical treatment of the formation, during Coulomb explosion, of highly excited neutral H atoms for strongly-driven hydrogen molecule. This process, where after the laser field is turned off, one electron escapes to the continuum while the other occupies a Rydberg state, was recently reported in an experimental study in Phys. Rev. Lett 102, 113002 (2009). We find that two-electron effects are important in order to correctly account for all pathways leading to highly excited neutral hydrogen formation [1]. We identify two pathways where the electron that escapes to the continuum does so either very quickly or after remaining bound for a few periods of the laser field. These two pathways of highly excited neutral H formation have distinct traces in the probability distribution of the escaping electron momentum components. [4pt] [1] A. Emmanouilidou, C. Lazarou, A. Staudte and U. Eichmann, Phys. Rev. A (Rapid) 85 011402 (2012).

Leveraging Electron Transfer Dissociation for Site Selective Radical Generation: Applications for Peptide Epimer Analysis

NASA Astrophysics Data System (ADS)

Lyon, Yana A.; Beran, Gregory; Julian, Ryan R.

2017-07-01

Traditional electron-transfer dissociation (ETD) experiments operate through a complex combination of hydrogen abundant and hydrogen deficient fragmentation pathways, yielding c and z ions, side-chain losses, and disulfide bond scission. Herein, a novel dissociation pathway is reported, yielding homolytic cleavage of carbon-iodine bonds via electronic excitation. This observation is very similar to photodissociation experiments where homolytic cleavage of carbon-iodine bonds has been utilized previously, but ETD activation can be performed without addition of a laser to the mass spectrometer. Both loss of iodine and loss of hydrogen iodide are observed, with the abundance of the latter product being greatly enhanced for some peptides after additional collisional activation. These observations suggest a novel ETD fragmentation pathway involving temporary storage of the electron in a charge-reduced arginine side chain. Subsequent collisional activation of the peptide radical produced by loss of HI yields spectra dominated by radical-directed dissociation, which can be usefully employed for identification of peptide isomers, including epimers.

Alternative Pathway of Metronidazole Activation in Trichomonas vaginalis Hydrogenosomes

PubMed Central

Hrdý, Ivan; Cammack, Richard; Stopka, Pavel; Kulda, Jaroslav; Tachezy, Jan

2005-01-01

Metronidazole and related 5-nitroimidazoles are the only available drugs in the treatment of human urogenital trichomoniasis caused by the protozoan parasite Trichomonas vaginalis. The drugs are activated to cytotoxic anion radicals by their reduction within the hydrogenosomes. It has been established that electrons required for metronidazole activation are released from pyruvate by the activity of pyruvate:ferredoxin oxidoreductase and transferred to the drug by a low-redox-potential carrier, ferredoxin. Here we describe a novel pathway involved in the drug activation within the hydrogenosome. The source of electrons is malate, another major hydrogenosomal substrate, which is oxidatively decarboxylated to pyruvate and CO2 by NAD-dependent malic enzyme. The electrons released during this reaction are transferred from NADH to ferredoxin by NADH dehydrogenase homologous to the catalytic module of mitochondrial complex I, which uses ferredoxin as electron acceptor. Trichomonads acquire high-level metronidazole resistance only after both pyruvate- and malate-dependent pathways of metronidazole activation are eliminated from the hydrogenosomes. PMID:16304169

Discriminating response groups in metabolic and regulatory pathway networks.

PubMed

Van Hemert, John L; Dickerson, Julie A

2012-04-01

Analysis of omics experiments generates lists of entities (genes, metabolites, etc.) selected based on specific behavior, such as changes in response to stress or other signals. Functional interpretation of these lists often uses category enrichment tests using functional annotations like Gene Ontology terms and pathway membership. This approach does not consider the connected structure of biochemical pathways or the causal directionality of events. The Omics Response Group (ORG) method, described in this work, interprets omics lists in the context of metabolic pathway and regulatory networks using a statistical model for flow within the networks. Statistical results for all response groups are visualized in a novel Pathway Flow plot. The statistical tests are based on the Erlang distribution model under the assumption of independent and identically Exponential-distributed random walk flows through pathways. As a proof of concept, we applied our method to an Escherichia coli transcriptomics dataset where we confirmed common knowledge of the E.coli transcriptional response to Lipid A deprivation. The main response is related to osmotic stress, and we were also able to detect novel responses that are supported by the literature. We also applied our method to an Arabidopsis thaliana expression dataset from an abscisic acid study. In both cases, conventional pathway enrichment tests detected nothing, while our approach discovered biological processes beyond the original studies. We created a prototype for an interactive ORG web tool at http://ecoserver.vrac.iastate.edu/pathwayflow (source code is available from https://subversion.vrac.iastate.edu/Subversion/jlv/public/jlv/pathwayflow). The prototype is described along with additional figures and tables in Supplementary Material. julied@iastate.edu Supplementary data are available at Bioinformatics online.

Simple Kinematic Pathway Approach (KPA) to Catchment-scale Travel Time and Water Age Distributions

NASA Astrophysics Data System (ADS)

Soltani, S. S.; Cvetkovic, V.; Destouni, G.

2017-12-01

The distribution of catchment-scale water travel times is strongly influenced by morphological dispersion and is partitioned between hillslope and larger, regional scales. We explore whether hillslope travel times are predictable using a simple semi-analytical "kinematic pathway approach" (KPA) that accounts for dispersion on two levels of morphological and macro-dispersion. The study gives new insights to shallow (hillslope) and deep (regional) groundwater travel times by comparing numerical simulations of travel time distributions, referred to as "dynamic model", with corresponding KPA computations for three different real catchment case studies in Sweden. KPA uses basic structural and hydrological data to compute transient water travel time (forward mode) and age (backward mode) distributions at the catchment outlet. Longitudinal and morphological dispersion components are reflected in KPA computations by assuming an effective Peclet number and topographically driven pathway length distributions, respectively. Numerical simulations of advective travel times are obtained by means of particle tracking using the fully-integrated flow model MIKE SHE. The comparison of computed cumulative distribution functions of travel times shows significant influence of morphological dispersion and groundwater recharge rate on the compatibility of the "kinematic pathway" and "dynamic" models. Zones of high recharge rate in "dynamic" models are associated with topographically driven groundwater flow paths to adjacent discharge zones, e.g. rivers and lakes, through relatively shallow pathway compartments. These zones exhibit more compatible behavior between "dynamic" and "kinematic pathway" models than the zones of low recharge rate. Interestingly, the travel time distributions of hillslope compartments remain almost unchanged with increasing recharge rates in the "dynamic" models. This robust "dynamic" model behavior suggests that flow path lengths and travel times in shallow hillslope compartments are controlled by topography, and therefore application and further development of the simple "kinematic pathway" approach is promising for their modeling.

Evaluation of diffuse and preferential flow pathways of infiltrated precipitation and irrigation using oxygen and hydrogen isotopes

NASA Astrophysics Data System (ADS)

Ma, Bin; Liang, Xing; Liu, Shaohua; Jin, Menggui; Nimmo, John R.; Li, Jing

2017-05-01

Subsurface-water flow pathways in three different land-use areas (non-irrigated grassland, poplar forest, and irrigated arable land) in the central North China Plain were investigated using oxygen (18O) and hydrogen (2H) isotopes in samples of precipitation, soils, and groundwater. Soil water in the top 10 cm was significantly affected by both evaporation and infiltration. Water at 10-40 cm depth in the grassland and arable land, and 10-60 cm in poplar forest, showed a relatively short residence time, as a substantial proportion of antecedent soil water was mixed with a 92-mm storm infiltration event, whereas below those depths (down to 150 cm), depleted δ18O spikes suggested that some storm water bypassed the shallow soil layers. Significant differences, in soil-water content and δ18O values, within a small area, suggested that the proportion of immobile soil water and water flowing in subsurface pathways varies depending on local vegetation cover, soil characteristics and irrigation applications. Soil-water δ18O values revealed that preferential flow and diffuse flow coexist. Preferential flow was active within the root zone, independent of antecedent soil-water content, in both poplar forest and arable land, whereas diffuse flow was observed in grassland. The depleted δ18O spikes at 20-50 cm depth in the arable land suggested the infiltration of irrigation water during the dry season. Temporal isotopic variations in precipitation were subdued in the shallow groundwater, suggesting more complete mixing of different input waters in the unsaturated zone before reaching the shallow groundwater.

Preferential flow estimates to an agricultural tile drain with implications for glyphosate transport

USGS Publications Warehouse

Stone, W.W.; Wilson, J.T.

2006-01-01

Agricultural subsurface drains, commonly referred to as tile drains, are potentially significant pathways for the movement of fertilizers and pesticides to streams and ditches in much of the Midwest. Preferential flow in the unsaturated zone provides a route for water and solutes to bypass the soil matrix and reach tile drains faster than predicted by traditional displacement theory. This paper uses chloride concentrations to estimate preferential flow contributions to a tile drain during two storms in May 2004. Chloride, a conservative anion, was selected as the tracer because of differences in chloride concentrations between the two sources of water to the tile drain, preferential and matrix flow. A strong correlation between specific conductance and chloride concentration provided a mechanism to estimate chloride concentrations in the tile drain throughout the storm hydrographs. A simple mixing analysis was used to identify the preferential flow component of the storm hydrograph. During two storms, preferential flow contributed 11 and 51% of total storm tile drain flow; the peak contributions, 40 and 81%, coincided with the peak tile drain flow. Positive relations between glyphosate [N-(phosphonomethyl)glycine] concentrations and preferential flow for the two storms suggest that preferential flow is an important transport pathway to the tile drain. ?? ASA, CSSA, SSSA.

21 CFR 1020.20 - Cold-cathode gas discharge tubes.

Code of Federal Regulations, 2014 CFR

2014-04-01

... discharge tubes designed to demonstrate the effects of a flow of electrons or the production of x-radiation... electron flow is produced and sustained by ionization of contained gas atoms and ion bombardment of the... the ions of one sign produced in air when all electrons liberated by photons in a volume element of...

21 CFR 1020.20 - Cold-cathode gas discharge tubes.

Code of Federal Regulations, 2012 CFR

2012-04-01

... discharge tubes designed to demonstrate the effects of a flow of electrons or the production of x-radiation... electron flow is produced and sustained by ionization of contained gas atoms and ion bombardment of the... the ions of one sign produced in air when all electrons liberated by photons in a volume element of...

21 CFR 1020.20 - Cold-cathode gas discharge tubes.

Code of Federal Regulations, 2013 CFR

2013-04-01

... discharge tubes designed to demonstrate the effects of a flow of electrons or the production of x-radiation... electron flow is produced and sustained by ionization of contained gas atoms and ion bombardment of the... the ions of one sign produced in air when all electrons liberated by photons in a volume element of...

21 CFR 1020.20 - Cold-cathode gas discharge tubes.

Code of Federal Regulations, 2011 CFR

2011-04-01

... discharge tubes designed to demonstrate the effects of a flow of electrons or the production of x-radiation... electron flow is produced and sustained by ionization of contained gas atoms and ion bombardment of the... the ions of one sign produced in air when all electrons liberated by photons in a volume element of...

Application of a Transient Storage Zone Model o Soil Pipeflow Tracer Injection Experiments

USDA-ARS?s Scientific Manuscript database

Soil pipes, defined here as discrete preferential flow paths generally parallel to the slope, are important subsurface flow pathways that play a role in many soil erosion phenomena. However, limited research has been performed on quantifying and characterizing their flow and transport characteristic...

Simultaneous cathodoluminescence and electron microscopy cytometry of cellular vesicles labeled with fluorescent nanodiamonds

NASA Astrophysics Data System (ADS)

Nagarajan, Sounderya; Pioche-Durieu, Catherine; Tizei, Luiz H. G.; Fang, Chia-Yi; Bertrand, Jean-Rémi; Le Cam, Eric; Chang, Huan-Cheng; Treussart, François; Kociak, Mathieu

2016-06-01

Light and Transmission Electron Microscopies (LM and TEM) hold potential in bioimaging owing to the advantages of fast imaging of multiple cells with LM and ultrastructure resolution offered by TEM. Integrated or correlated LM and TEM are the current approaches to combine the advantages of both techniques. Here we propose an alternative in which the electron beam of a scanning TEM (STEM) is used to excite concomitantly the luminescence of nanoparticle labels (a process known as cathodoluminescence, CL), and image the cell ultrastructure. This CL-STEM imaging allows obtaining luminescence spectra and imaging ultrastructure simultaneously. We present a proof of principle experiment, showing the potential of this technique in image cytometry of cell vesicular components. To label the vesicles we used fluorescent diamond nanocrystals (nanodiamonds, NDs) of size ~150 nm coated with different cationic polymers, known to trigger different internalization pathways. Each polymer was associated with a type of ND with a different emission spectrum. With CL-STEM, for each individual vesicle, we were able to measure (i) their size with nanometric resolution, (ii) their content in different ND labels, and realize intracellular component cytometry. In contrast to the recently reported organelle flow cytometry technique that requires cell sonication, CL-STEM-based image cytometry preserves the cell integrity and provides a much higher resolution in size. Although this novel approach is still limited by a low throughput, the automatization of data acquisition and image analysis, combined with improved intracellular targeting, should facilitate applications in cell biology at the subcellular level.Light and Transmission Electron Microscopies (LM and TEM) hold potential in bioimaging owing to the advantages of fast imaging of multiple cells with LM and ultrastructure resolution offered by TEM. Integrated or correlated LM and TEM are the current approaches to combine the advantages of both techniques. Here we propose an alternative in which the electron beam of a scanning TEM (STEM) is used to excite concomitantly the luminescence of nanoparticle labels (a process known as cathodoluminescence, CL), and image the cell ultrastructure. This CL-STEM imaging allows obtaining luminescence spectra and imaging ultrastructure simultaneously. We present a proof of principle experiment, showing the potential of this technique in image cytometry of cell vesicular components. To label the vesicles we used fluorescent diamond nanocrystals (nanodiamonds, NDs) of size ~150 nm coated with different cationic polymers, known to trigger different internalization pathways. Each polymer was associated with a type of ND with a different emission spectrum. With CL-STEM, for each individual vesicle, we were able to measure (i) their size with nanometric resolution, (ii) their content in different ND labels, and realize intracellular component cytometry. In contrast to the recently reported organelle flow cytometry technique that requires cell sonication, CL-STEM-based image cytometry preserves the cell integrity and provides a much higher resolution in size. Although this novel approach is still limited by a low throughput, the automatization of data acquisition and image analysis, combined with improved intracellular targeting, should facilitate applications in cell biology at the subcellular level. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01908k

Pathway for recovery of photo-degraded polymer solar cells by post degradation thermal anneal

DOE PAGES

Bhattacharya, J.; Joshi, P. H.; Biswas, Rana; ...

2017-02-16

The photo-degradation of polymer solar cells is a critical challenge preventing its commercial deployment. We experimentally fabricate organic solar cells and characterize their degradation under solar simulators in an environmental chamber under nitrogen flow, without exposure to oxygen and moisture. We have developed a thermally stable inverted organic solar cell architecture in which light induced degradation of device characteristics can be reversibly annealed to the pristine values. The stable inverted cells utilized MoO x layers that are thermally treated immediately after their deposition on the organic layer, and before metal cathode deposition. Organic solar cells that are photo-degraded in themore » presence of oxygen, however show irreversible degradation that cannot be thermally recovered. The decrease of organic solar cell characteristics correlates with increases in mid-gap electronic states, measured using capacitance spectroscopy and dark current. It is likely the photo-induced defect states caused by local H motion from the alkyl chains to the aromatic backbone, can be reversibly annealed at elevated temperatures after photo-degradation. Finally, our results provide a pathway for improving the stability of organic photovoltaics.« less

Enhanced limonene production in cyanobacteria reveals photosynthesis limitations.

PubMed

Wang, Xin; Liu, Wei; Xin, Changpeng; Zheng, Yi; Cheng, Yanbing; Sun, Su; Li, Runze; Zhu, Xin-Guang; Dai, Susie Y; Rentzepis, Peter M; Yuan, Joshua S

2016-12-13

Terpenes are the major secondary metabolites produced by plants, and have diverse industrial applications as pharmaceuticals, fragrance, solvents, and biofuels. Cyanobacteria are equipped with efficient carbon fixation mechanism, and are ideal cell factories to produce various fuel and chemical products. Past efforts to produce terpenes in photosynthetic organisms have gained only limited success. Here we engineered the cyanobacterium Synechococcus elongatus PCC 7942 to efficiently produce limonene through modeling guided study. Computational modeling of limonene flux in response to photosynthetic output has revealed the downstream terpene synthase as a key metabolic flux-controlling node in the MEP (2-C-methyl-d-erythritol 4-phosphate) pathway-derived terpene biosynthesis. By enhancing the downstream limonene carbon sink, we achieved over 100-fold increase in limonene productivity, in contrast to the marginal increase achieved through stepwise metabolic engineering. The establishment of a strong limonene flux revealed potential synergy between photosynthate output and terpene biosynthesis, leading to enhanced carbon flux into the MEP pathway. Moreover, we show that enhanced limonene flux would lead to NADPH accumulation, and slow down photosynthesis electron flow. Fine-tuning ATP/NADPH toward terpene biosynthesis could be a key parameter to adapt photosynthesis to support biofuel/bioproduct production in cyanobacteria.

Enhanced limonene production in cyanobacteria reveals photosynthesis limitations

PubMed Central

Wang, Xin; Liu, Wei; Xin, Changpeng; Zheng, Yi; Cheng, Yanbing; Sun, Su; Li, Runze; Zhu, Xin-Guang; Dai, Susie Y.; Rentzepis, Peter M.; Yuan, Joshua S.

2016-01-01

Terpenes are the major secondary metabolites produced by plants, and have diverse industrial applications as pharmaceuticals, fragrance, solvents, and biofuels. Cyanobacteria are equipped with efficient carbon fixation mechanism, and are ideal cell factories to produce various fuel and chemical products. Past efforts to produce terpenes in photosynthetic organisms have gained only limited success. Here we engineered the cyanobacterium Synechococcus elongatus PCC 7942 to efficiently produce limonene through modeling guided study. Computational modeling of limonene flux in response to photosynthetic output has revealed the downstream terpene synthase as a key metabolic flux-controlling node in the MEP (2-C-methyl-d-erythritol 4-phosphate) pathway-derived terpene biosynthesis. By enhancing the downstream limonene carbon sink, we achieved over 100-fold increase in limonene productivity, in contrast to the marginal increase achieved through stepwise metabolic engineering. The establishment of a strong limonene flux revealed potential synergy between photosynthate output and terpene biosynthesis, leading to enhanced carbon flux into the MEP pathway. Moreover, we show that enhanced limonene flux would lead to NADPH accumulation, and slow down photosynthesis electron flow. Fine-tuning ATP/NADPH toward terpene biosynthesis could be a key parameter to adapt photosynthesis to support biofuel/bioproduct production in cyanobacteria. PMID:27911807

Cloning and Analysis of the Alternative Oxidase Gene of Neurospora Crassa

PubMed Central

Li, Q.; Ritzel, R. G.; McLean, LLT.; McIntosh, L.; Ko, T.; Bertrand, H.; Nargang, F. E.

1996-01-01

Mitochondria of Neurospora crassa contain a cyanide-resistant alternative respiratory pathway in addition to the cytochrome pathway. The alternative oxidase is present only when electron flow through the cytochrome chain is restricted. Both genomic and cDNA copies for the alternative oxidase gene have been isolated and analyzed. The sequence of the predicted protein is homologous to that of other species. The mRNA for the alternative oxidase is scarce in wild-type cultures grown under normal conditions, but it is abundant in cultures grown in the presence of chloramphenicol, an inhibitor of mitochondrial protein synthesis, or in mutants deficient in mitochondrial cytochromes. Thus, induction of alternative oxidase appears to be at the transcriptional level. Restriction fragment length polymorphism mapping of the isolated gene demonstrated that it is located in a position corresponding to the aod-1 locus. Sequence analysis of mutant aod-1 alleles reveals mutations affecting the coding sequence of the alternative oxidase. The level of aod-1 mRNA in an aod-2 mutant strain that had been grown in the presence of chloramphenicol was reduced several fold relative to wild-type, supporting the hypothesis that the product of aod-2 is required for optimal expression of aod-1. PMID:8770590

Pathway for recovery of photo-degraded polymer solar cells by post degradation thermal anneal

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

Bhattacharya, J.; Joshi, P. H.; Biswas, Rana

The photo-degradation of polymer solar cells is a critical challenge preventing its commercial deployment. We experimentally fabricate organic solar cells and characterize their degradation under solar simulators in an environmental chamber under nitrogen flow, without exposure to oxygen and moisture. We have developed a thermally stable inverted organic solar cell architecture in which light induced degradation of device characteristics can be reversibly annealed to the pristine values. The stable inverted cells utilized MoO x layers that are thermally treated immediately after their deposition on the organic layer, and before metal cathode deposition. Organic solar cells that are photo-degraded in themore » presence of oxygen, however show irreversible degradation that cannot be thermally recovered. The decrease of organic solar cell characteristics correlates with increases in mid-gap electronic states, measured using capacitance spectroscopy and dark current. It is likely the photo-induced defect states caused by local H motion from the alkyl chains to the aromatic backbone, can be reversibly annealed at elevated temperatures after photo-degradation. Finally, our results provide a pathway for improving the stability of organic photovoltaics.« less

Modeling sediment trapping in a vegetative filter accounting for converging overland flow

Treesearch

M. J. Helmers; D. E. Eisenhauer; T. G. Franti; M. G. Dosskey

2005-01-01

Vegetative filters (VF) are used to remove sediment and other pollutants from overland flow. When modeling the hydrology of VF, it is often assumed that overland flow is planar, but our research indicated that it can be two-dimensional with converging and diverging pathways. Our hypothesis is that flow convergence will negatively influence the sediment trapping...

Water-mediated electron transfer between protein redox centers.

PubMed

Migliore, Agostino; Corni, Stefano; Felice, Rosa Di; Molinari, Elisa

2007-04-12

Recent experimental and theoretical investigations show that water molecules between or near redox partners can significantly affect their electron-transfer (ET) properties. Here we study the effects of intervening water molecules on the electron self-exchange reaction of azurin (Az), by performing a conformational sampling on the water medium and by using a newly developed ab initio method to calculate transfer integrals between molecular redox sites. We show that the insertion of water molecules at the interface between the copper active sites of Az dimers slightly increases the overall ET rate, while some favorable water conformations can considerably enhance the ET kinetics. These features are traced back to the interplay of two competing factors: the electrostatic interaction between the water and protein subsystems (mainly opposing the ET process for the water arrangements drawn from MD simulations) and the effectiveness of water in mediating ET coupling pathways. Such an interplay provides a physical basis for the found absence of correlation between the electronic couplings derived through ab initio electronic structure calculations and the related quantities obtained through the Empirical Pathways (EP) method. In fact, the latter does not account for electrostatic effects on the transfer integrals. Thus, we conclude that the water-mediated electron tunneling is not controlled by the geometry of a single physical pathway. We discuss the results in terms of the interplay between different ET pathways controlled by the conformational changes of one of the water molecules via its electrostatic influence. Finally, we examine the dynamical effects of the interfacial water and check the validity of the Condon approximation.

Electron concentration distribution in a glow discharge in air flow

NASA Astrophysics Data System (ADS)

Mukhamedzianov, R. B.; Gaisin, F. M.; Sabitov, R. A.

1989-04-01

Electron concentration distributions in a glow discharge in longitudinal and vortex air flows are determined from the attenuation of the electromagnetic wave passing through the plasma using microwave probes. An analysis of the distribution curves obtained indicates that electron concentration decreases in the direction of the anode. This can be explained by charge diffusion toward the chamber walls and electron recombination and sticking within the discharge.

Innovation Incubator: LiquidCool Solutions Technical Evaluation. Laboratory Study and Demonstration Results of a Directed-Flow, Liquid Submerged Server for High-Efficiency Data Centers

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

Kozubal, Eric J

LiquidCool Solutions (LCS) has developed liquid submerged server (LSS) technology that changes the way computer electronics are cooled. The technology provides an option to cool electronics by the direct contact flow of dielectric fluid (coolant) into a sealed enclosure housing all the electronics of a single server. The intimate dielectric fluid contact with electronics improves the effectiveness of heat removal from the electronics.

Dielectric barrier structure with hollow electrodes and its recoil effect

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

Yu, Shuang; Chen, Qunzhi; Liu, Jiahui

2015-06-15

A dielectric barrier structure with hollow electrodes (HEDBS), in which gas flow oriented parallel to the electric field, was proposed. Results showed that with this structure, air can be effectively ignited, forming atmospheric low temperature plasma, and the proposed HEDBS could achieve much higher electron density (5 × 10{sup 15}/cm{sup 3}). It was also found that the flow condition, including outlet diameter and flow rate, played a key role in the evolution of electron density. Optical emission spectroscopy diagnostic results showed that the concentration of reactive species had the same variation trend as the electron density. The simulated distribution of discharge gasmore » flow indicated that the HEDBS had a strong recoil effect on discharge gas, and could efficiently promote generating electron density as well as reactive species.« less

The investigation of substituent effects on the fragmentation pathways of pentacoordinated phenoxyspirophosphoranes by ESI-MSn.

PubMed

Cui, Xiaoyan; Sun, Can; Zhao, Pei; Wang, Yanyan; Guo, Yanchun; Zhao, Yufen; Cao, Shuxia

2018-04-01

The fragmentation pathways of pentacoordinated phenoxyspirophosphoranes were investigated in the positive mode by electrospray ionization multistage mass spectrometry. The results demonstrate that the sodium adducts of the title compounds undergo two competitive fragmentation pathways, and the fragmentation patterns are heavily dependent on the various substituent patterns at the phenolic group. An electron-withdrawing substituent at the ortho-position always results in the removal of a corresponding phenol analogue, while cleavage by spiroring opening becomes the predominant fragmentation pathway if an electron-donating substituent is at the phenolic group. The substituent effects on the competitive fragmentation pathways were further elucidated by theoretical calculations, single crystal structure analysis, and high-resolution mass spectrometry. The results contribute to the understanding of the gas-phase fragmentation reactions and the structure identification of spirophosphorane analogues by electrospray ionization multistage mass spectrometry. Copyright © 2018 John Wiley & Sons, Ltd.

Surface-directed capillary system; theory, experiments and applications.

PubMed

Bouaidat, Salim; Hansen, Ole; Bruus, Henrik; Berendsen, Christian; Bau-Madsen, Niels Kristian; Thomsen, Peter; Wolff, Anders; Jonsmann, Jacques

2005-08-01

We present a capillary flow system for liquid transport in microsystems. Our simple microfluidic system consists of two planar parallel surfaces, separated by spacers. One of the surfaces is entirely hydrophobic, the other mainly hydrophobic, but with hydrophilic pathways defined on it by photolithographic means. By controlling the wetting properties of the surfaces in this manner, the liquid can be confined to certain areas defined by the hydrophilic pathways. This technique eliminates the need for alignment of the two surfaces. Patterned plasma-polymerized hexafluoropropene constitutes the hydrophobic areas, whereas the untreated glass surface constitutes the hydrophilic pathways. We developed a theoretical model of the capillary flow and obtained analytical solutions which are in good agreement with the experimental results. The capillarity-driven microflow system was also used to pattern and immobilize biological material on planar substrates: well-defined 200 microm wide strips of human cells (HeLa) and fluorescence labelled proteins (fluorescein isothiocyanate-labelled bovine serum albumin, i.e., FITC-BSA) were fabricated using the capillary flow system presented here.

Planktonic food webs revisited: Reanalysis of results from the linear inverse approach

NASA Astrophysics Data System (ADS)

Hlaili, Asma Sakka; Niquil, Nathalie; Legendre, Louis

2014-01-01

Identification of the trophic pathway that dominates a given planktonic assemblage is generally based on the distribution of biomasses among food-web compartments, or better, the flows of materials or energy among compartments. These flows are obtained by field observations and a posteriori analyses, including the linear inverse approach. In the present study, we re-analysed carbon flows obtained by inverse analysis at 32 stations in the global ocean and one large lake. Our results do not support two "classical" views of plankton ecology, i.e. that the herbivorous food web is dominated by mesozooplankton grazing on large phytoplankton, and the microbial food web is based on microzooplankton significantly consuming bacteria; our results suggest instead that phytoplankton are generally grazed by microzooplankton, of which they are the main food source. Furthermore, we identified the "phyto-microbial food web", where microzooplankton largely feed on phytoplankton, in addition to the already known "poly-microbial food web", where microzooplankton consume more or less equally various types of food. These unexpected results led to a (re)definition of the conceptual models corresponding to the four trophic pathways we found to exist in plankton, i.e. the herbivorous, multivorous, and two types of microbial food web. We illustrated the conceptual trophic pathways using carbon flows that were actually observed at representative stations. The latter can be calibrated to correspond to any field situation. Our study also provides researchers and managers with operational criteria for identifying the dominant trophic pathway in a planktonic assemblage, these criteria being based on the values of two carbon ratios that could be calculated from flow values that are relatively easy to estimate in the field.

Cerebrospinal and Interstitial Fluid Transport via the Glymphatic Pathway Modeled by Optimal Mass Transport

PubMed Central

Ratner, Vadim; Gao, Yi; Lee, Hedok; Elkin, Rena; Nedergaard, Maiken; Benveniste, Helene; Tannenbaum, Allen

2017-01-01

The glymphatic pathway is a system which facilitates continuous cerebrospinal fluid (CSF) and interstitial fluid (ISF) exchange and plays a key role in removing waste products from the rodent brain. Dysfunction of the glymphatic pathway may be implicated in the pathophysiology of Alzheimer's disease. Intriguingly, the glymphatic system is most active during deep wave sleep general anesthesia. By using paramagnetic tracers administered into CSF of rodents, we previously showed the utility of MRI in characterizing a macroscopic whole brain view of glymphatic transport but we have yet to define and visualize the specific flow patterns. Here we have applied an alternative mathematical analysis approach to a dynamic time series of MRI images acquired every 4 min over ∼3 hrs in anesthetized rats, following administration of a small molecular weight paramagnetic tracer into the CSF reservoir of the cisterna magna. We use Optimal Mass Transport (OMT) to model the glymphatic flow vector field, and then analyze the flow to find the network of CSF-ISF flow channels. We use 3D visualization computational tools to visualize the OMT defined network of CSF-ISF flow channels in relation to anatomical and vascular key landmarks from the live rodent brain. The resulting OMT model of the glymphatic transport network agrees largely with the current understanding of the glymphatic transport patterns defined by dynamic contrast-enhanced MRI revealing key CSF transport pathways along the ventral surface of the brain with a trajectory towards the pineal gland, cerebellum, hypothalamus and olfactory bulb. In addition, the OMT analysis also revealed some interesting previously unnoticed behaviors regarding CSF transport involving parenchymal streamlines moving from ventral reservoirs towards the surface of the brain, olfactory bulb and large central veins. PMID:28323163

Cerebrospinal and interstitial fluid transport via the glymphatic pathway modeled by optimal mass transport.

PubMed

Ratner, Vadim; Gao, Yi; Lee, Hedok; Elkin, Rena; Nedergaard, Maiken; Benveniste, Helene; Tannenbaum, Allen

2017-05-15

The glymphatic pathway is a system which facilitates continuous cerebrospinal fluid (CSF) and interstitial fluid (ISF) exchange and plays a key role in removing waste products from the rodent brain. Dysfunction of the glymphatic pathway may be implicated in the pathophysiology of Alzheimer's disease. Intriguingly, the glymphatic system is most active during deep wave sleep general anesthesia. By using paramagnetic tracers administered into CSF of rodents, we previously showed the utility of MRI in characterizing a macroscopic whole brain view of glymphatic transport but we have yet to define and visualize the specific flow patterns. Here we have applied an alternative mathematical analysis approach to a dynamic time series of MRI images acquired every 4min over ∼3h in anesthetized rats, following administration of a small molecular weight paramagnetic tracer into the CSF reservoir of the cisterna magna. We use Optimal Mass Transport (OMT) to model the glymphatic flow vector field, and then analyze the flow to find the network of CSF-ISF flow channels. We use 3D visualization computational tools to visualize the OMT defined network of CSF-ISF flow channels in relation to anatomical and vascular key landmarks from the live rodent brain. The resulting OMT model of the glymphatic transport network agrees largely with the current understanding of the glymphatic transport patterns defined by dynamic contrast-enhanced MRI revealing key CSF transport pathways along the ventral surface of the brain with a trajectory towards the pineal gland, cerebellum, hypothalamus and olfactory bulb. In addition, the OMT analysis also revealed some interesting previously unnoticed behaviors regarding CSF transport involving parenchymal streamlines moving from ventral reservoirs towards the surface of the brain, olfactory bulb and large central veins. Copyright © 2017. Published by Elsevier Inc.

The influence of alternative pathways of respiration that utilize branched-chain amino acids following water shortage in Arabidopsis.

PubMed

Pires, Marcel V; Pereira Júnior, Adilson A; Medeiros, David B; Daloso, Danilo M; Pham, Phuong Anh; Barros, Kallyne A; Engqvist, Martin K M; Florian, Alexandra; Krahnert, Ina; Maurino, Veronica G; Araújo, Wagner L; Fernie, Alisdair R

2016-06-01

During dark-induced senescence isovaleryl-CoA dehydrogenase (IVDH) and D-2-hydroxyglutarate dehydrogenase (D-2HGDH) act as alternate electron donors to the ubiquinol pool via the electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase (ETF/ETFQO) pathway. However, the role of this pathway in response to other stresses still remains unclear. Here, we demonstrated that this alternative pathway is associated with tolerance to drought in Arabidopsis. In comparison with wild type (WT) and lines overexpressing D-2GHDH, loss-of-function etfqo-1, d2hgdh-2 and ivdh-1 mutants displayed compromised respiration rates and were more sensitive to drought. Our results demonstrated that an operational ETF/ETFQO pathway is associated with plants' ability to withstand drought and to recover growth once water becomes replete. Drought-induced metabolic reprogramming resulted in an increase in tricarboxylic acid (TCA) cycle intermediates and total amino acid levels, as well as decreases in protein, starch and nitrate contents. The enhanced levels of the branched-chain amino acids in loss-of-function mutants appear to be related to their increased utilization as substrates for the TCA cycle under water stress. Our results thus show that mitochondrial metabolism is highly active during drought stress responses and provide support for a role of alternative respiratory pathways within this response. © 2015 John Wiley & Sons Ltd.

High-performance colorimeter with an electronic bubble gate for use in miniaturized continuous-flow analyzers.

PubMed

Neeley, W E; Wardlaw, S C; Yates, T; Hollingsworth, W G; Swinnen, M E

1976-02-01

We describe a high-performance colorimeter with an electronic bubble gate for use with miniaturized continuous-flow analyzers. The colorimeter has a flow-through cuvette with optically flat quartz windows that allows a bubbled stream to pass freely without any breakup or retention of bubbles. The fluid volume in the light path is only 1.8 mul. The electronic bubble gate selectively removes that portion of the photodector signal produced by the air bubbles passing through the flow cell and allows that portion of the signal attributable to the fluid segment to pass to the recorder. The colorimeter is easy to use, rugged, inexpensive, and requires minimal adjustments.

Negative Magnetoresistance in Viscous Flow of Two-Dimensional Electrons.

PubMed

Alekseev, P S

2016-10-14

At low temperatures, in very clean two-dimensional (2D) samples, the electron mean free path for collisions with static defects and phonons becomes greater than the sample width. Under this condition, the electron transport occurs by formation of a viscous flow of an electron fluid. We study the viscous flow of 2D electrons in a magnetic field perpendicular to the 2D layer. We calculate the viscosity coefficients as the functions of magnetic field and temperature. The off-diagonal viscosity coefficient determines the dispersion of the 2D hydrodynamic waves. The decrease of the diagonal viscosity in magnetic field leads to negative magnetoresistance which is temperature and size dependent. Our analysis demonstrates that this viscous mechanism is responsible for the giant negative magnetoresistance recently observed in the ultrahigh-mobility GaAs quantum wells. We conclude that 2D electrons in those structures in moderate magnetic fields should be treated as a viscous fluid.

Negative Magnetoresistance in Viscous Flow of Two-Dimensional Electrons

NASA Astrophysics Data System (ADS)

Alekseev, P. S.

2016-10-01

At low temperatures, in very clean two-dimensional (2D) samples, the electron mean free path for collisions with static defects and phonons becomes greater than the sample width. Under this condition, the electron transport occurs by formation of a viscous flow of an electron fluid. We study the viscous flow of 2D electrons in a magnetic field perpendicular to the 2D layer. We calculate the viscosity coefficients as the functions of magnetic field and temperature. The off-diagonal viscosity coefficient determines the dispersion of the 2D hydrodynamic waves. The decrease of the diagonal viscosity in magnetic field leads to negative magnetoresistance which is temperature and size dependent. Our analysis demonstrates that this viscous mechanism is responsible for the giant negative magnetoresistance recently observed in the ultrahigh-mobility GaAs quantum wells. We conclude that 2D electrons in those structures in moderate magnetic fields should be treated as a viscous fluid.

Electron transfer in biology

NASA Astrophysics Data System (ADS)

Williams, R. J. P.

Electron transfer is one of the key reactions of biology not just in catalysis of oxidation/reduction reactions but in the conversion of sources of energy such as light to usable form for chemical transformations. There are then two intriguing problems. What is the nature of the matrix in which electrons flow in a biological cell after the initial charge separation due for example to the absorption of light. Here we are examining biological structures similar to man's electronic wires and the construction must be of low resistance in what are apparently insulators - organic polymers. It has been found that the electronic conduction system is largely made from metallo-proteins associated with lipid membranes. We understand much about these biological wires today. The second problem concerns the conversion of the energy captured from the light into usable chemical form. The major synthetic step in the production of biological polymers, including proteins, DNA, RNA, polysaccharides and fats, is condensation, i.e. the removal of water in the formation of amides, esters and so on. Now these condensation reactions are driven in biology by using a drying agent in water, namely the anhydride, pyrophosphate, in a special compound ATP, adenosine triphosphate. The central problem is to discover exactly how the flow of electrons can be related to the synthesis of (bound) pyrophosphate. (In a thermodynamic sense pyrophosphate is a water soluble kinetically stable drying agent comparable with solid P2O5.) In the biological systems the connection between these different classes of reaction, electron transfer and condensation, is known to be via the production of an energized gradient of protons across the biological membrane which arises from the flow of electrons across the same membrane in the electron transport wires of biology. However we do not understand thoroughly the steps which lead from electron flow in a membrane to proton gradients in that membrane, i.e. electron/proton coupling. Again we do not understand thoroughly how subsequently the proton gradient across a membrane makes ATP, pyrophosphate. Today there is good experimental evidence as to the likely answers in principle. These analyse the coupling devices in mechanical terms. In this article I describe at first the 'wires' of biology, uncoupled simple electron flow, and then go on to the ways in which electron flow could be transduced by mechanical devices, also proteins, into proton gradients and then ATP. This will be termed coupled electron flow. The objective of the article is to stimulate participation by physical chemists in the further description of biological energy capture from light or the oxidation of hydrocarbons to a form suitable for driving chemical syntheses in a controlled manner.

Mutual synergy between catalase and peroxidase activities of the bifunctional enzyme KatG is facilitated by electron hole-hopping within the enzyme.

PubMed

Njuma, Olive J; Davis, Ian; Ndontsa, Elizabeth N; Krewall, Jessica R; Liu, Aimin; Goodwin, Douglas C

2017-11-10

KatG is a bifunctional, heme-dependent enzyme in the front-line defense of numerous bacterial and fungal pathogens against H 2 O 2 -induced oxidative damage from host immune responses. Contrary to the expectation that catalase and peroxidase activities should be mutually antagonistic, peroxidatic electron donors (PxEDs) enhance KatG catalase activity. Here, we establish the mechanism of synergistic cooperation between these activities. We show that at low pH values KatG can fully convert H 2 O 2 to O 2 and H 2 O only if a PxED is present in the reaction mixture. Stopped-flow spectroscopy results indicated rapid initial rates of H 2 O 2 disproportionation slowing concomitantly with the accumulation of ferryl-like heme states. These states very slowly returned to resting ( i.e. ferric) enzyme, indicating that they represented catalase-inactive intermediates. We also show that an active-site tryptophan, Trp-321, participates in off-pathway electron transfer. A W321F variant in which the proximal tryptophan was replaced with a non-oxidizable phenylalanine exhibited higher catalase activity and less accumulation of off-pathway heme intermediates. Finally, rapid freeze-quench EPR experiments indicated that both WT and W321F KatG produce the same methionine-tyrosine-tryptophan (MYW) cofactor radical intermediate at the earliest reaction time points and that Trp-321 is the preferred site of off-catalase protein oxidation in the native enzyme. Of note, PxEDs did not affect the formation of the MYW cofactor radical but could reduce non-productive protein-based radical species that accumulate during reaction with H 2 O 2 Our results suggest that catalase-inactive intermediates accumulate because of off-mechanism oxidation, primarily of Trp-321, and PxEDs stimulate KatG catalase activity by preventing the accumulation of inactive intermediates. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Electron Tunneling, a Quantum Probe for the Quantum World of Nanotechnology

ERIC Educational Resources Information Center

Hipps, K. W.; Scudiero, L.

2005-01-01

A quantum-mechanical probe is essential to study the quantum world, which is provided by electron tunneling. A spectroscopic mapping to image the electron-transport pathways on a sub-molecular scale is used.

A Study of the Effects of High Power Pulsed 2450 MHz Microwaves, ELF modulated Microwaves, and ELF Fields on Human Lymphocytes and Selected Cell Lines

DTIC Science & Technology

1993-01-27

Considerable effect was expended in investigating shifts in intercellular calcium of one particular cell line, Jurket, using flow cytometry methods. No...culture. The following analysis were used to characterize the immortalized cell lines: flow cytometry , electron microscopy, two-dimensional protein gel...further characterized by flow cytometry , electron microscopy, two dimensional protein electrophoresis and nuclear run-off assay. Flow cytometric analysis of

Global gyrokinetic simulations of intrinsic rotation in ASDEX Upgrade Ohmic L-mode plasmas

NASA Astrophysics Data System (ADS)

Hornsby, W. A.; Angioni, C.; Lu, Z. X.; Fable, E.; Erofeev, I.; McDermott, R.; Medvedeva, A.; Lebschy, A.; Peeters, A. G.; The ASDEX Upgrade Team

2018-05-01

Non-linear, radially global, turbulence simulations of ASDEX Upgrade (AUG) plasmas are performed and the nonlinear generated intrinsic flow shows agreement with the intrinsic flow gradients measured in the core of Ohmic L-mode plasmas at nominal parameters. Simulations utilising the kinetic electron model show hollow intrinsic flow profiles as seen in a predominant number of experiments performed at similar plasma parameters. In addition, significantly larger flow gradients are seen than in a previous flux-tube analysis (Hornsby et al 2017 Nucl. Fusion 57 046008). Adiabatic electron model simulations can show a flow profile with opposing sign in the gradient with respect to a kinetic electron simulation, implying a reversal in the sign of the residual stress due to kinetic electrons. The shaping of the intrinsic flow is strongly determined by the density gradient profile. The sensitivity of the residual stress to variations in density profile curvature is calculated and seen to be significantly stronger than to neoclassical flows (Hornsby et al 2017 Nucl. Fusion 57 046008). This variation is strong enough on its own to explain the large variations in the intrinsic flow gradients seen in some AUG experiments. Analysis of the symmetry breaking properties of the turbulence shows that profile shearing is the dominant mechanism in producing a finite parallel wave-number, with turbulence gradient effects contributing a smaller portion of the parallel wave-vector.

Using proteomic data to assess a genome-scale "in silico" model of metal reducing bacteria in the simulation of field-scale uranium bioremediation

NASA Astrophysics Data System (ADS)

Yabusaki, S.; Fang, Y.; Wilkins, M. J.; Long, P.; Rifle IFRC Science Team

2011-12-01

A series of field experiments in a shallow alluvial aquifer at a former uranium mill tailings site have demonstrated that indigenous bacteria can be stimulated with acetate to catalyze the conversion of hexavalent uranium in a groundwater plume to immobile solid-associated uranium in the +4 oxidation state. While this bioreduction of uranium has been shown to lower groundwater concentrations below actionable standards, a viable remediation methodology will need a mechanistic, predictive and quantitative understanding of the microbially-mediated reactions that catalyze the reduction of uranium in the context of site-specific processes, properties, and conditions. At the Rifle IFRC site, we are investigating the impacts on uranium behavior of pulsed acetate amendment, acetate-oxidizing iron and sulfate reducing bacteria, seasonal water table variation, spatially-variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. The simulation of three-dimensional, variably saturated flow and biogeochemical reactive transport during a uranium bioremediation field experiment includes a genome-scale in silico model of Geobacter sp. to represent the Fe(III) terminal electron accepting process (TEAP). The Geobacter in silico model of cell-scale physiological metabolic pathways is comprised of hundreds of intra-cellular and environmental exchange reactions. One advantage of this approach is that the TEAP reaction stoichiometry and rate are now functions of the metabolic status of the microorganism. The linkage of in silico model reactions to specific Geobacter proteins has enabled the use of groundwater proteomic analyses to assess the accuracy of the model under evolving hydrologic and biogeochemical conditions. In this case, the largest predicted fluxes through in silico model reactions generally correspond to high abundances of proteins linked to those reactions (e.g. the condensation reaction catalyzed by the protein citrate synthase that generates citrate from acetyl-CoA and oxaloacetate). Model discrepancies with the proteomic data, such as the prediction of shifts associated with nitrogen limitation, revealed pathways in the in silico code that could be modified to more accurately predict metabolic processes that occur in the subsurface. The potential outcome of this approach is the engineering of electron donor (e.g., acetate), terminal electron acceptor [e.g., U(VI)], and biogeochemical conditions that enhance the desired metabolic pathways of the target microorganism(s) to effect cost-effective uranium bioreduction.

Fluorescence particle detection using microfluidics and planar optoelectronic elements

NASA Astrophysics Data System (ADS)

Kettlitz, Siegfried W.; Moosmann, Carola; Valouch, Sebastian; Lemmer, Uli

2014-05-01

Detection of fluorescent particles is an integral part of flow cytometry for analysis of selectively stained cells. Established flow cytometer designs achieve great sensitivity and throughput but require bulky and expensive components which prohibit mass production of small single-use point-of-care devices. The use of a combination of innovative technologies such as roll-to-roll printed microuidics with integrated optoelectronic components such as printed organic light emitting diodes and printed organic photodiodes enables tremendous opportunities in cost reduction, miniaturization and new application areas. In order to harvest these benefits, the optical setup requires a redesign to eliminate the need for lenses, dichroic mirrors and lasers. We investigate the influence of geometric parameters on the performance of a thin planar design which uses a high power LED as planar light source and a PIN-photodiode as planar detector. Due to the lack of focusing optics and inferior optical filters, the device sensitivity is not yet on par with commercial state of the art flow cytometer setups. From noise measurements, electronic and optical considerations we deduce possible pathways of improving the device performance. We identify that the sensitivity is either limited by dark noise for very short apertures or by noise from background light for long apertures. We calculate the corresponding crossover length. For the device design we conclude that a low device thickness, low particle velocity and short aperture length are necessary to obtain optimal sensitivity.

Call-Center Based Disease Management of Pediatric Asthmatics

DTIC Science & Technology

2005-04-01

study locations. Purchase peak flow meters. Prepare and reproduce patient education materials, and informed consent work sheets. Contract Oracle data...identified. Electronic peak flow meters have been purchased. Patient education materials and informed consent documents have been reproduced. A web-based...Research Center * Study population identified via military and Foundation Health databases * Electronic peak flow meters purchased * Patient education materials

Analysis of fast chlorophyll fluorescence rise (O-K-J-I-P) curves in green fruits indicates electron flow limitations at the donor side of PSII and the acceptor sides of both photosystems.

PubMed

Kalachanis, Dimitrios; Manetas, Yiannis

2010-07-01

Limited evidence up to now indicates low linear photosynthetic electron flow and CO(2) assimilation rates in non-foliar chloroplasts. In this investigation, we used chlorophyll fluorescence techniques to locate possible limiting steps in photosystem function in exposed, non-stressed green fruits (both pericarps and seeds) of three species, while corresponding leaves served as controls. Compared with leaves, fruit photosynthesis was characterized by less photon trapping and less quantum yields of electron flow, while the non-photochemical quenching was higher and potentially linked to enhanced carotenoid/chlorophyll ratios. Analysis of fast chlorophyll fluorescence rise curves revealed possible limitations both in the donor (oxygen evolving complex) and the acceptor (Q(A)(-)--> intermediate carriers) sides of photosystem II (PSII) indicating innately low PSII photochemical activity. On the other hand, PSI was characterized by faster reduction of its final electron acceptors and their small pool sizes. We argue that the fast reductive saturation of final PSI electron acceptors may divert electrons back to intermediate carriers facilitating a cyclic flow around PSI, while the partial inactivation of linear flow precludes strong reduction of plastoquinone. As such, the photosynthetic attributes of fruit chloroplasts may act to replenish the ATP lost because of hypoxia usually encountered in sink organs with high diffusive resistance to gas exchange.

Flow-induced protein kinase A–CREB pathway acts via BMP signaling to promote HSC emergence

PubMed Central

Kim, Peter Geon; Nakano, Haruko; Das, Partha P.; Chen, Michael J.; Rowe, R. Grant; Chou, Stephanie S.; Ross, Samantha J.; Sakamoto, Kathleen M.; Zon, Leonard I.; Schlaeger, Thorsten M.; Orkin, Stuart H.; Nakano, Atsushi

2015-01-01

Fluid shear stress promotes the emergence of hematopoietic stem cells (HSCs) in the aorta–gonad–mesonephros (AGM) of the developing mouse embryo. We determined that the AGM is enriched for expression of targets of protein kinase A (PKA)–cAMP response element-binding protein (CREB), a pathway activated by fluid shear stress. By analyzing CREB genomic occupancy from chromatin-immunoprecipitation sequencing (ChIP-seq) data, we identified the bone morphogenetic protein (BMP) pathway as a potential regulator of CREB. By chemical modulation of the PKA–CREB and BMP pathways in isolated AGM VE-cadherin+ cells from mid-gestation embryos, we demonstrate that PKA–CREB regulates hematopoietic engraftment and clonogenicity of hematopoietic progenitors, and is dependent on secreted BMP ligands through the type I BMP receptor. Finally, we observed blunting of this signaling axis using Ncx1-null embryos, which lack a heartbeat and intravascular flow. Collectively, we have identified a novel PKA–CREB–BMP signaling pathway downstream of shear stress that regulates HSC emergence in the AGM via the endothelial-to-hematopoietic transition. PMID:25870201

Surface Proton Transfer Promotes Four-Electron Oxygen Reduction on Gold Nanocrystal Surfaces in Alkaline Solution

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

Lu, Fang; Zhang, Yu; Liu, Shizhong

Four-electron oxygen reduction reaction (4e-ORR), as a key pathway in energy conversion, is preferred over the two-electron reduction pathway that falls short in dissociating dioxygen molecules. Gold (Au) surfaces exhibit high sensitivity of the ORR pathway to its atomic structures. The long-standing puzzle remains unsolved why the Au surfaces with {100} sub-facets were exceptionally capable to catalyze the 4e-ORR in alkaline solution, though limited within a narrow potential window. Herein we report the discovery of a dominant 4e-ORR over the whole potential range on {310} surface of Au nanocrystal shaped as truncated ditetragonal prism (TDP). In contrast, ORR pathways onmore » single-crystalline facets of shaped nanoparticles, including {111} on nano-octahedra and {100} on nano-cubes, are similar to their single-crystal counterparts. Combining our experimental results with density functional theory calculations, we elucidate the key role of surface proton transfers from co-adsorbed H 2O molecules in activating the facet- and potential-dependent 4e ORR on Au in alkaline solutions. These results elucidate how surface atomic structures determine the reaction pathways via bond scission and formation among weakly adsorbed water and reaction intermediates. The new insight helps in developing facet-specific nanocatalysts for various reactions.« less

Surface Proton Transfer Promotes Four-Electron Oxygen Reduction on Gold Nanocrystal Surfaces in Alkaline Solution

DOE PAGES

Lu, Fang; Zhang, Yu; Liu, Shizhong; ...

2017-05-11

Four-electron oxygen reduction reaction (4e-ORR), as a key pathway in energy conversion, is preferred over the two-electron reduction pathway that falls short in dissociating dioxygen molecules. Gold (Au) surfaces exhibit high sensitivity of the ORR pathway to its atomic structures. The long-standing puzzle remains unsolved why the Au surfaces with {100} sub-facets were exceptionally capable to catalyze the 4e-ORR in alkaline solution, though limited within a narrow potential window. Herein we report the discovery of a dominant 4e-ORR over the whole potential range on {310} surface of Au nanocrystal shaped as truncated ditetragonal prism (TDP). In contrast, ORR pathways onmore » single-crystalline facets of shaped nanoparticles, including {111} on nano-octahedra and {100} on nano-cubes, are similar to their single-crystal counterparts. Combining our experimental results with density functional theory calculations, we elucidate the key role of surface proton transfers from co-adsorbed H 2O molecules in activating the facet- and potential-dependent 4e ORR on Au in alkaline solutions. These results elucidate how surface atomic structures determine the reaction pathways via bond scission and formation among weakly adsorbed water and reaction intermediates. The new insight helps in developing facet-specific nanocatalysts for various reactions.« less

Evaluation of diffuse and preferential flow pathways of infiltratedprecipitation and irrigation using oxygen and hydrogen isotopes

USGS Publications Warehouse

Ma, Bin; Liang, Xing; Liu, Shaohua; Jin, Menggui; Nimmo, John R.; Li, Jingxin

2017-01-01

Subsurface-water flow pathways in three different land-use areas (non-irrigated grassland, poplar forest, and irrigated arable land) in the central North China Plain were investigated using oxygen (18O) and hydrogen (2H) isotopes in samples of precipitation, soils, and groundwater. Soil water in the top 10 cm was significantly affected by both evaporation and infiltration. Water at 10–40 cm depth in the grassland and arable land, and 10–60 cm in poplar forest, showed a relatively short residence time, as a substantial proportion of antecedent soil water was mixed with a 92-mm storm infiltration event, whereas below those depths (down to 150 cm), depleted δ18O spikes suggested that some storm water bypassed the shallow soil layers. Significant differences, in soil-water content and δ18O values, within a small area, suggested that the proportion of immobile soil water and water flowing in subsurface pathways varies depending on local vegetation cover, soil characteristics and irrigation applications. Soil-water δ18O values revealed that preferential flow and diffuse flow coexist. Preferential flow was active within the root zone, independent of antecedent soil-water content, in both poplar forest and arable land, whereas diffuse flow was observed in grassland. The depleted δ18O spikes at 20–50 cm depth in the arable land suggested the infiltration of irrigation water during the dry season. Temporal isotopic variations in precipitation were subdued in the shallow groundwater, suggesting more complete mixing of different input waters in the unsaturated zone before reaching the shallow groundwater.

Assessing the Ability of Vegetation Indices to Identify Shallow Subsurface Water Flow Pathways from Hyperspectral Imagery Using Machine Learning: Application

NASA Astrophysics Data System (ADS)

Doctor, K.; Byers, J. M.

2017-12-01

Shallow underground water flow pathways expressed as slight depressions are common in the land surface. Under conditions of saturated overland flow, such as during heavy rain or snow melt, these areas of preferential flow might appear on the surface as very shallow flowing streams. When there is no water flowing in these ephemeral channels it can be difficult to identify them. It is especially difficult to discern the slight depressions above the subsurface water flow pathways (SWFP) when the area is covered by vegetation. Since the soil moisture content in these SWFP is often greater than the surrounding area, the vegetation growing on top of these channels shows different vigor and moisture content than the vegetation growing above the non-SWFP area. Vegetation indices (VI) are used in visible and near infrared (VNIR) hyperspectral imagery to enhance biophysical properties of vegetation, and so the brightness values between vegetation atop SWFP and the surrounding vegetation were highlighted. We performed supervised machine learning using ground-truth class labels to determine the conditional probability of a SWFP at a given pixel given either the spectral distribution or VI at that pixel. The training data estimates the probability distributions to a determined finite sampling accuracy for a binary Naïve Bayes classifier between SWFP and non-SWFP. The ground-truth data provides a test bed for understanding the ability to build SWFP classifiers using hyperspectral imagery. SWFP were distinguishable in the imagery within corn and grass fields and in areas with low-lying vegetation. However, the training data is limited to particular types of terrain and vegetation cover in the Shenandoah Valley, Virginia and this would limit the resulting classifier. Further training data could extend its use to other environments.

Cyclooxygenase-2 Selectively Controls Renal Blood Flow Through a Novel PPARβ/δ-Dependent Vasodilator Pathway.

PubMed

Kirkby, Nicholas S; Sampaio, Walkyria; Etelvino, Gisele; Alves, Daniele T; Anders, Katie L; Temponi, Rafael; Shala, Fisnik; Nair, Anitha S; Ahmetaj-Shala, Blerina; Jiao, Jing; Herschman, Harvey R; Xiaomeng, Wang; Wahli, Walter; Santos, Robson A; Mitchell, Jane A

2018-02-01

Cyclooxygenase-2 (COX-2) is an inducible enzyme expressed in inflammation and cancer targeted by nonsteroidal anti-inflammatory drugs. COX-2 is also expressed constitutively in discreet locations where its inhibition drives gastrointestinal and cardiovascular/renal side effects. Constitutive COX-2 expression in the kidney regulates renal function and blood flow; however, the global relevance of the kidney versus other tissues to COX-2-dependent blood flow regulation is not known. Here, we used a microsphere deposition technique and pharmacological COX-2 inhibition to map the contribution of COX-2 to regional blood flow in mice and compared this to COX-2 expression patterns using luciferase reporter mice. Across all tissues studied, COX-2 inhibition altered blood flow predominantly in the kidney, with some effects also seen in the spleen, adipose, and testes. Of these sites, only the kidney displayed appreciable local COX-2 expression. As the main site where COX-2 regulates blood flow, we next analyzed the pathways involved in kidney vascular responses using a novel technique of video imaging small arteries in living tissue slices. We found that the protective effect of COX-2 on renal vascular function was associated with prostacyclin signaling through PPARβ/δ (peroxisome proliferator-activated receptor-β/δ). These data demonstrate the kidney as the principle site in the body where local COX-2 controls blood flow and identifies a previously unreported PPARβ/δ-mediated renal vasodilator pathway as the mechanism. These findings have direct relevance to the renal and cardiovascular side effects of drugs that inhibit COX-2, as well as the potential of the COX-2/prostacyclin/PPARβ/δ axis as a therapeutic target in renal disease. © 2018 The Authors.

Quantum Calculations of Electron Tunneling in Respiratory Complex III.

PubMed

Hagras, Muhammad A; Hayashi, Tomoyuki; Stuchebrukhov, Alexei A

2015-11-19

The most detailed and comprehensive to date study of electron transfer reactions in the respiratory complex III of aerobic cells, also known as bc1 complex, is reported. In the framework of the tunneling current theory, electron tunneling rates and atomistic tunneling pathways between different redox centers were investigated for all electron transfer reactions comprising different stages of the proton-motive Q-cycle. The calculations reveal that complex III is a smart nanomachine, which under certain conditions undergoes conformational changes gating electron transfer, or channeling electrons to specific pathways. One-electron tunneling approximation was adopted in the tunneling calculations, which were performed using hybrid Broken-Symmetry (BS) unrestricted DFT/ZINDO levels of theory. The tunneling orbitals were determined using an exact biorthogonalization scheme that uniquely separates pairs of tunneling orbitals with small overlaps out of the remaining Franck-Condon orbitals with significant overlap. Electron transfer rates in different redox pairs show exponential distance dependence, in agreement with the reported experimental data; some reactions involve coupled proton transfer. Proper treatment of a concerted two-electron bifurcated tunneling reaction at the Q(o) site is given.

Creating a bio-hybrid signal transduction pathway: opening a new channel of communication between cells and machines.

PubMed

Yarkoni, Orr; Donlon, Lynn; Frankel, Daniel

2012-12-01

Manipulation of signal transduction pathways presents a viable mechanism to interface cells with electronics. In this work, we present a two-step signal transduction pathway involving cellular and electronic transduction elements. In order to circumvent many of the conventional difficulties encountered when harnessing chemical signalling for the purpose of electronics communication, gaseous nitric oxide (NO) was selected as the signalling molecule. By genetic engineering of the nitric oxide synthase protein eNOS and insertion of light-oxygen-voltage (LOV) domains, we have created a photoactive version of the protein. The novel chimeric eNOS was found to be capable of producing NO in response to excitation by visible light. By coupling these mutant cells to a surface modified platinum electrode, it was possible to convert an optical signal into a chemical one, followed by subsequent conversion of the chemical signal into an electrical output.

OH- Initiated Heterogeneous Oxidation of Saturated Organic Aerosols in the Presence of SO2: Uptake Kinetics and Product Identification.

NASA Astrophysics Data System (ADS)

Richards-Henderson, N. K.; Ward, M.; Goldstein, A. H.; Wilson, K. R.

2014-12-01

Gas-phase oxidation mechanisms for organic gases are often used as a starting point to understand heterogeneous oxidation. The reaction of a simple alkane hydrocarbon by OH proceeds through hydrogen abstraction and under ambient conditions leads to peroxy radical (RO2) formation. RO2 can further react to form: (1) smaller molecular weight products (i.e. fragmentation) via alkoxy radical formation and dissociation and/or (2) higher molecular weight products with oxygenated functional groups (i.e. functionalization). The ability to perturb these two pathways (functionalization vs. fragmentation) is critical for understanding the detailed reaction mechanism that control atmospheric aging chemistry of particles. At high temperatures the presence of sulfur dioxide (SO2) during organic-OH gas-phase oxidation enhances the fragmentation pathway leading to increased alkoxy formation. It is unknown if a comparative affect occurs at room temperature during a heterogeneous reaction. We used the heterogeneous reaction of OH radicals with sub-micron squalane particles in the presence and absence of SO2 as a model system to explore changes in individual mechanistic pathways. Detailed kinetic measurements were made in a flow tube reactor using a vacuum ultraviolet (VUV) photoionization aerosol mass spectrometer and oxidation products are identified from samples collected on quartz filters using thermal desorption two-dimensional chromatographic separation and ionization by either VUV (10.5 eV) or electron impact (70 eV), with detection by high resolution time of flight mass spectrometry (GCxGC-VUV/EI-HRTOFMS). In the presence of SO2 the yields of alcohols were enhanced compared to without SO2, suggesting that the alkoxy formation pathway was dominant. The results from this work will provide an experimentally-confirmed kinetic framework that could be used to model atmospheric aging mechanisms.

miR-34a mediates oxaliplatin resistance of colorectal cancer cells by inhibiting macroautophagy via transforming growth factor-β/Smad4 pathway

PubMed Central

Sun, Chen; Wang, Fu-Jing; Zhang, Hao-Gang; Xu, Xun-Zheng; Jia, Rui-Chun; Yao, Lei; Qiao, Peng-Fei

2017-01-01

AIM To investigate whether microRNA (miR)-34a mediates oxaliplatin (OXA) resistance of colorectal cancer (CRC) cells by inhibiting macroautophagy via the transforming growth factor (TGF)-β/Smad4 pathway. METHODS miR-34a expression levels were detected in CRC tissues and CRC cell lines by quantitative real-time polymerase chain reaction. Computational search, functional luciferase assay and western blotting were used to demonstrate the downstream target of miR-34a in CRC cells. Cell viability was measured with Cell Counting Kit-8. Apoptosis and macroautophagy of CRC cells were analyzed by flow cytometry and transmission electron microscopy, and expression of beclin I and LC3-II was detected by western blotting. RESULTS Expression of miR-34a was significantly reduced while expression of TGF-β and Smad4 was increased in CRC patients treated with OXA-based chemotherapy. OXA treatment also resulted in decreased miR-34a levels and increased TGF-β and Smad4 levels in both parental cells and the OXA-resistant CRC cells. Activation of macroautophagy contributed to OXA resistance in CRC cells. Expression levels of Smad4 and miR-34a in CRC patients had a significant inverse correlation and overexpressing miR-34a inhibited macroautophagy activation by directly targeting Smad4 through the TGF-β/Smad4 pathway. OXA-induced downregulation of miR-34a and increased drug resistance by activating macroautophagy in CRC cells. CONCLUSION miR-34a mediates OXA resistance of CRC by inhibiting macroautophagy via the TGF-β/Smad4 pathway. PMID:28348487

Tetrahydrothiophene 1-oxide as an electron acceptor for Escherichia coli.

PubMed Central

Meganathan, R; Schrementi, J

1987-01-01

Escherichia coli used tetrahydrothiophene 1-oxide (THTO) as an electron acceptor for anaerobic growth with glycerol as a carbon source; the THTO was reduced to tetrahydrothiophene. Cell extracts also reduced THTO to tetrahydrothiophene in the presence of a variety of electron donors. Chlorate-resistant (chl) mutants (chlA, chlB, chlD, and chlE) were unable to grow with THTO as the electron acceptor. However, growth and THTO reduction by the chlD mutant were restored by high concentrations of molybdate. Similarly, mutants of E. coli that are blocked in the menaquinone (vitamin K2) biosynthetic pathway, i.e., menB, menC, and menD mutants, did not grow with THTO as an electron acceptor. Growth and THTO reduction were restored in these mutants by the presence of appropriate intermediates of the vitamin K biosynthetic pathway. PMID:3294808

Particle flows to shape and voltage surface discontinuities in the electron sheath surrounding a high voltage solar array in LEO

NASA Technical Reports Server (NTRS)

Metz, Roger N.

1991-01-01

This paper discusses the numerical modeling of electron flows from the sheath surrounding high positively biased objects in LEO (Low Earth Orbit) to regions of voltage or shape discontinuity on the biased surfaces. The sheath equations are derived from the Two-fluid, Warm Plasma Model. An equipotential corner and a plane containing strips of alternating voltage bias are treated in two dimensions. A self-consistent field solution of the sheath equations is outlined and is pursued through one cycle. The electron density field is determined by numerical solution of Poisson's equation for the electrostatic potential in the sheath using the NASCAP-LEO relation between electrostatic potential and charge density. Electron flows are calculated numerically from the electron continuity equation. Magnetic field effects are not treated.

Visualization and Hierarchical Analysis of Flow in Discrete Fracture Network Models

NASA Astrophysics Data System (ADS)

Aldrich, G. A.; Gable, C. W.; Painter, S. L.; Makedonska, N.; Hamann, B.; Woodring, J.

2013-12-01

Flow and transport in low permeability fractured rock is primary in interconnected fracture networks. Prediction and characterization of flow and transport in fractured rock has important implications in underground repositories for hazardous materials (eg. nuclear and chemical waste), contaminant migration and remediation, groundwater resource management, and hydrocarbon extraction. We have developed methods to explicitly model flow in discrete fracture networks and track flow paths using passive particle tracking algorithms. Visualization and analysis of particle trajectory through the fracture network is important to understanding fracture connectivity, flow patterns, potential contaminant pathways and fast paths through the network. However, occlusion due to the large number of highly tessellated and intersecting fracture polygons preclude the effective use of traditional visualization methods. We would also like quantitative analysis methods to characterize the trajectory of a large number of particle paths. We have solved these problems by defining a hierarchal flow network representing the topology of particle flow through the fracture network. This approach allows us to analyses the flow and the dynamics of the system as a whole. We are able to easily query the flow network, and use paint-and-link style framework to filter the fracture geometry and particle traces based on the flow analytics. This allows us to greatly reduce occlusion while emphasizing salient features such as the principal transport pathways. Examples are shown that demonstrate the methodology and highlight how use of this new method allows quantitative analysis and characterization of flow and transport in a number of representative fracture networks.

The influence of ZnO-SnO2 nanoparticles and activated carbon on the photocatalytic degradation of toluene using continuous flow mode

PubMed Central

Rangkooy, Hossein Ali; Tanha, Fatemeh; Jaafarzadeh, Neamat; Mohammadbeigi, Abolfazl

2017-01-01

The present study examined the gas-phase photocatalytic degradation of toluene using ZnO-SnO2 nanocomposite supported on activated carbon in a photocatalytic reactor. Toluene was selected as a model pollutant from volatile organic compounds to determine the pathway of photocatalytic degradation and the factors influencing this degradation. The ZnO-SnO2 nanocomposite was synthesized through co-precipitation method in a ratio of 2:1 and then supported on activated carbon. The immobilization of ZnO-SnO2 nanocomposite on activated carbon was determined by the surface area and scanning electron micrograph technique proposed by Brunauer, Emmett, and Teller. The laboratory findings showed that the highest efficiency was 40% for photocatalytic degradation of toluene. The results also indicated that ZnO-SnO2 nano-oxides immobilization on activated carbon had a synergic effect on photocatalytic degradation of toluene. Use of a hybrid photocatalytic system (ZnO/SnO2 nano coupled oxide) and application of absorbent (activated carbon) may be efficient and effective technique for refinement of toluene from air flow. PMID:29497487

Control of Oxidative Sulfur Metabolism of Chlorobium limicola forma thiosulfatophilum

PubMed Central

Cork, Douglas; Mathers, Jeremy; Maka, Andrea; Srnak, Anna

1985-01-01

A metered blend of anaerobic-grade N2, CO2, and H2S gases was introduced into an illuminated, 800-ml liquid volume, continuously stirred tank reactor. The system, described as an anaerobic gas-to-liquid phase fed-batch reactor, was used to investigate the effects of H2S flow rate and light energy on the accumulation of oxidized sulfur compounds formed by the photoautotroph Chlorobium limicola forma thiosulfatophilum during growth. Elemental sulfur was formed and accumulated in stoichiometric quantities when light energy and H2S molar flow rate levels were optimally adjusted in the presence of nonlimiting CO2. Deviation from the optimal H2S and light energy levels resulted in either oxidation of sulfur or complete inhibition of sulfide oxidation. Based on these observations, a model of sulfide and sulfur oxidases electrochemically coupled to the photosynthetic reaction center of Chlorobium spp. is presented. The dynamic deregulation of oxidative pathways may be a mechanism for supplying the photosynthetic reaction center with a continuous source of electrons during periods of varying light and substrate availability, as in pond ecosystems where Chlorobium spp. are found. Possible applications for a sulfide gas removal process are discussed. PMID:16346713

A Review of Darcy's Law: Limitations and Alternatives for Predicting Solute Transport

NASA Astrophysics Data System (ADS)

Steenhuis, Tammo; Kung, K.-J. Sam; Jaynes, Dan; Helling, Charles S.; Gish, Tim; Kladivko, Eileen

2016-04-01

Darcy's Law that was derived originally empirically 160 years ago, has been used successfully in calculating the (Darcy) flux in porous media throughout the world. However, field and laboratory experiments have demonstrated that the Darcy flux employed in the convective disperse equation could only successfully predict solute transport under two conditions: (1) uniformly or densely packed porous media; and (2) field soils under relatively dry condition. Employing the Darcy flux for solute transport in porous media with preferential flow pathways was problematic. In this paper we examine the theoretical background behind these field and laboratory observations and then provide an alternative to predict solute movement. By examining the characteristics of the momentum conservation principles on which Darcy's law is based, we show under what conditions Darcy flux can predict solute transport in porous media of various complexity. We find that, based on several case studies with capillary pores, Darcy's Law inherently merges momentum and in that way erases information on pore-scale velocities. For that reason the Darcy flux cannot predict flow in media with preferential flow conduits where individual pore velocities are essential in predicting the shape of the breakthrough curve and especially "the early arrival" of solutes. To overcome the limitations of the assumption in Darcy's law, we use Jury's conceptualization and employ the measured chemical breakthrough curve as input to characterize the impact of individual preferential flow pathways on chemical transport. Specifically, we discuss how best to take advantage of Jury's conceptualization to extract the pore-scale flow velocity to accurately predict chemical transport through soils with preferential flow pathways.

Kinetics of interprotein electron transfer between cytochrome c6 and the soluble CuA domain of cyanobacterial cytochrome c oxidase.

PubMed

Paumann, Martina; Feichtinger, Markus; Bernroitner, Margit; Goldfuhs, Judith; Jakopitsch, Christa; Furtmüller, Paul G; Regelsberger, Günther; Peschek, Günter A; Obinger, Christian

2004-10-08

Cytochrome c6 is a soluble metalloprotein located in the periplasmic space and the thylakoid lumen of many cyanobacteria and is known to carry electrons from cytochrome b6f to photosystem I. The CuA domain of cytochrome c oxidase, the terminal enzyme which catalyzes the four-electron reduction of molecular oxygen in the respiratory chains of mitochondria and many bacteria, also has a periplasmic location. In order to test whether cytochrome c6 could also function as a donor for cytochrome c oxidase, we investigated the kinetics of the electron transfer between recombinant cytochrome c6 (produced in high yield in Escherichia coli by coexpressing the maturation proteins encoded by the ccmA-H gene cluster) and the recombinant soluble CuA domain (i.e., the donor binding and electron entry site) of subunit II of cytochrome c oxidase from Synechocystis PCC 6803. The forward and the reverse electron transfer reactions were studied by the stopped-flow technique and yielded apparent bimolecular rate constants of (3.3 +/- 0.3) x 10(5) M(-1) s(-1) and (3.9 +/- 0.1) x 10(6) M(-1) s(-1), respectively, in 5 mM potassium phosphate buffer, pH 7, containing 20 mM potassium chloride and 25 degrees C. This corresponds to an equilibrium constant Keq of 0.085 in the physiological direction (DeltarG'0 = 6.1 kJ/mol). The reduction of the CuA fragment by cytochrome c6 is almost independent on ionic strength, which is in contrast to the reaction of the CuA domain with horse heart cytochrome c, which decreases with increasing ionic strength. The findings are discussed with respect to the potential role of cytochrome c6 as mobile electron carrier in both cyanobacterial electron transport pathways. Copyright 2004 Federation of European Biochemical Societies

Multiple pathways for woody plant establishment on floodplains at local to regional scales

USGS Publications Warehouse

Cooper, D.J.; Andersen, D.C.; Chimner, Rodney A.

2003-01-01

1. The structure and functioning of riverine ecosystems is dependent upon regional setting and the interplay of hydrologic regime and geomorphologic processes. We used a retrospective analysis to study recruitment along broad, alluvial valley segments (parks) and canyon segments of the unregulated Yampa River and the regulated Green River in the upper Colorado River basin, USA. We precisely aged 811 individuals of Populus deltoides ssp. wislizenii (native) and Tamarix ramosissima (exotic) from 182 wooded patches and determined the elevation and character of the germination surface for each. We used logistic regression to relate recruitment events (presence or absence of cohort) to five flow and two weather parameters.2. Woody plant establishment occurred via multiple pathways at patch, reach and segment scales. Recruitment occurred through establishment on (1) vertically accreting bars in the unregulated alluvial valley, (2) high alluvial floodplain surfaces during rare large flood events, (3) vertically accreting channel margin deposits in canyon pools and eddies, (4) vertically accreting intermittent/abandoned channels, (5) low elevation gravel bars and debris fans in canyons during multi-year droughts, and (6) bars and channels formed prior to flow regulation on the dammed river during controlled flood events.3. The Yampa River's peak flow was rarely included in models estimating the likelihood that recruitment would occur in any year. Flow variability and the interannual pattern of flows, rather than individual large floods, control most establishment.4. Regulation of the Green River flow since 1962 has had different effects on woody vegetation recruitment in canyons and valleys. The current regime mimics drought in a canyon setting, accelerating Tamarix invasion whereas in valleys the ongoing geomorphic adjustment of the channel, combined with reduced flow variability, has nearly eliminated Populus establishment.5. A single year's flow or a particular pattern of flows over a sequence of years, whether natural or man-made, produces different recruitment opportunities in alluvial and canyon reaches, in diverse landforms within a particular river reach, and for Populus and Tamarix. The design of flows to restore riparian ecosystems must consider these multiple pathways and adjust the seasonal timing, magnitude and interannual frequency of flows to match the desired outcome.

Spheromak plasma flow injection into a torus chamber and the HIST plasmas

NASA Astrophysics Data System (ADS)

Hatuzaki, Akinori

2005-10-01

The importance of plasma flow or two-fluid effect is recognized in understanding the relaxed states of high-beta torus plasmas, start-up and current drive by non-coaxial helicity injection, magnetic reconnection and plasma dynamo in fusion, laboratory and space plasmas. As a new approach to create a flowing two-fluid plasma equilibrium, we have tried to inject tangentially the plasma flow with spheromak-type magnetic configurations into a torus vacuum chamber with an external toroidal magnetic field (TF) coil. In the initial experiments, the RFP-like configuration with helical magnetic structures was realized in the torus vessel. The ion flow measurement with Mach probes showed that the ion flow keeps the same direction despite the reversal of the toroidal current and the axial electric field. The ion fluid comes to flow in the opposite direction to the electron fluid by the reversal of TF. This result suggests that not only electron but also ion flow contributes significantly on the reversed toroidal current. In this case, the ratio of ui to the electron flow velocity ue is estimated as ui/ue ˜ 1/2. We also will inject the spheromak flow into the HIST spherical torus plasmas to examine the possibilities to embedding the two-fluid effect in the ST plasmas.

Fluctuations, Electron Transport, and Flow Shear in 2D Axial, Azimuthal (z-θ) Hybrid Hall Thruster Simulations.

NASA Astrophysics Data System (ADS)

Fernandez, Eduardo; Gascon, Nicolas; Knoll, Aaron; Scharfe, Michelle; Cappelli, Mark

2007-11-01

Motivated by the inability of radial-axial (r-z) simulations to properly treat cross-field electron transport in Hall thrusters, a novel 2D z-θ model has been implemented. In common with many r-z descriptions, the simulation is hybrid in nature and assumes quasi-neutrality. Unlike r-z models, electron transport is not enhanced with an ad-hoc mobility coefficient; instead it is given by collisional or ``classical'' terms as well as ``anomalous'' contributions associated with azimuthal electric field fluctuations. Results indicate that anomalous transport dominates classical transport for most of the channel and near field, except in a strong electron flow shear region near the channel exit. The correlation between flow shear, fluctuation behavior, and electron transport will be examined, along with experimental data from the Stanford Hall Thruster. Our findings make a strong link to the turbulent transport suppression mechanism by flow shear seen in fusion devices. The scheme for combining the r-z and z-θ descriptions into an upcoming 3D hybrid model will be presented.

Brain Networks Shaping Religious Belief

PubMed Central

Deshpande, Gopikrishna; Krueger, Frank; Thornburg, Matthew P.; Grafman, Jordan Henry

2014-01-01

Abstract We previously demonstrated with functional magnetic resonance imaging (fMRI) that religious belief depends upon three cognitive dimensions, which can be mapped to specific brain regions. In the present study, we considered these co-activated regions as nodes of three networks each one corresponding to a particular dimension, corresponding to each dimension and examined the causal flow within and between these networks to address two important hypotheses that remained untested in our previous work. First, we hypothesized that regions involved in theory of mind (ToM) are located upstream the causal flow and drive non-ToM regions, in line with theories attributing religion to the evolution of ToM. Second, we hypothesized that differences in directional connectivity are associated with differences in religiosity. To test these hypotheses, we performed a multivariate Granger causality-based directional connectivity analysis of fMRI data to demonstrate the causal flow within religious belief-related networks. Our results supported both hypotheses. Religious subjects preferentially activated a pathway from inferolateral to dorsomedial frontal cortex to monitor the intent and involvement of supernatural agents (SAs; intent-related ToM). Perception of SAs engaged pathways involved in fear regulation and affective ToM. Religious beliefs are founded both on propositional statements for doctrine, but also on episodic memory and imagery. Beliefs based on doctrine engaged a pathway from Broca's to Wernicke's language areas. Beliefs related to everyday life experiences engaged pathways involved in imagery. Beliefs implying less involved SAs and evoking imagery activated a pathway from right lateral temporal to occipital regions. This pathway was more active in non-religious compared to religious subjects, suggesting greater difficulty and procedural demands for imagining and processing the intent of SAs. Insights gained by Granger connectivity analysis inform us about the causal binding of individual regions activated during religious belief processing. PMID:24279687

Brain networks shaping religious belief.

PubMed

Kapogiannis, Dimitrios; Deshpande, Gopikrishna; Krueger, Frank; Thornburg, Matthew P; Grafman, Jordan Henry

2014-02-01

We previously demonstrated with functional magnetic resonance imaging (fMRI) that religious belief depends upon three cognitive dimensions, which can be mapped to specific brain regions. In the present study, we considered these co-activated regions as nodes of three networks each one corresponding to a particular dimension, corresponding to each dimension and examined the causal flow within and between these networks to address two important hypotheses that remained untested in our previous work. First, we hypothesized that regions involved in theory of mind (ToM) are located upstream the causal flow and drive non-ToM regions, in line with theories attributing religion to the evolution of ToM. Second, we hypothesized that differences in directional connectivity are associated with differences in religiosity. To test these hypotheses, we performed a multivariate Granger causality-based directional connectivity analysis of fMRI data to demonstrate the causal flow within religious belief-related networks. Our results supported both hypotheses. Religious subjects preferentially activated a pathway from inferolateral to dorsomedial frontal cortex to monitor the intent and involvement of supernatural agents (SAs; intent-related ToM). Perception of SAs engaged pathways involved in fear regulation and affective ToM. Religious beliefs are founded both on propositional statements for doctrine, but also on episodic memory and imagery. Beliefs based on doctrine engaged a pathway from Broca's to Wernicke's language areas. Beliefs related to everyday life experiences engaged pathways involved in imagery. Beliefs implying less involved SAs and evoking imagery activated a pathway from right lateral temporal to occipital regions. This pathway was more active in non-religious compared to religious subjects, suggesting greater difficulty and procedural demands for imagining and processing the intent of SAs. Insights gained by Granger connectivity analysis inform us about the causal binding of individual regions activated during religious belief processing.

Elliptic flow of electrons from beauty-hadron decays extracted from Pb-Pb collision data at √{s_NN} = 2.76 TeV

NASA Astrophysics Data System (ADS)

Moreira de Godoy, D.; Herrmann, F.; Klasen, M.; Klein-Bösing, C.; Suaide, A. A. P.

2018-05-01

We present a calculation of the elliptic flow of electrons from beauty-hadron decays in semi-central Pb-Pb collisions at centre-of-mass energy per colliding nucleon pair, represented as √{s_NN}, of 2.76 TeV. The result is obtained by the subtraction of the charm-quark contribution in the elliptic flow of electrons from heavy-flavour hadron decays in semi-central Pb-Pb collisions at √{s_NN} = 2.76 TeV recently made publicly available by the ALICE collaboration.

Higher-than-ballistic conduction of viscous electron flows

PubMed Central

Guo, Haoyu; Ilseven, Ekin; Falkovich, Gregory; Levitov, Leonid S.

2017-01-01

Strongly interacting electrons can move in a neatly coordinated way, reminiscent of the movement of viscous fluids. Here, we show that in viscous flows, interactions facilitate transport, allowing conductance to exceed the fundamental Landauer’s ballistic limit Gball. The effect is particularly striking for the flow through a viscous point contact, a constriction exhibiting the quantum mechanical ballistic transport at T=0 but governed by electron hydrodynamics at elevated temperatures. We develop a theory of the ballistic-to-viscous crossover using an approach based on quasi-hydrodynamic variables. Conductance is found to obey an additive relation G=Gball+Gvis, where the viscous contribution Gvis dominates over Gball in the hydrodynamic limit. The superballistic, low-dissipation transport is a generic feature of viscous electronics. PMID:28265079

The role of zonal flows in the saturation of multi-scale gyrokinetic turbulence

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

Staebler, G. M.; Candy, J.; Howard, N. T.

2016-06-15

The 2D spectrum of the saturated electric potential from gyrokinetic turbulence simulations that include both ion and electron scales (multi-scale) in axisymmetric tokamak geometry is analyzed. The paradigm that the turbulence is saturated when the zonal (axisymmetic) ExB flow shearing rate competes with linear growth is shown to not apply to the electron scale turbulence. Instead, it is the mixing rate by the zonal ExB velocity spectrum with the turbulent distribution function that competes with linear growth. A model of this mechanism is shown to be able to capture the suppression of electron-scale turbulence by ion-scale turbulence and the thresholdmore » for the increase in electron scale turbulence when the ion-scale turbulence is reduced. The model computes the strength of the zonal flow velocity and the saturated potential spectrum from the linear growth rate spectrum. The model for the saturated electric potential spectrum is applied to a quasilinear transport model and shown to accurately reproduce the electron and ion energy fluxes of the non-linear gyrokinetic multi-scale simulations. The zonal flow mixing saturation model is also shown to reproduce the non-linear upshift in the critical temperature gradient caused by zonal flows in ion-scale gyrokinetic simulations.« less

The role of zonal flows in the saturation of multi-scale gyrokinetic turbulence

DOE PAGES

Staebler, Gary M.; Candy, John; Howard, Nathan T.; ...

2016-06-29

The 2D spectrum of the saturated electric potential from gyrokinetic turbulence simulations that include both ion and electron scales (multi-scale) in axisymmetric tokamak geometry is analyzed. The paradigm that the turbulence is saturated when the zonal (axisymmetic) ExB flow shearing rate competes with linear growth is shown to not apply to the electron scale turbulence. Instead, it is the mixing rate by the zonal ExB velocity spectrum with the turbulent distribution function that competes with linear growth. A model of this mechanism is shown to be able to capture the suppression of electron-scale turbulence by ion-scale turbulence and the thresholdmore » for the increase in electron scale turbulence when the ion-scale turbulence is reduced. The model computes the strength of the zonal flow velocity and the saturated potential spectrum from the linear growth rate spectrum. The model for the saturated electric potential spectrum is applied to a quasilinear transport model and shown to accurately reproduce the electron and ion energy fluxes of the non-linear gyrokinetic multi-scale simulations. Finally, the zonal flow mixing saturation model is also shown to reproduce the non-linear upshift in the critical temperature gradient caused by zonal flows in ionscale gyrokinetic simulations.« less

Flow directionality, mountain barriers and functional traits determine diatom metacommunity structuring of high mountain streams.

PubMed

Dong, Xiaoyu; Li, Bin; He, Fengzhi; Gu, Yuan; Sun, Meiqin; Zhang, Haomiao; Tan, Lu; Xiao, Wen; Liu, Shuoran; Cai, Qinghua

2016-04-19

Stream metacommunities are structured by a combination of local (environmental filtering) and regional (dispersal) processes. The unique characters of high mountain streams could potentially determine metacommunity structuring, which is currently poorly understood. Aiming at understanding how these characters influenced metacommunity structuring, we explored the relative importance of local environmental conditions and various dispersal processes, including through geographical (overland), topographical (across mountain barriers) and network (along flow direction) pathways in shaping benthic diatom communities. From a trait perspective, diatoms were categorized into high-profile, low-profile and motile guild to examine the roles of functional traits. Our results indicated that both environmental filtering and dispersal processes influenced metacommunity structuring, with dispersal contributing more than environmental processes. Among the three pathways, stream corridors were primary pathway. Deconstructive analysis suggested different responses to environmental and spatial factors for each of three ecological guilds. However, regardless of traits, dispersal among streams was limited by mountain barriers, while dispersal along stream was promoted by rushing flow in high mountain stream. Our results highlighted that directional processes had prevailing effects on metacommunity structuring in high mountain streams. Flow directionality, mountain barriers and ecological guilds contributed to a better understanding of the roles that mountains played in structuring metacommunity.

Observation of the avalanche of runaway electrons in air in a strong electric field.

PubMed

Gurevich, A V; Mesyats, G A; Zybin, K P; Yalandin, M I; Reutova, A G; Shpak, V G; Shunailov, S A

2012-08-24

The generation of an avalanche of runaway electrons is demonstrated for the first time in a laboratory experiment. Two flows of runaway electrons are formed sequentially in an extended air discharge gap at the stage of delay of a pulsed breakdown. The first, picosecond, runaway electron flow is emitted in the cathode region where the field is enhanced. Being accelerated in the gap, this beam generates electrons due to impact ionization. These secondary electrons form a delayed avalanche of runaway electrons if the field is strong enough. The properties of the avalanche correspond to the existing notions about the runaway breakdown in air. The measured current of the avalanche exceeds up to an order the current of the initiating electron beam.

Observation of the Avalanche of Runaway Electrons in Air in a Strong Electric Field

NASA Astrophysics Data System (ADS)

Gurevich, A. V.; Mesyats, G. A.; Zybin, K. P.; Yalandin, M. I.; Reutova, A. G.; Shpak, V. G.; Shunailov, S. A.

2012-08-01

The generation of an avalanche of runaway electrons is demonstrated for the first time in a laboratory experiment. Two flows of runaway electrons are formed sequentially in an extended air discharge gap at the stage of delay of a pulsed breakdown. The first, picosecond, runaway electron flow is emitted in the cathode region where the field is enhanced. Being accelerated in the gap, this beam generates electrons due to impact ionization. These secondary electrons form a delayed avalanche of runaway electrons if the field is strong enough. The properties of the avalanche correspond to the existing notions about the runaway breakdown in air. The measured current of the avalanche exceeds up to an order the current of the initiating electron beam.

Nonmonotonic magnetoresistance of a two-dimensional viscous electron-hole fluid in a confined geometry

NASA Astrophysics Data System (ADS)

Alekseev, P. S.; Dmitriev, A. P.; Gornyi, I. V.; Kachorovskii, V. Yu.; Narozhny, B. N.; Titov, M.

2018-02-01

Ultrapure conductors may exhibit hydrodynamic transport where the collective motion of charge carriers resembles the flow of a viscous fluid. In a confined geometry (e.g., in ultra-high-quality nanostructures), the electronic fluid assumes a Poiseuille-type flow. Applying an external magnetic field tends to diminish viscous effects leading to large negative magnetoresistance. In two-component systems near charge neutrality, the hydrodynamic flow of charge carriers is strongly affected by the mutual friction between the two constituents. At low fields, the magnetoresistance is negative, however, at high fields the interplay between electron-hole scattering, recombination, and viscosity results in a dramatic change of the flow profile: the magnetoresistance changes its sign and eventually becomes linear in very high fields. This nonmonotonic magnetoresistance can be used as a fingerprint to detect viscous flow in two-component conducting systems.

Pump and Flow Control Subassembly of Thermal Control Subsystem for Photovoltaic Power Module

NASA Technical Reports Server (NTRS)

Motil, Brian; Santen, Mark A.

1993-01-01

The pump and flow control subassembly (PFCS) is an orbital replacement unit (ORU) on the Space Station Freedom photovoltaic power module (PVM). The PFCS pumps liquid ammonia at a constant rate of approximately 1170 kg/hr while providing temperature control by flow regulation between the radiator and the bypass loop. Also, housed within the ORU is an accumulator to compensate for fluid volumetric changes as well as the electronics and firmware for monitoring and control of the photovoltaic thermal control system (PVTCS). Major electronic functions include signal conditioning, data interfacing and motor control. This paper will provide a description of each major component within the PFCS along with performance test data. In addition, this paper will discuss the flow control algorithm and describe how the nickel hydrogen batteries and associated power electronics will be thermally controlled through regulation of coolant flow to the radiator.

Viscous electron flow in mesoscopic two-dimensional electron gas

NASA Astrophysics Data System (ADS)

Gusev, G. M.; Levin, A. D.; Levinson, E. V.; Bakarov, A. K.

2018-02-01

We report electrical and magneto transport measurements in mesoscopic size, two-dimensional (2D) electron gas in a GaAs quantum well. Remarkably, we find that the probe configuration and sample geometry strongly affects the temperature evolution of local resistance. We attribute all transport properties to the presence of hydrodynamic effects. Experimental results confirm the theoretically predicted significance of viscous flow in mesoscopic devices.

Paclitaxel suppresses proliferation and induces apoptosis through regulation of ROS and the AKT/MAPK signaling pathway in canine mammary gland tumor cells.

PubMed

Ren, Xiaoli; Zhao, Bingbing; Chang, Hongjian; Xiao, Min; Wu, Yuhong; Liu, Yun

2018-06-01

Paclitaxel is a diterpenoid compound, derived from the pacific yew (Taxus brevifolia) berry, which exhibits antineoplastic effects against various types of cancer. However, the antitumor effects and the molecular mechanisms of paclitaxel on canine CHMm cells remain to be elucidated. The aim of the present study was to investigate the antitumor effects of paclitaxel on CHMm cells and identify relevant signal transduction pathways modulated by paclitaxel using multiple methods including MTT assay, flow cytometry, acridine orange/ethidium bromide staining, transmission electron microscopy, determination of cellular reactive oxygen species (ROS), superoxide dismutase (SOD) and malondiadehyde (MDA) and western blotting, the data indicated that paclitaxel decreased cell viability, induced G2/M‑phase cell cycle arrest, suppressed the expression of cyclin B1 and induced apoptosis in a dose‑dependent manner. In addition, paclitaxel upregulated the expression of Bax and cytochrome c, but reduced expression of apoptosis regulator Bcl‑2, resulting in activation of caspase‑3, chromatin condensation, karyopyknosis, intracellular vacuolization, increased production of ROS and MDA, and decreased activity of SOD. However, these effects were inhibited when CHMm cells were treated with N‑acetyl‑L‑cysteine. Furthermore, treatment with paclitaxel inhibited the level of of phospho (p)‑RAC‑α serine/threonine‑protein kinase (AKT) and p‑ribosomal protein S6 kinase proteins, and promoted phosphorylation of P38 mitogen‑activated protein kinase (MAPK) and p‑90 kDa ribosomal protein S6 kinase 1 proteins in CHMm cells. It was observed that paclitaxel in combination with pharmacological inhibitors of the P38 and phosphatidylinositol‑4,5‑bisphosphate 3‑kinase (PI3K) signaling pathways (SB203580 and LY294002, respectively) exerted synergistic inhibitory effects on the proliferation of the CHMm cells. The results of the present study demonstrated that paclitaxel inhibited tumor cell proliferation by increasing intrinsic apoptosis through inhibition of the PI3K/AKT signaling pathway and activation of MAPK signaling pathway in CHMm cells.

Personalized Guideline-Based Treatment Recommendations Using Natural Language Processing Techniques.

PubMed

Becker, Matthias; Böckmann, Britta

2017-01-01

Clinical guidelines and clinical pathways are accepted and proven instruments for quality assurance and process optimization. Today, electronic representation of clinical guidelines exists as unstructured text, but is not well-integrated with patient-specific information from electronic health records. Consequently, generic content of the clinical guidelines is accessible, but it is not possible to visualize the position of the patient on the clinical pathway, decision support cannot be provided by personalized guidelines for the next treatment step. The Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT) provides common reference terminology as well as the semantic link for combining the pathways and the patient-specific information. This paper proposes a model-based approach to support the development of guideline-compliant pathways combined with patient-specific structured and unstructured information using SNOMED CT. To identify SNOMED CT concepts, a software was developed to extract SNOMED CT codes out of structured and unstructured German data to map these with clinical pathways annotated in accordance with the systematized nomenclature.

Competing charge transfer pathways at the photosystem II-electrode interface

PubMed Central

Zhang, Jenny Z.; Sokol, Katarzyna P.; Paul, Nicholas; Romero, Elisabet; van Grondelle, Rienk; Reisner, Erwin

2016-01-01

The integration of the water-oxidation enzyme, photosystem II (PSII), into electrodes allows the electrons extracted from water-oxidation to be harnessed for enzyme characterization and driving novel endergonic reactions. However, PSII continues to underperform in integrated photoelectrochemical systems despite extensive optimization efforts. Here, we performed protein-film photoelectrochemistry on spinach and Thermosynechococcus elongatus PSII, and identified a competing charge transfer pathway at the enzyme-electrode interface that short-circuits the known water-oxidation pathway: photo-induced O2 reduction occurring at the chlorophyll pigments. This undesirable pathway is promoted by the embedment of PSII in an electron-conducting matrix, a common strategy of enzyme immobilization. Anaerobicity helps to recover the PSII photoresponses, and unmasked the onset potentials relating to the QA/QB charge transfer process. These findings have imparted a fuller understanding of the charge transfer pathways within PSII and at photosystem-electrode interfaces, which will lead to more rational design of pigment-containing photoelectrodes in general. PMID:27723748

Ultrasonic selectivity on depressing photosynthesis of cyanobacteria and green algae probed by chlorophyll-a fluorescence transient.

PubMed

Duan, Zhipeng; Tan, Xiao; Li, Niegui

2017-10-01

Ultrasound can inhibit cyanobacterial growth through rupturing cells, but this pathway frequently has the risk to release intercellular toxin (e.g., microcystin). Depressing photosynthesis without cell disruption may provide a new strategy to control cyanobacterial blooms using ultrasound, especially Microcystis blooms. In this work, Microcystis aeruginosa (toxic cyanobacteria) and Chlorella pyrenoidosa (typical green algae) were chosen as model microalgae to verify this hypothesis. Results showed that ultrasound has the ability to inhibit cyanobacterial photosynthesis significantly and selectively. Specifically, sonication damaged Q A , a tightly bound one-electron acceptor, and blocked electron flow at Q B , a two-electron acceptor, in the photosystem II (PSII) of M. aeruginosa when it was exposed for 60 s (35 kHz, 0.043 W/cm 3 ). Moreover, 44.8% of the reaction centers (RCs) in the PSII of M. aeruginosa were transferred into inactive ones (RC si s), and the cell concentration decreased by 32.5% after sonication for 300 s. By contrast, only 7.9% of RC si occurred in C. pyrenoidosa, and cell concentration and chlorophyll-a content reduced by 18.7% and 9.3%, respectively. Differences in both species (i.e., cell structures) might be responsible for the varying levels to sonication. This research suggests that cyanobacteria, especially Microcystis, could be controlled by ultrasound via damaging their PSIIs.

Analysis of the Exhumation Pathways Experienced in the Cascades Range

NASA Astrophysics Data System (ADS)

Giles, S. M.; Pesek, M.; Perez, N. D.

2017-12-01

The Cascades volcanic arc is the result of subduction of the Juan de Fuca plate beneath North America. The Cascades trend north to south and create a modern orographic precipitation gradient that focuses precipitation along the western flank of the range. However, the deformation style changes from shortening in the north to extension in the south. This experimental design is an ideal location to test how surface and tectonic processes contribute to rock uplift in orogens. In the Oregon Cascades, zircon U-Pb geochronology, and multiple thermochronologic techniques (apatite U-Pb, zircon U-Th/He) will be applied to an intrusive rock exposed along a west-flowing river to investigate the exhumation pathway. These intrusive rocks are capped by late Miocene basalt flows, constraining the timing of surface exposure. The results of this study will define a time-temperature pathway and be compared with existing exhumation constraints from the Washington Cascades to determine whether the exhumation pathways may correspond to the changing structural regimes or consistent climate patterns along strike.

Thalamocortical and corticothalamic pathways differentially contribute to goal-directed behaviors in the rat

PubMed Central

Alcaraz, Fabien; Fresno, Virginie; Marchand, Alain R; Kremer, Eric J; Coutureau, Etienne

2018-01-01

Highly distributed neural circuits are thought to support adaptive decision-making in volatile and complex environments. Notably, the functional interactions between prefrontal and reciprocally connected thalamic nuclei areas may be important when choices are guided by current goal value or action-outcome contingency. We examined the functional involvement of selected thalamocortical and corticothalamic pathways connecting the dorsomedial prefrontal cortex (dmPFC) and the mediodorsal thalamus (MD) in the behaving rat. Using a chemogenetic approach to inhibit projection-defined dmPFC and MD neurons during an instrumental learning task, we show that thalamocortical and corticothalamic pathways differentially support goal attributes. Both pathways participate in adaptation to the current goal value, but only thalamocortical neurons are required to integrate current causal relationships. These data indicate that antiparallel flow of information within thalamocortical circuits may convey qualitatively distinct aspects of adaptive decision-making and highlight the importance of the direction of information flow within neural circuits. PMID:29405119

Preferential pathways in complex fracture systems and their influence on large scale transport

NASA Astrophysics Data System (ADS)

Willmann, M.; Mañé, R.; Tyukhova, A.

2017-12-01

Many subsurface applications in complex fracture systems require large-scale predictions. Precise predictions are difficult because of the existence of preferential pathways at different scales. The intrinsic complexity of fracture systems increases within fractured sedimentary formations, because also the coupling of fractures and matrix has to be taken into account. This interplay of fracture system and the sedimentary matrix is strongly controlled by the actual fracture aperture of an individual fracture. And an effective aperture cannot be easily be determined because of the preferential pathways along the fracture plane. We investigate the influence of these preferential pathways on large scale solute transport and upscale the aperture. By explicitly modeling flow and particle tracking in individual fractures, we develop a new effective transport aperture, which is weighted by the aperture along the preferential paths, a Lagrangian aperture. We show that this new aperture is consistently larger than existing definitions of effective flow and transport apertures. Finally, we apply our results to a fractured sedimentary formation in Northern Switzerland.

Splash flow from a metal plate hit by an electron beam pulse

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

Garcia, M., LLNL

1997-09-01

When a pulsed electron beam hits a metal plate with sufficient energy a volume of the metal becomes hot fluid that subsequently sprays out of the plate. A second pulse of electrons traveling toward the plate would scatter and degrade before impacting the solid plate because of its encounter with the diffuse material of the initial splash. People designing electron beam machines for use as pulsed radiation sources wish to eliminate the interaction between the electrons and the splash because they want sharp radiation pulses emitted from the solid plate. This report presents a compressible fluid model of this splashmore » flow and compares specific cases with experiments and comprehensive calculations performed by B. DeVolder and others at the Los Alamos National Laboratory, see reference (1). My aim was to develop as simple a theory as possible to calculate the speed and density of the splash flow. I have used both simplifying assumptions and mathematical approximations to develop convenient formulas. As I wished to make a clear and interesting presentation of this work to a diverse audience that includes people outside the specialty of fluid dynamics, some of my descriptions may seem wordier than necessary. The plan of the report is as follows. In the section called ``energy deposition`` I describe how an electron beam deposits energy in a solid plate, converting some of the material into a hot fluid. The initial temperature of this fluid is the key parameter in determining the nature of the subsequent flow; an explicit formula is shown. Flow occurs in two regions: along a streamtube within the metal plate and as an expanding plume outside the metal plate. Flow within the plate is described in the section called ``isentropic flow.`` This flow occurs as expansion waves move at the speed of sound through the streamtube. The analysis of this flow provides a formula for the mass flow over time from the plate into the external splash. The section called ``centered expansion`` elaborates on the nature of certain approximations I have made in treating the wave phenomena in both the streamtube and splash flows. The section called ``splash flow`` presents a formula to describe the material density as a function of space and time outside the plate. This formula depends on the time- dependent material density at the plate, which was found during the streamtube analysis. The section called ``examples`` shows the results of specific calculations and a comparison to computational and experimental results described in reference (1). The final section, ``possible future work,`` poses new questions.« less

Soil Susceptibility to Macropore Flow Across a Desert-Oasis Ecotone of the Hexi Corridor, Northwest China

NASA Astrophysics Data System (ADS)

Zhang, Yongyong; Zhao, Wenzhi; He, Jianhua; Fu, Li

2018-02-01

Macropore flow not only provides a fast pathway for water and solute transport and increases the risks of water and nutrient loss but also enhances soil aeration and groundwater recharge. However, macropore flow characteristics in irrigated oasis soils subject to continuous crop cultivation are poorly understood. This study was to investigate the effect of continuous cultivation on soil properties and macropore flow and to quantify the changes in macropore flow characteristics in an old oasis field (>50 years of cultivation, OOF), young oasis field (20 years, YOF), and adjacent uncultivated sandy area (0 year, USL) in Northwest China. Triplicate soil samples were collected from each site to investigate soil properties. Dye tracer experiments with also three replicates were conducted at each site. The degree of macropore flow (i.e., parameters of macropore flow) was highest at the OOF, intermediate at the YOF, and minimal at the USL. The macropore flow fraction (i.e., fraction of total infiltration flows through macropore flow pathways) at the OOF was 3.4 times greater than at the USL. The heterogeneous infiltration pattern at the OOF was dominated by macropore flow, while funnel flow was predominant at the USL. Long-term irrigation with silt-laden river water has increased silt + clay contents of the oasis soils. Irrigation and high-input crop cultivation also increased organic matter. These changes in soil properties contributed to the interaggregate voids formation. The conversion of native desert soils to irrigated croplands increases the degree of macropore flow, which might enhance groundwater recharge in the desert-oasis ecotone.

Electron Transport Controls Glutamine Synthetase Activity in the Facultative Heterotrophic Cyanobacterium Synechocystis sp. PCC 6803.

PubMed Central

Reyes, J. C.; Crespo, J. L.; Garcia-Dominguez, M.; Florencio, F. J.

1995-01-01

Glutamine synthetase (GS) from Synechocystis sp. PCC 6803 was inactivated in vivo by transferring cells from light to darkness or by incubation with the photosynthetic inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea but not with 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone. Addition of glucose prevented both dark and 3-(3,4-dichlorophenyl)-1,1-dimethylurea GS inactivation. In a Synechocystis psbE-psbF mutant (T1297) lacking photosystem II, glucose was required to maintain active GS, even in the light. However, in nitrogen-starved T1297 cells the removal of glucose did not affect GS activity. The fact that dark-inactivated GS was reactivated in vitro by the same treatments that reactivate the ammonium-inactivated GS points out that both nitrogen metabolism and redox state of the cells lead to the same molecular regulatory mechanism in the control of GS activity. Using GS antibodies we detected that dark-inactivated GS displayed a different electrophoretic migration with respect to the active form in nondenaturing polyacrylamide gel electrophoresis but not in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The possible pathway to modulate GS activity by the electron transport flow in Synechocystis cells is discussed. PMID:12228640

Ciprofloxacin induces oxidative stress in duckweed (Lemna minor L.): Implications for energy metabolism and antibiotic-uptake ability.

PubMed

Gomes, Marcelo Pedrosa; Gonçalves, Cíntia Almeida; de Brito, Júlio César Moreira; Souza, Amanda Miranda; da Silva Cruz, Fernanda Vieira; Bicalho, Elisa Monteze; Figueredo, Cleber Cunha; Garcia, Queila Souza

2017-04-15

We investigate the physiological responses and antibiotic-uptake capacity of Lemna minor exposed to ciprofloxacin. Ciprofloxacin (Cipro) induced toxic effects and hormesis in plants by significantly modifying photosynthesis and respiration pathways. A toxic effect was induced by a concentration ≥1.05mg ciprofloxacin l -1 while hormesis occurs at the lowest concentration studied (0.75mg ciprofloxacin l -1 ). By impairing normal electron flow in the respiratory electron transport chain, ciprofloxacin induces hydrogen peroxide (H 2 O 2 ) production. The ability of plants to cope with H 2 O 2 accumulation using antioxidant systems resulted in stimulation/deleterious effects to photosynthesis by Cipro. Cipro-induced oxidative stress was also associated with the ability of L. minor plants to uptake the antibiotic and, therefore, with plant-uptake capacity. Our results indicate that instead of being a photosystem II binding molecule, Cipro induces oxidative stress by targeting the mitochondrial ETC, which would explain the observed effects of the antibiotic on non-target eukaryotic organisms. The selection of plants species with a high capacity to tolerate oxidative stress may constitute a strategy to be used in Cipro-remediation programs. Copyright © 2017 Elsevier B.V. All rights reserved.

Compact Electron Gun Based on Secondary Emission Through Ionic Bombardment

PubMed Central

Diop, Babacar; Bonnet, Jean; Schmid, Thomas; Mohamed, Ajmal

2011-01-01

We present a new compact electron gun based on the secondary emission through ionic bombardment principle. The driving parameters to develop such a gun are to obtain a quite small electron gun for an in-flight instrument performing Electron Beam Fluorescence measurements (EBF) on board of a reentry vehicle in the upper atmosphere. These measurements are useful to characterize the gas flow around the vehicle in terms of gas chemical composition, temperatures and velocity of the flow which usually presents thermo-chemical non-equilibrium. Such an instrument can also be employed to characterize the upper atmosphere if placed on another carrier like a balloon. In ground facilities, it appears as a more practical tool to characterize flows in wind tunnel studies or as an alternative to complex electron guns in industrial processes requiring an electron beam. We describe in this paper the gun which has been developed as well as its different features which have been characterized in the laboratory. PMID:22163896

A residence-time-based transport approach for the groundwater pathway in performance assessment models

NASA Astrophysics Data System (ADS)

Robinson, Bruce A.; Chu, Shaoping

2013-03-01

This paper presents the theoretical development and numerical implementation of a new modeling approach for representing the groundwater pathway in risk assessment or performance assessment model of a contaminant transport system. The model developed in the present study, called the Residence Time Distribution (RTD) Mixing Model (RTDMM), allows for an arbitrary distribution of fluid travel times to be represented, to capture the effects on the breakthrough curve of flow processes such as channelized flow and fast pathways and complex three-dimensional dispersion. Mathematical methods for constructing the model for a given RTD are derived directly from the theory of residence time distributions in flowing systems. A simple mixing model is presented, along with the basic equations required to enable an arbitrary RTD to be reproduced using the model. The practical advantages of the RTDMM include easy incorporation into a multi-realization probabilistic simulation; computational burden no more onerous than a one-dimensional model with the same number of grid cells; and straightforward implementation into available flow and transport modeling codes, enabling one to then utilize advanced transport features of that code. For example, in this study we incorporated diffusion into the stagnant fluid in the rock matrix away from the flowing fractures, using a generalized dual porosity model formulation. A suite of example calculations presented herein showed the utility of the RTDMM for the case of a radioactive decay chain, dual porosity transport and sorption.

Transverse electron-scale instability in relativistic shear flows.

PubMed

Alves, E P; Grismayer, T; Fonseca, R A; Silva, L O

2015-08-01

Electron-scale surface waves are shown to be unstable in the transverse plane of a sheared flow in an initially unmagnetized collisionless plasma, not captured by (magneto)hydrodynamics. It is found that these unstable modes have a higher growth rate than the closely related electron-scale Kelvin-Helmholtz instability in relativistic shears. Multidimensional particle-in-cell simulations verify the analytic results and further reveal the emergence of mushroomlike electron density structures in the nonlinear phase of the instability, similar to those observed in the Rayleigh Taylor instability despite the great disparity in scales and different underlying physics. This transverse electron-scale instability may play an important role in relativistic and supersonic sheared flow scenarios, which are stable at the (magneto)hydrodynamic level. Macroscopic (≫c/ωpe) fields are shown to be generated by this microscopic shear instability, which are relevant for particle acceleration, radiation emission, and to seed magnetohydrodynamic processes at long time scales.

Anaerobic humus and Fe(III) reduction and electron transport pathway by a novel humus-reducing bacterium, Thauera humireducens SgZ-1.

PubMed

Ma, Chen; Yu, Zhen; Lu, Qin; Zhuang, Li; Zhou, Shun-Gui

2015-04-01

In this study, an anaerobic batch experiment was conducted to investigate the humus- and Fe(III)-reducing ability of a novel humus-reducing bacterium, Thauera humireducens SgZ-1. Inhibition tests were also performed to explore the electron transport pathways with various electron acceptors. The results indicate that in anaerobic conditions, strain SgZ-1 possesses the ability to reduce a humus analog, humic acids, soluble Fe(III), and Fe(III) oxides. Acetate, propionate, lactate, and pyruvate were suitable electron donors for humus and Fe(III) reduction by strain SgZ-1, while fermentable sugars (glucose and sucrose) were not. UV-visible spectra obtained from intact cells of strain SgZ-1 showed absorption peaks at 420, 522, and 553 nm, characteristic of c-type cytochromes (cyt c). Dithionite-reduced cyt c was reoxidized by Fe-EDTA and HFO (hydrous ferric oxide), which suggests that cyt c within intact cells of strain SgZ-1 has the ability to donate electrons to extracellular Fe(III) species. Inhibition tests revealed that dehydrogenases, quinones, and cytochromes b/c (cyt b/c) were involved in reduction of AQS (9, 10-anthraquinone-2-sulfonic acid, humus analog) and oxygen. In contrast, only NADH dehydrogenase was linked to electron transport to HFO, while dehydrogenases and cyt b/c were found to participate in the reduction of Fe-EDTA. Thus, various different electron transport pathways are employed by strain SgZ-1 for different electron acceptors. The results from this study help in understanding the electron transport processes and environmental responses of the genus Thauera.

[The electronic health record: computerised provider order entry and the electronic instruction document as new functionalities].

PubMed

Derikx, Joep P M; Erdkamp, Frans L G; Hoofwijk, A G M

2013-01-01

An electronic health record (EHR) should provide 4 key functionalities: (a) documenting patient data; (b) facilitating computerised provider order entry; (c) displaying the results of diagnostic research; and (d) providing support for healthcare providers in the clinical decision-making process.- Computerised provider order entry into the EHR enables the electronic receipt and transfer of orders to ancillary departments, which can take the place of handwritten orders.- By classifying the computer provider order entries according to disorders, digital care pathways can be created. Such care pathways could result in faster and improved diagnostics.- Communicating by means of an electronic instruction document that is linked to a computerised provider order entry facilitates the provision of healthcare in a safer, more efficient and auditable manner.- The implementation of a full-scale EHR has been delayed as a result of economic, technical and legal barriers, as well as some resistance by physicians.

Oxidative bioelectrocatalysis: From natural metabolic pathways to synthetic metabolons and minimal enzyme cascades.

PubMed

Minteer, Shelley D

2016-05-01

Anodic bioelectrodes for biofuel cells are more complex than cathodic bioelectrodes for biofuel cells, because laccase and bilirubin oxidase can individually catalyze four electron reduction of oxygen to water, whereas most anodic enzymes only do a single two electron oxidation of a complex fuel (i.e. glucose oxidase oxidizing glucose to gluconolactone while generating 2 electrons of the total 24 electrons), so enzyme cascades are typically needed for complete oxidation of the fuel. This review article will discuss the lessons learned from natural metabolic pathways about multi-step oxidation and how those lessons have been applied to minimal or artificial enzyme cascades. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson. Copyright © 2015. Published by Elsevier B.V.

The electron drift velocity, ion acoustic speed and irregularity drifts in high-latitude E-region

NASA Astrophysics Data System (ADS)

Uspensky, M. V.; Pellinen, R. J.; Janhunen, P.

2008-10-01

The purpose of this study is to examine the STARE irregularity drift velocity dependence on the EISCAT line-of-sight (los or l-o-s) electron drift velocity magnitude, VE×Blos, and the flow angle ΘN,F (superscript N and/or F refer to the STARE Norway and Finland radar). In the noon-evening sector the flow angle dependence of Doppler velocities, VirrN,F, inside and outside the Farley-Buneman (FB) instability cone (|VE×Blos|>Cs and |VE×Blos||VE×Blos|. Both features (a and b) as well as the weak flow angle velocity dependence indicate that the l-o-s electron drift velocity cannot be the sole factor which controls the motion of the backscatter ~1-m irregularities at large flow angles. Importantly, the backscatter was collected at aspect angle ~1° and flow angle Θ>60°, where linear fluid and kinetic theories invariably predict negative growth rates. At least qualitatively, all the facts can be reasonably explained by nonlinear wave-wave coupling found and described by Kudeki and Farley (1989), Lu et al. (2008) for the equatorial electrojet and studied in numerical simulation by Otani and Oppenheim (1998, 2006).

Phloem transport in gymnosperms: a question of pressure and resistance.

PubMed

Liesche, Johannes; Schulz, Alexander

2018-01-04

Even in the highest trees, carbon is efficiently distributed from leaves to heterotrophic tissues like fruit, flowers and roots. This long-distance transport happens in the highly specialized sieve elements of the phloem. In gymnosperms, sieve element anatomy appears to be less suited for mass flow of phloem sap than that of angiosperms. This review covers available data on gymnosperm phloem to evaluate if it functions differently from that of angiosperms. Although current evidence suggests that, despite a higher pathway resistance, a single source-to-sink turgor pressure gradient can drive mass flow, several questions remain unanswered. These include how endoplasmic reticulum-complexes in sieve elements influence flow, as well as what the effect of symplasmic coupling along the whole phloem pathway could be. Copyright © 2017 Elsevier Ltd. All rights reserved.

Do ray cells provide a pathway for radial water movement in the stems of conifer trees?

Treesearch

David M. Barnard; Barbara Lachenbruch; Katherine A. McCulloh; Peter Kitin; Frederick C. Meinzer

2013-01-01

The pathway of radial water movement in tree stems presents an unknown with respect to whole-tree hydraulics. Radial profiles have shown substantial axial sap flow in deeper layers of sapwood (that may lack direct connection to transpiring leaves), which suggests the existence of a radial pathway for water movement. Rays in tree stems include ray tracheids and/or ray...

A comparative study of single-temperature and two-temperature accretion flows around black holes

NASA Astrophysics Data System (ADS)

Dihingia, Indu Kalpa; Das, Santabrata; Mandal, Samir

2018-02-01

We study the properties of sub-Keplerian accretion disk around a stationary black hole, considering bremsstrahlung, synchrotron and Comptonization of synchrotron photons as radiative cooling mechanisms active in the disk. We obtain the solutions of two-temperature global accretion flow (TTAF) and compare it with the results obtained from single-temperature (STAF) model. We observe that flow properties, in particular, the radial profile of electron and ion temperatures differ noticeably in the adopted models for flows with identical boundary conditions fixed at the outer edge of the disk. Since the electron temperature is one of the key factors to regulate the radiative processes, we argue that physically motivated description of electron temperature needs to be considered in studying the astrophysical phenomena around black holes.

Enhancement of the water flow velocity through carbon nanotubes resulting from the radius dependence of the friction due to electron excitations

NASA Astrophysics Data System (ADS)

Sokoloff, J. B.

2018-03-01

Secchi et al. [Nature (London) 537, 210 (2016), 10.1038/nature19315] observed a large enhancement of the permeability and slip length in carbon nanotubes when the tube radius is of the order of 15 nm, but not in boron nitride nanotubes. It will be pointed out that none of the parameters that appear in the usual molecular dynamics treatments of water flow in carbon nanotubes have a length scale comparable to 15 nm, which could account for the observed flow velocity enhancement. It will be demonstrated here, however, that if the friction force between the water and the tube walls in carbon nanotubes is dominated by friction due to electron excitations in the tube walls, the enhanced flow can be accounted for by a reduction in the contribution to the friction due to electron excitations in the wall, resulting from the dependence of the electron energy band gap on the tube radius.

KML001 Induces Apoptosis and Autophagic Cell Death in Prostate Cancer Cells via Oxidative Stress Pathway

PubMed Central

You, Dalsan; Kim, Yunlim; Jang, Myoung Jin; Lee, Chunwoo; Jeong, In Gab; Cho, Yong Mee; Hwang, Jung Jin; Hong, Jun Hyuk; Ahn, Hanjong; Kim, Choung-Soo

2015-01-01

We investigated the effects of KML001 (NaAsO2, sodium metaarsenite, Kominox), an orally bioavailable arsenic compound, on the growth and death of human prostate cancer cells and its mechanism of action. Growth inhibition was assessed by cytotoxicity assays in the presence or absence of inhibitor of apoptosis, inhibitor of autophagy or antioxidant N-Acetyl-L-cysteine to study mechanism of cell death induced by KML001 in PC3, DU145 and LNCaP prostate cancer cell lines. Electron microscopy, flow cytometry and Western blotting were used to study apoptotic and autophagic mechanisms. The DU145 xenograft model was used to determine the efficacy of KML001 in vivo. KML001 decreased the viability of cells and increased the percentage of annexin V-positive cells dose-dependently in prostate cancer cells, and LNCaP cells were more sensitive to KML001 than PC3 or DU145 cells. Electron microscopy revealed typical apoptotic characters and autophagic vacuoles in cells treated with KML001. Exposure to KML001 in prostate cancer cells induced apoptosis and autophagy in a time- and dose-dependent manner. KML001 induced dose-dependent accumulation of reactive oxygen species, and scavenging the reactive oxygen species with N-Acetyl-L-cysteine reduced LC3 and cleaved poly (ADP-ribose) polymerase. KML001 significantly inhibited tumor growth in the DU145 xenograft model. In addition, significant decrease of proliferation and significant increases of apoptosis and autophagy were observed in KML001-treated tumors than in vehicle-treated tumors. Exposure of human prostate cancer cells to KML001 induced both apoptosis and autophagic cell death via oxidative stress pathway. And KML001 had an antiproliferative effect on DU145 cells in xenograft mice. PMID:26352139

KML001 Induces Apoptosis and Autophagic Cell Death in Prostate Cancer Cells via Oxidative Stress Pathway.

PubMed

You, Dalsan; Kim, Yunlim; Jang, Myoung Jin; Lee, Chunwoo; Jeong, In Gab; Cho, Yong Mee; Hwang, Jung Jin; Hong, Jun Hyuk; Ahn, Hanjong; Kim, Choung-Soo

2015-01-01

We investigated the effects of KML001 (NaAsO2, sodium metaarsenite, Kominox), an orally bioavailable arsenic compound, on the growth and death of human prostate cancer cells and its mechanism of action. Growth inhibition was assessed by cytotoxicity assays in the presence or absence of inhibitor of apoptosis, inhibitor of autophagy or antioxidant N-Acetyl-L-cysteine to study mechanism of cell death induced by KML001 in PC3, DU145 and LNCaP prostate cancer cell lines. Electron microscopy, flow cytometry and Western blotting were used to study apoptotic and autophagic mechanisms. The DU145 xenograft model was used to determine the efficacy of KML001 in vivo. KML001 decreased the viability of cells and increased the percentage of annexin V-positive cells dose-dependently in prostate cancer cells, and LNCaP cells were more sensitive to KML001 than PC3 or DU145 cells. Electron microscopy revealed typical apoptotic characters and autophagic vacuoles in cells treated with KML001. Exposure to KML001 in prostate cancer cells induced apoptosis and autophagy in a time- and dose-dependent manner. KML001 induced dose-dependent accumulation of reactive oxygen species, and scavenging the reactive oxygen species with N-Acetyl-L-cysteine reduced LC3 and cleaved poly (ADP-ribose) polymerase. KML001 significantly inhibited tumor growth in the DU145 xenograft model. In addition, significant decrease of proliferation and significant increases of apoptosis and autophagy were observed in KML001-treated tumors than in vehicle-treated tumors. Exposure of human prostate cancer cells to KML001 induced both apoptosis and autophagic cell death via oxidative stress pathway. And KML001 had an antiproliferative effect on DU145 cells in xenograft mice.

Calcium delivery and storage in plant leaves: exploring the link with water flow.

PubMed

Gilliham, Matthew; Dayod, Maclin; Hocking, Bradleigh J; Xu, Bo; Conn, Simon J; Kaiser, Brent N; Leigh, Roger A; Tyerman, Stephen D

2011-04-01

Calcium (Ca) is a unique macronutrient with diverse but fundamental physiological roles in plant structure and signalling. In the majority of crops the largest proportion of long-distance calcium ion (Ca(2+)) transport through plant tissues has been demonstrated to follow apoplastic pathways, although this paradigm is being increasingly challenged. Similarly, under certain conditions, apoplastic pathways can dominate the proportion of water flow through plants. Therefore, tissue Ca supply is often found to be tightly linked to transpiration. Once Ca is deposited in vacuoles it is rarely redistributed, which results in highly transpiring organs amassing large concentrations of Ca ([Ca]). Meanwhile, the nutritional flow of Ca(2+) must be regulated so it does not interfere with signalling events. However, water flow through plants is itself regulated by Ca(2+), both in the apoplast via effects on cell wall structure and stomatal aperture, and within the symplast via Ca(2+)-mediated gating of aquaporins which regulates flow across membranes. In this review, an integrated model of water and Ca(2+) movement through plants is developed and how this affects [Ca] distribution and water flow within tissues is discussed, with particular emphasis on the role of aquaporins.

[Hemodynamic phenomena in retrobulhar and eyeball vessels].

PubMed

Modrzejewska, Monika

2011-01-01

The purpose of this review was to evaluate factors connected with blood flow and indices regulating vascular diameter and some parameters influencing retrobulbar circulation such as type of vascular resistance, anatomical structure of vascular wall and vessel lumen. Neurogenic and angiogenic factors, rheological blood composition, presence of anatomical and pathological obstructions on blood flow pathway as well as degree of development of collateral circulation pathways--have influence on the volume and blood flow velocity in eyeball. There were discussed bulbar circulation hemodynamics, emphasizing the importance of perfusion pressure. The role of risk factors was underlined for pathological lesions in vessels supplying blood to eyeball and in ophthalmic artery (OA) and its collaterals, in central retinal artery (CRA) as well as posterior ciliary arteries (PCAs), and in venous system carrying away blood from eye. IN CONCLUSION--the results of many studies of retrobulbar blood flow in different types of ophthalmic diseases of the vascular etiopathogenesis indicate that registry of the mean values of blood flow parameters and vascular resistance indices parallel to measurement of blood flow spectrum in OA, CRA, PCAs arteries, might contribute much information to explain or to evaluate nature of pathological changes in retinal and choroidal circulation.

Insights into electron flux through manipulation of fermentation conditions and assessment of protein expression profiles in Clostridium thermocellum.

PubMed

Rydzak, Thomas; Grigoryan, Marina; Cunningham, Zack J; Krokhin, Oleg V; Ezzati, Peyman; Cicek, Nazim; Levin, David B; Wilkins, John A; Sparling, Richard

2014-01-01

While annotation of the genome sequence of Clostridium thermocellum has allowed predictions of pathways catabolizing cellobiose to end products, ambiguities have persisted with respect to the role of various proteins involved in electron transfer reactions. A combination of growth studies modulating carbon and electron flow and multiple reaction monitoring (MRM) mass spectrometry measurements of proteins involved in central metabolism and electron transfer was used to determine the key enzymes involved in channeling electrons toward fermentation end products. Specifically, peptides belonging to subunits of ferredoxin-dependent hydrogenase and NADH:ferredoxin oxidoreductase (NFOR) were low or below MRM detection limits when compared to most central metabolic proteins measured. The significant increase in H2 versus ethanol synthesis in response to either co-metabolism of pyruvate and cellobiose or hypophosphite mediated pyruvate:formate lyase inhibition, in conjunction with low levels of ferredoxin-dependent hydrogenase and NFOR, suggest that highly expressed putative bifurcating hydrogenases play a substantial role in reoxidizing both reduced ferredoxin and NADH simultaneously. However, product balances also suggest that some of the additional reduced ferredoxin generated through increased flux through pyruvate:ferredoxin oxidoreductase must be ultimately converted into NAD(P)H either directly via NADH-dependent reduced ferredoxin:NADP(+) oxidoreductase (NfnAB) or indirectly via NADPH-dependent hydrogenase. While inhibition of hydrogenases with carbon monoxide decreased H2 production 6-fold and redirected flux from pyruvate:ferredoxin oxidoreductase to pyruvate:formate lyase, the decrease in CO2 was only 20 % of that of the decrease in H2, further suggesting that an alternative redox system coupling ferredoxin and NAD(P)H is active in C. thermocellum in lieu of poorly expressed ferredoxin-dependent hydrogenase and NFOR.

Higher-than-ballistic conduction of viscous electron flows.

PubMed

Guo, Haoyu; Ilseven, Ekin; Falkovich, Gregory; Levitov, Leonid S

2017-03-21

Strongly interacting electrons can move in a neatly coordinated way, reminiscent of the movement of viscous fluids. Here, we show that in viscous flows, interactions facilitate transport, allowing conductance to exceed the fundamental Landauer's ballistic limit [Formula: see text] The effect is particularly striking for the flow through a viscous point contact, a constriction exhibiting the quantum mechanical ballistic transport at [Formula: see text] but governed by electron hydrodynamics at elevated temperatures. We develop a theory of the ballistic-to-viscous crossover using an approach based on quasi-hydrodynamic variables. Conductance is found to obey an additive relation [Formula: see text], where the viscous contribution [Formula: see text] dominates over [Formula: see text] in the hydrodynamic limit. The superballistic, low-dissipation transport is a generic feature of viscous electronics.

Coherence, Energy and Charge Transfers in De-Excitation Pathways of Electronic Excited State of Biomolecules in Photosynthesis

NASA Astrophysics Data System (ADS)

Bohr, Henrik G.; Malik, F. Bary

2013-11-01

The observed multiple de-excitation pathways of photo-absorbed electronic excited state in the peridinin-chlorophyll complex, involving both energy and charge transfers among its constituents, are analyzed using the bio-Auger (B-A) theory. It is also shown that the usually used Förster-Dexter theory, which does not allow for charge transfer, is a special case of B-A theory. The latter could, under appropriate circumstances, lead to excimers.

Efficient and Effective Change Principles in Active Videogames

PubMed Central

Fenner, Ashley A.; Howie, Erin K.; Feltz, Deborah L.; Gray, Cindy M.; Lu, Amy Shirong; Mueller, Florian “Floyd”; Simons, Monique; Barnett, Lisa M.

2015-01-01

Abstract Active videogames have the potential to enhance population levels of physical activity but have not been successful in achieving this aim to date. This article considers a range of principles that may be important to the design of effective and efficient active videogames from diverse discipline areas, including behavioral sciences (health behavior change, motor learning, and serious games), business production (marketing and sales), and technology engineering and design (human–computer interaction/ergonomics and flow). Both direct and indirect pathways to impact on population levels of habitual physical activity are proposed, along with the concept of a game use lifecycle. Examples of current active and sedentary electronic games are used to understand how such principles may be applied. Furthermore, limitations of the current usage of theoretical principles are discussed. A suggested list of principles for best practice in active videogame design is proposed along with suggested research ideas to inform practice to enhance physical activity. PMID:26181680

Efficient and Effective Change Principles in Active Videogames.

PubMed

Straker, Leon M; Fenner, Ashley A; Howie, Erin K; Feltz, Deborah L; Gray, Cindy M; Lu, Amy Shirong; Mueller, Florian Floyd; Simons, Monique; Barnett, Lisa M

2015-02-01

Active videogames have the potential to enhance population levels of physical activity but have not been successful in achieving this aim to date. This article considers a range of principles that may be important to the design of effective and efficient active videogames from diverse discipline areas, including behavioral sciences (health behavior change, motor learning, and serious games), business production (marketing and sales), and technology engineering and design (human-computer interaction/ergonomics and flow). Both direct and indirect pathways to impact on population levels of habitual physical activity are proposed, along with the concept of a game use lifecycle. Examples of current active and sedentary electronic games are used to understand how such principles may be applied. Furthermore, limitations of the current usage of theoretical principles are discussed. A suggested list of principles for best practice in active videogame design is proposed along with suggested research ideas to inform practice to enhance physical activity.

Blue and red light-induced germination of resting spores in the red-tide diatom Leptocylindrus danicus.

PubMed

Shikata, Tomoyuki; Iseki, Mineo; Matsunaga, Shigeru; Higashi, Sho-ichi; Kamei, Yasuhiro; Watanabe, Masakatsu

2011-01-01

Photophysiological and pharmacological approaches were used to examine light-induced germination of resting spores in the red-tide diatom Leptocylindrus danicus. The equal-quantum action spectrum for photogermination had peaks at about 440 nm (blue light) and 680 nm (red light), which matched the absorption spectrum of the resting spore chloroplast, as well as photosynthetic action spectra reported for other diatoms. DCMU, an inhibitor of photosynthetic electron flow near photosystem II, completely blocked photogermination. These results suggest that the photosynthetic system is involved in the photoreception process of light-induced germination. Results of pharmacological studies of the downstream signal transduction pathway suggested that Ca(2+) influx is the closest downstream neighbor, followed by steps involving calmodulin, nitric oxide synthase, guanylyl cyclase, protein-tyrosine-phosphatase, protein kinase C and actin polymerization and translation. © 2011 The Authors. Photochemistry and Photobiology © 2011 The American Society of Photobiology.

Multi-layer multi-configuration time-dependent Hartree (ML-MCTDH) approach to the correlated exciton-vibrational dynamics in the FMO complex

NASA Astrophysics Data System (ADS)

Schulze, Jan; Shibl, Mohamed F.; Al-Marri, Mohammed J.; Kühn, Oliver

2016-05-01

The coupled quantum dynamics of excitonic and vibrational degrees of freedom is investigated for high-dimensional models of the Fenna-Matthews-Olson complex. This includes a seven- and an eight-site model with 518 and 592 harmonic vibrational modes, respectively. The coupling between local electronic transitions and vibrations is described within the Huang-Rhys model using parameters that are obtained by discretization of an experimental spectral density. Different pathways of excitation energy flow are analyzed in terms of the reduced one-exciton density matrix, focussing on the role of vibrational and vibronic excitations. Distinct features due to both competing time scales of vibrational and exciton motion and vibronically assisted transfer are observed. The question of the effect of initial state preparation is addressed by comparing the case of an instantaneous Franck-Condon excitation at a single site with that of a laser field excitation.

A quest for macroinvertebrate indicators of flow conditions in small, suburban stream

EPA Science Inventory

Alteration of hydrologic variability is considered a key pathway by which urbanization affects stream assemblages; however, understanding the mechanisms of alteration remains a challenge. One approach is to identify biological metrics that show distinct responses to flows, which ...

X-ray Microtomography of Intermittency in Multiphase Flow at Steady State Using a Differential Imaging Method

NASA Astrophysics Data System (ADS)

Gao, Ying; Lin, Qingyang; Bijeljic, Branko; Blunt, Martin J.

2017-12-01

We imaged the steady state flow of brine and decane in Bentheimer sandstone. We devised an experimental method based on differential imaging to examine how flow rate impacts impact the pore-scale distribution of fluids during coinjection. This allows us to elucidate flow regimes (connected, or breakup of the nonwetting phase pathways) for a range of fractional flows at two capillary numbers, Ca, namely 3.0 × 10-7 and 7.5 × 10-6. At the lower Ca, for a fixed fractional flow, the two phases appear to flow in connected unchanging subnetworks of the pore space, consistent with conventional theory. At the higher Ca, we observed that a significant fraction of the pore space contained sometimes oil and sometimes brine during the 1 h scan: this intermittent occupancy, which was interpreted as regions of the pore space that contained both fluid phases for some time, is necessary to explain the flow and dynamic connectivity of the oil phase; pathways of always oil-filled portions of the void space did not span the core. This phase was segmented from the differential image between the 30 wt % KI brine image and the scans taken at each fractional flow. Using the grey scale histogram distribution of the raw images, the oil proportion in the intermittent phase was calculated. The pressure drops at each fractional flow at low and high flow rates were measured by high-precision differential pressure sensors. The relative permeabilities and fractional flow obtained by our experiment at the mm-scale compare well with data from the literature on cm-scale samples.

Sonic hedgehog pathway activation increases mitochondrial abundance and activity in hippocampal neurons

PubMed Central

Yao, Pamela J.; Manor, Uri; Petralia, Ronald S.; Brose, Rebecca D.; Wu, Ryan T. Y.; Ott, Carolyn; Wang, Ya-Xian; Charnoff, Ari; Lippincott-Schwartz, Jennifer; Mattson, Mark P.

2017-01-01

Mitochondria are essential organelles whose biogenesis, structure, and function are regulated by many signaling pathways. We present evidence that, in hippocampal neurons, activation of the Sonic hedgehog (Shh) signaling pathway affects multiple aspects of mitochondria. Mitochondrial mass was increased significantly in neurons treated with Shh. Using biochemical and fluorescence imaging analyses, we show that Shh signaling activity reduces mitochondrial fission and promotes mitochondrial elongation, at least in part, via suppression of the mitochondrial fission protein dynamin-like GTPase Drp1. Mitochondria from Shh-treated neurons were more electron-dense, as revealed by electron microscopy, and had higher membrane potential and respiratory activity. We further show that Shh protects neurons against a variety of stresses, including the mitochondrial poison rotenone, amyloid β-peptide, hydrogen peroxide, and high levels of glutamate. Collectively our data suggest a link between Shh pathway activity and the physiological properties of mitochondria in hippocampal neurons. PMID:27932496

Comparison of different two-pathway models for describing the combined effect of DO and nitrite on the nitrous oxide production by ammonia-oxidizing bacteria.

PubMed

Lang, Longqi; Pocquet, Mathieu; Ni, Bing-Jie; Yuan, Zhiguo; Spérandio, Mathieu

2017-02-01

The aim of this work is to compare the capability of two recently proposed two-pathway models for predicting nitrous oxide (N 2 O) production by ammonia-oxidizing bacteria (AOB) for varying ranges of dissolved oxygen (DO) and nitrite. The first model includes the electron carriers whereas the second model is based on direct coupling of electron donors and acceptors. Simulations are confronted to extensive sets of experiments (43 batches) from different studies with three different microbial systems. Despite their different mathematical structures, both models could well and similarly describe the combined effect of DO and nitrite on N 2 O production rate and emission factor. The model-predicted contributions for nitrifier denitrification pathway and hydroxylamine pathway also matched well with the available isotopic measurements. Based on sensitivity analysis, calibration procedures are described and discussed for facilitating the future use of those models.

Direct cooled power electronics substrate

DOEpatents

Wiles, Randy H [Powell, TN; Wereszczak, Andrew A [Oak Ridge, TN; Ayers, Curtis W [Kingston, TN; Lowe, Kirk T [Knoxville, TN

2010-09-14

The disclosure describes directly cooling a three-dimensional, direct metallization (DM) layer in a power electronics device. To enable sufficient cooling, coolant flow channels are formed within the ceramic substrate. The direct metallization layer (typically copper) may be bonded to the ceramic substrate, and semiconductor chips (such as IGBT and diodes) may be soldered or sintered onto the direct metallization layer to form a power electronics module. Multiple modules may be attached to cooling headers that provide in-flow and out-flow of coolant through the channels in the ceramic substrate. The modules and cooling header assembly are preferably sized to fit inside the core of a toroidal shaped capacitor.

Initiation with an electron beam of chemical reactions of interest for visible wavelength lasers

NASA Technical Reports Server (NTRS)

Whittier, J. S.; Cool, T. A.

1976-01-01

A description is given of the first results obtained with a new shock tube-electron beam facility designed to provide a versatile means for the systematic search for laser operation among several candidate metal atom-oxidizer systems. According to the current experimental approach, metal atoms are obtained in the vapor phase by the dissociation of metal compounds. A shock tube is employed to provide a short duration flow through an array of 29 supersonic flow-mixing nozzles. A high energy electron accelerator is used for the rapid initiation of chemical reaction in a mixed flow of encapsulated metal and oxidizer.

A metal-free organic-inorganic aqueous flow battery.

PubMed

Huskinson, Brian; Marshak, Michael P; Suh, Changwon; Er, Süleyman; Gerhardt, Michael R; Galvin, Cooper J; Chen, Xudong; Aspuru-Guzik, Alán; Gordon, Roy G; Aziz, Michael J

2014-01-09

As the fraction of electricity generation from intermittent renewable sources--such as solar or wind--grows, the ability to store large amounts of electrical energy is of increasing importance. Solid-electrode batteries maintain discharge at peak power for far too short a time to fully regulate wind or solar power output. In contrast, flow batteries can independently scale the power (electrode area) and energy (arbitrarily large storage volume) components of the system by maintaining all of the electro-active species in fluid form. Wide-scale utilization of flow batteries is, however, limited by the abundance and cost of these materials, particularly those using redox-active metals and precious-metal electrocatalysts. Here we describe a class of energy storage materials that exploits the favourable chemical and electrochemical properties of a family of molecules known as quinones. The example we demonstrate is a metal-free flow battery based on the redox chemistry of 9,10-anthraquinone-2,7-disulphonic acid (AQDS). AQDS undergoes extremely rapid and reversible two-electron two-proton reduction on a glassy carbon electrode in sulphuric acid. An aqueous flow battery with inexpensive carbon electrodes, combining the quinone/hydroquinone couple with the Br2/Br(-) redox couple, yields a peak galvanic power density exceeding 0.6 W cm(-2) at 1.3 A cm(-2). Cycling of this quinone-bromide flow battery showed >99 per cent storage capacity retention per cycle. The organic anthraquinone species can be synthesized from inexpensive commodity chemicals. This organic approach permits tuning of important properties such as the reduction potential and solubility by adding functional groups: for example, we demonstrate that the addition of two hydroxy groups to AQDS increases the open circuit potential of the cell by 11% and we describe a pathway for further increases in cell voltage. The use of π-aromatic redox-active organic molecules instead of redox-active metals represents a new and promising direction for realizing massive electrical energy storage at greatly reduced cost.

The vertical hydraulic conductivity of an aquitard at two spatial scales

USGS Publications Warehouse

Hart, D.J.; Bradbury, K.R.; Feinstein, D.T.

2006-01-01

Aquitards protect underlying aquifers from contaminants and limit recharge to those aquifers. Understanding the mechanisms and quantity of ground water flow across aquitards to underlying aquifers is essential for ground water planning and assessment. We present results of laboratory testing for shale hydraulic conductivities, a methodology for determining the vertical hydraulic conductivity (Kv) of aquitards at regional scales and demonstrate the importance of discrete flow pathways across aquitards. A regional shale aquitard in southeastern Wisconsin, the Maquoketa Formation, was studied to define the role that an aquitard plays in a regional ground water flow system. Calibration of a regional ground water flow model for southeastern Wisconsin using both predevelopment steady-state and transient targets suggested that the regional Kv of the Maquoketa Formation is 1.8 ?? 10 -11 m/s. The core-scale measurements of the Kv of the Maquoketa Formation range from 1.8 ?? 10-14 to 4.1 ?? 10-12 m/s. Flow through some additional pathways in the shale, potential fractures or open boreholes, can explain the apparent increase of the regional-scale Kv. Based on well logs, erosional windows or high-conductivity zones seem unlikely pathways. Fractures cutting through the entire thickness of the shale spaced 5 km apart with an aperture of 50 microns could provide enough flow across the aquitard to match that provided by an equivalent bulk Kv of 1.8 ?? 10-11 m/s. In a similar fashion, only 50 wells of 0.1 m radius open to aquifers above and below the shale and evenly spaced 10 km apart across southeastern Wisconsin can match the model Kv. Copyright ?? 2005 National Ground Water Association.

Self-generated zonal flows in the plasma turbulence driven by trapped-ion and trapped-electron instabilities

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

Drouot, T.; Gravier, E.; Reveille, T.

This paper presents a study of zonal flows generated by trapped-electron mode and trapped-ion mode micro turbulence as a function of two plasma parameters—banana width and electron temperature. For this purpose, a gyrokinetic code considering only trapped particles is used. First, an analytical equation giving the predicted level of zonal flows is derived from the quasi-neutrality equation of our model, as a function of the density fluctuation levels and the banana widths. Then, the influence of the banana width on the number of zonal flows occurring in the system is studied using the gyrokinetic code. Finally, the impact of themore » temperature ratio T{sub e}/T{sub i} on the reduction of zonal flows is shown and a close link is highlighted between reduction and different gyro-and-bounce-average ion and electron density fluctuation levels. This reduction is found to be due to the amplitudes of gyro-and-bounce-average density perturbations n{sub e} and n{sub i} gradually becoming closer, which is in agreement with the analytical results given by the quasi-neutrality equation.« less

Electron Energization and Mixing Observed by MMS in the Vicinity of an Electron Diffusion Region During Magnetopause Reconnection

NASA Technical Reports Server (NTRS)

Chen, Li-Jen; Hesse, Michael; Wang, Shan; Gershman, Daniel; Ergun, Robert; Pollock, Craig; Torbert, Roy; Bessho, Naoki; Daughton, William; Dorelli, John;

Electron energization and mixing observed by MMS in the vicinity of an electron diffusion region during magnetopause reconnection

NASA Astrophysics Data System (ADS)

Chen, Li-Jen; Hesse, Michael; Wang, Shan; Gershman, Daniel; Ergun, Robert; Pollock, Craig; Torbert, Roy; Bessho, Naoki; Daughton, William; Dorelli, John; Giles, Barbara; Strangeway, Robert; Russell, Christopher; Khotyaintsev, Yuri; Burch, Jim; Moore, Thomas; Lavraud, Benoit; Phan, Tai; Avanov, Levon

2016-06-01

Measurements from the Magnetospheric Multiscale (MMS) mission are reported to show distinct features of electron energization and mixing in the diffusion region of the terrestrial magnetopause reconnection. At the ion jet and magnetic field reversals, distribution functions exhibiting signatures of accelerated meandering electrons are observed at an electron out-of-plane flow peak. The meandering signatures manifested as triangular and crescent structures are established features of the electron diffusion region (EDR). Effects of meandering electrons on the electric field normal to the reconnection layer are detected. Parallel acceleration and mixing of the inflowing electrons with exhaust electrons shape the exhaust flow pattern. In the EDR vicinity, the measured distribution functions indicate that locally, the electron energization and mixing physics is captured by two-dimensional reconnection, yet to account for the simultaneous four-point measurements, translational invariant in the third dimension must be violated on the ion-skin-depth scale.

Alternative ground states enable pathway switching in biological electron transfer

DOE PAGES

Abriata, Luciano A.; Alvarez-Paggi, Damian; Ledesma, Gabirela N.; ...

2012-10-10

Electron transfer is the simplest chemical reaction and constitutes the basis of a large variety of biological processes, such as photosynthesis and cellular respiration. Nature has evolved specific proteins and cofactors for these functions. The mechanisms optimizing biological electron transfer have been matter of intense debate, such as the role of the protein milieu between donor and acceptor sites. Here we propose a mechanism regulating long-range electron transfer in proteins. Specifically, we report a spectroscopic, electrochemical, and theoretical study on WT and single-mutant CuA redox centers from Thermus thermophilus, which shows that thermal fluctuations may populate two alternative ground-state electronicmore » wave functions optimized for electron entry and exit, respectively, through two different and nearly perpendicular pathways. In conclusion, these findings suggest a unique role for alternative or “invisible” electronic ground states in directional electron transfer. Moreover, it is shown that this energy gap and, therefore, the equilibrium between ground states can be fine-tuned by minor perturbations, suggesting alternative ways through which protein–protein interactions and membrane potential may optimize and regulate electron–proton energy transduction.« less

Sulforaphane Protects against High Cholesterol-Induced Mitochondrial Bioenergetics Impairments, Inflammation, and Oxidative Stress and Preserves Pancreatic β-Cells Function.

PubMed

Carrasco-Pozo, Catalina; Tan, Kah Ni; Gotteland, Martin; Borges, Karin

2017-01-01

Cholesterol plays an important role in inducing pancreatic β -cell dysfunction, leading to an impaired insulin secretory response to glucose. This study aimed to determine the protective effects of sulforaphane, a natural isothiocyanate Nrf2-inducer, against cholesterol-induced pancreatic β -cells dysfunction, through molecular and cellular mechanisms involving mitochondrial bioenergetics. Sulforaphane prevented cholesterol-induced alterations in the coupling efficiency of mitochondrial respiration, improving ATP turnover and spare capacity, and averted the impairment of the electron flow at complexes I, II, and IV. Sulforaphane also attenuated the cholesterol-induced activation of the NF κ B pathway, normalizing the expression of pro- and anti-inflammatory cytokines. In addition, it also inhibited the decrease in sirtuin 1 expression and greatly increased Pgc-1α expression in Min6 cells. Sulforaphane increased the expression of antioxidant enzymes downstream of the Nrf2 pathway and prevented lipid peroxidation induced by cholesterol. The antioxidant and anti-inflammatory properties of sulforaphane and its ability to protect and improve mitochondrial bioenergetic function contribute to its protective action against cholesterol-induced pancreatic β -cell dysfunction. Our data provide a scientifically tested foundation upon which sulforaphane can be developed as nutraceutical to preserve β -cell function and eventually control hyperglycemia.

Sulforaphane Protects against High Cholesterol-Induced Mitochondrial Bioenergetics Impairments, Inflammation, and Oxidative Stress and Preserves Pancreatic β-Cells Function

PubMed Central

Tan, Kah Ni; Gotteland, Martin

2017-01-01

Cholesterol plays an important role in inducing pancreatic β-cell dysfunction, leading to an impaired insulin secretory response to glucose. This study aimed to determine the protective effects of sulforaphane, a natural isothiocyanate Nrf2-inducer, against cholesterol-induced pancreatic β-cells dysfunction, through molecular and cellular mechanisms involving mitochondrial bioenergetics. Sulforaphane prevented cholesterol-induced alterations in the coupling efficiency of mitochondrial respiration, improving ATP turnover and spare capacity, and averted the impairment of the electron flow at complexes I, II, and IV. Sulforaphane also attenuated the cholesterol-induced activation of the NFκB pathway, normalizing the expression of pro- and anti-inflammatory cytokines. In addition, it also inhibited the decrease in sirtuin 1 expression and greatly increased Pgc-1α expression in Min6 cells. Sulforaphane increased the expression of antioxidant enzymes downstream of the Nrf2 pathway and prevented lipid peroxidation induced by cholesterol. The antioxidant and anti-inflammatory properties of sulforaphane and its ability to protect and improve mitochondrial bioenergetic function contribute to its protective action against cholesterol-induced pancreatic β-cell dysfunction. Our data provide a scientifically tested foundation upon which sulforaphane can be developed as nutraceutical to preserve β-cell function and eventually control hyperglycemia. PMID:28386307

EGCG protects against homocysteine-induced human umbilical vein endothelial cells apoptosis by modulating mitochondrial-dependent apoptotic signaling and PI3K/Akt/eNOS signaling pathways.

PubMed

Liu, Shumin; Sun, Zhengwu; Chu, Peng; Li, Hailong; Ahsan, Anil; Zhou, Ziru; Zhang, Zonghui; Sun, Bin; Wu, Jingjun; Xi, Yalin; Han, Guozhu; Lin, Yuan; Peng, Jinyong; Tang, Zeyao

2017-05-01

Homocysteine (Hcy) induced vascular endothelial injury leads to the progression of endothelial dysfunction in atherosclerosis. Epigallocatechin gallate (EGCG), a natural dietary antioxidant, has been applied to protect against atherosclerosis. However, the underlying protective mechanism of EGCG has not been clarified. The present study investigated the mechanism of EGCG protected against Hcy-induced human umbilical vein endothelial cells (HUVECs) apoptosis. Methyl thiazolyl tetrazolium assay (MTT), transmission electron microscope, fluorescent staining, flow cytometry, western blot were used in this study. The study has demonstrated that EGCG suppressed Hcy-induced endothelial cell morphological changes and reactive oxygen species (ROS) generation. Moreover, EGCG dose-dependently prevented Hcy-induced HUVECs cytotoxicity and apoptotic biochemical changes such as reducing mitochondrial membrane potential (MMP), decreasing Bcl-2/Bax protein ratio and activating caspase-9 and 3. In addition, EGCG enhanced the protein ratio of p-Akt/Akt, endothelial nitric oxide synthase (eNOS) activation and nitric oxide (NO) formation in injured cells. In conclusion, the present study shows that EGCG prevents Hcy-induced HUVECs apoptosis via modulating mitochondrial apoptotic and PI3K/Akt/eNOS signaling pathways. Furthermore, the results indicate that EGCG is likely to represent a potential therapeutic strategy for atherosclerosis associated with Hyperhomocysteinemia (HHcy).

Hepatoma tissue culture (HTC) cells as a model for investigating the effects of low concentrations of herbicide on cell structure and function.

PubMed

Malatesta, M; Perdoni, F; Santin, G; Battistelli, S; Muller, S; Biggiogera, M

2008-12-01

Previous studies on mice fed genetically modified (GM) soybean demonstrated modifications of the mitochondrial functions and of the transcription/splicing pathways in hepatocytes. The cause(s) of these alterations could not be conclusively established but, since the GM soybean used is tolerant to glyphosate and was treated with the glyphosate-containing herbicide Roundup , the possibility exists that the effects observed may be due to herbicide residues. In order to verify this hypothesis, we treated HTC cells with 1-10mM Roundup and analysed cellular features by flow cytometry, fluorescence and electron microscopy. Under these experimental conditions, the death rate and the general morphology of HTC cells were not affected, as well as most of the cytoplasmic organelles. However, in HTC-treated cells, lysosome density increased and mitochondrial membranes modified indicating a decline in the respiratory activity. Moreover, nuclei underwent morpho-functional modifications suggestive of a decreased transcriptional/splicing activity. Although we cannot exclude that other factors than the presence of the herbicide residues could be responsible for the cellular modifications described in GM-fed mice, the concordance of the effects induced by low concentrations of Roundup on HTC cells suggests that the presence of Roundup residues could be one of the factors interfering with multiple metabolic pathways.

The Soil Foam Drainage Equation - an alternative model for unsaturated flow in porous media

NASA Astrophysics Data System (ADS)

Assouline, Shmuel; Lehmann, Peter; Hoogland, Frouke; Or, Dani

2017-04-01

The analogy between the geometry and dynamics of wet foam drainage and gravity drainage of unsaturated porous media expands modeling capabilities for capillary flows and supplements the standard Richards equation representation. The governing equation for draining foam (or a soil variant termed the soil foam drainage equation - SFDE) obviates the need for macroscopic unsaturated hydraulic conductivity function by an explicit account of diminishing flow pathway sizes as the medium gradually drains. Potential advantages of the proposed drainage foam formalism include direct description of transient flow without requiring constitutive functions; evolution of capillary cross sections that provides consistent description of self-regulating internal fluxes (e.g., towards field capacity); and a more intuitive geometrical picture of capillary flow across textural boundaries. We will present new and simple analytical expressions for drainage rates and volumes from unsaturated porous media subjected to different boundary conditions that are in good agreement with the numerical solution of the SFDE and experimental results. The foam drainage methodology expands the range of tools available for describing and quantifying unsaturated flows and provides geometrically tractable links between evolution of liquid configuration and flow dynamics in unsaturated porous media. The resulting geometrical representation of capillary drainage could improve understanding of colloid and pathogen transport. The explicit geometrical interpretation of flow pathways underlying the hydraulic functions used by the Richards equation offers new insights that benefit both approaches.

Three dimensional instabilities of an electron scale current sheet in collisionless magnetic reconnection

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

Jain, Neeraj; Büchner, Jörg; Max Planck Institute for Solar System Research, Justus-Von-Liebig-Weg-3, Göttingen

In collisionless magnetic reconnection, electron current sheets (ECS) with thickness of the order of an electron inertial length form embedded inside ion current sheets with thickness of the order of an ion inertial length. These ECS's are susceptible to a variety of instabilities which have the potential to affect the reconnection rate and/or the structure of reconnection. We carry out a three dimensional linear eigen mode stability analysis of electron shear flow driven instabilities of an electron scale current sheet using an electron-magnetohydrodynamic plasma model. The linear growth rate of the fastest unstable mode was found to drop with themore » thickness of the ECS. We show how the nature of the instability depends on the thickness of the ECS. As long as the half-thickness of the ECS is close to the electron inertial length, the fastest instability is that of a translational symmetric two-dimensional (no variations along flow direction) tearing mode. For an ECS half thickness sufficiently larger or smaller than the electron inertial length, the fastest mode is not a tearing mode any more and may have finite variations along the flow direction. Therefore, the generation of plasmoids in a nonlinear evolution of ECS is likely only when the half-thickness is close to an electron inertial length.« less

Azimuthal ExB drift of electrons induced by the radial electric field flowing through a longitudinal magnetic channel with non-magnetized ions

NASA Astrophysics Data System (ADS)

Akatsuka, Hiroshi; Takeda, Jun; Nezu, Atsushi

2016-09-01

To examine of the effect of the radial electric field on the azimuthal electron motion under E × B field for plasmas with magnetized electrons and non-magnetized ions, an experimental study is conducted by a stationary plasma flow. The argon plasma flow is generated by a DC arc generator under atmospheric pressure, followed by a cw expansion into a rarefied gas-wind tunnel with a uniform magnetic field 0 . 16 T. Inside one of the magnets, we set a ring electrode to apply the radial electric field. We applied an up-down probe for the analysis of the electron motion, where one of the tips is also used as a Langmuir probe to measure electron temperature, density and the space potential. We found that the order of the radial electric field is about several hundred V/m, which should be caused by the difference in the magnetization between electrons and ions. Electron saturation current indicates the existence of the E × B rotation of electrons, whose order is about 2000 - 4000 m/s. The order of the observed electron drift velocity is consistent with the theoretical value calculated from the applied magnetic field and the measured electric field deduced from the space potential.

Managing care pathways combining SNOMED CT, archetypes and an electronic guideline system.

PubMed

Bernstein, Knut; Andersen, Ulrich

2008-01-01

Today electronic clinical guideline systems exist, but they are not well integrated with electronic health records. This paper thus proposes that the patient's "position" in the pathway during the patient journey should be made visible to all involved healthcare parties and the patient. This requires that the generic knowledge, which is represented in the guidelines, is combined with the patient specific information - and then made accessible for all relevant parties. In addition to the decision support provided by the guideline system documentation support can be provided by templates based on archetypes. This paper provides a proposal for how the guideline system and the EHR can be integrated by the use of archetypes and SNOMED CT. SNOMED CT provides the common reference terminology and the semantic links between the systems. The proposal also includes the use of a National Patient Index for storing data about the patient's position in the pathway and for sharing this information by all involved parties.

Pathways of energy transfer in LHCII revealed by room-temperature 2D electronic spectroscopy.

PubMed

Wells, Kym L; Lambrev, Petar H; Zhang, Zhengyang; Garab, Gyözö; Tan, Howe-Siang

2014-06-21

We present here the first room-temperature 2D electronic spectroscopy study of energy transfer in the plant light-harvesting complex II, LHCII. Two-dimensional electronic spectroscopy has been used to study energy transfer dynamics in LHCII trimers from the chlorophyll b Qy band to the chlorophyll a Qy band. Observing cross-peak regions corresponding to couplings between different excitonic states reveals partially resolved fine structure at the exciton level that cannot be isolated by pump-probe or linear spectroscopy measurements alone. Global analysis of the data has been performed to identify the pathways and time constants of energy transfer. The measured waiting time (Tw) dependent 2D spectra are found to be composed of 2D decay-associated spectra with three timescales (0.3 ps, 2.3 ps and >20 ps). Direct and multistep cascading pathways from the high-energy chlorophyll b states to the lowest-energy chlorophyll a states have been resolved occurring on time scales of hundreds of femtoseconds to picoseconds.

Kynurenine pathway metabolites and enzymes involved in redox reactions.

PubMed

González Esquivel, D; Ramírez-Ortega, D; Pineda, B; Castro, N; Ríos, C; Pérez de la Cruz, V

2017-01-01

Oxido-reduction reactions are a fundamental part of the life due to support many vital biological processes as cellular respiration and glucose oxidation. In the redox reactions, one substance transfers one or more electrons to another substance. An important electron carrier is the coenzyme NAD + , which is involved in many metabolic pathways. De novo biosynthesis of NAD + is through the kynurenine pathway, the major route of tryptophan catabolism, which is sensitive to redox environment and produces metabolites with redox capacity, able to alter biological functions that are controlled by redox-responsive signaling pathways. Kynurenine pathway metabolites have been implicated in the physiology process and in the physiopathology of many diseases; processes that also share others factors as dysregulation of calcium homeostasis, mitochondrial dysfunction, oxidative stress, inflammation and cell death, which impact the redox environment. This review examines in detail the available evidence in which kynurenine pathway metabolites participate in redox reactions and their effect on cellular redox homeostasis, since the knowledge of the main factors and mechanisms that lead to cell death in many neurodegenative disorders and other pathologies, such as mitochondrial dysfunction, oxidative stress and kynurenines imbalance, will allow to develop therapies using them as targets. This article is part of the Special Issue entitled 'The Kynurenine Pathway in Health and Disease'. Copyright © 2016 Elsevier Ltd. All rights reserved.

Symmetry breaking and polarization of the C. elegans zygote by the polarity protein PAR-2.

PubMed

Zonies, Seth; Motegi, Fumio; Hao, Yingsong; Seydoux, Geraldine

2010-05-01

Polarization of the C. elegans zygote is initiated by ECT-2-dependent cortical flows, which mobilize the anterior PAR proteins (PAR-3, PAR-6 and PKC-3) away from the future posterior end of the embryo marked by the sperm centrosome. Here, we demonstrate the existence of a second, parallel and redundant pathway that can polarize the zygote in the absence of ECT-2-dependent cortical flows. This second pathway depends on the polarity protein PAR-2. We show that PAR-2 localizes to the cortex nearest the sperm centrosome even in the absence of cortical flows. Once on the cortex, PAR-2 antagonizes PAR-3-dependent recruitment of myosin, creating myosin flows that transport the anterior PAR complex away from PAR-2 in a positive-feedback loop. We propose that polarity in the C. elegans zygote is initiated by redundant ECT-2- and PAR-2-dependent mechanisms that lower PAR-3 levels locally, triggering a positive-feedback loop that polarizes the entire cortex.

Process mining routinely collected electronic health records to define real-life clinical pathways during chemotherapy.

PubMed

Baker, Karl; Dunwoodie, Elaine; Jones, Richard G; Newsham, Alex; Johnson, Owen; Price, Christopher P; Wolstenholme, Jane; Leal, Jose; McGinley, Patrick; Twelves, Chris; Hall, Geoff

2017-07-01

There is growing interest in the use of routinely collected electronic health records to enhance service delivery and facilitate clinical research. It should be possible to detect and measure patterns of care and use the data to monitor improvements but there are methodological and data quality challenges. Driven by the desire to model the impact of a patient self-test blood count monitoring service in patients on chemotherapy, we aimed to (i) establish reproducible methods of process-mining electronic health records, (ii) use the outputs derived to define and quantify patient pathways during chemotherapy, and (iii) to gather robust data which is structured to be able to inform a cost-effectiveness decision model of home monitoring of neutropenic status during chemotherapy. Electronic Health Records at a UK oncology centre were included if they had (i) a diagnosis of metastatic breast cancer and received adjuvant epirubicin and cyclosphosphamide chemotherapy or (ii) colorectal cancer and received palliative oxaliplatin and infusional 5-fluorouracil chemotherapy, and (iii) were first diagnosed with cancer between January 2004 and February 2013. Software and a Markov model were developed, producing a schematic of patient pathways during chemotherapy. Significant variance from the assumed care pathway was evident from the data. Of the 535 patients with breast cancer and 420 with colorectal cancer there were 474 and 329 pathway variants respectively. Only 27 (5%) and 26 (6%) completed the planned six cycles of chemotherapy without having unplanned hospital contact. Over the six cycles, 169 (31.6%) patients with breast cancer and 190 (45.2%) patients with colorectal cancer were admitted to hospital. The pathways of patients on chemotherapy are complex. An iterative approach to addressing semantic and data quality issues enabled the effective use of routinely collected patient records to produce accurate models of the real-life experiences of chemotherapy patients and generate clinically useful information. Very few patients experience the idealised patient pathway that is used to plan their care. A better understanding of real-life clinical pathways through process mining can contribute to care and data quality assurance, identifying unmet needs, facilitating quantification of innovation impact, communicating with stakeholders, and ultimately improving patient care and outcomes. Copyright © 2017 Elsevier B.V. All rights reserved.

Extension of the Mott-Gurney Law for a Bilayer Gap

NASA Astrophysics Data System (ADS)

Dubinov, A. E.; Kitayev, I. N.

2018-04-01

Steady drift states of an electron flow in a planar gap filled with a bilayer dielectric have been considered. Exact mathematical formulas have been derived that describe the distributions of the electrostatic potential and space charge limited electron flow current (extended Mott-Gurney law for a bilayer diode).

Compare Vehicle Technologies | Transportation Research | NREL

Science.gov Websites

electric car diagramming energy storage, power electronics, and climate control components, as well as storage, power electronics, and climate control components, as well as energy flow among components. 3-D control components, as well as energy flow among components. 3-D illustration of electric car diagramming

Flow Synthesis of Diaryliodonium Triflates

PubMed Central

2017-01-01

A safe and scalable synthesis of diaryliodonium triflates was achieved using a practical continuous-flow design. A wide array of electron-rich to electron-deficient arenes could readily be transformed to their respective diaryliodonium salts on a gram scale, with residence times varying from 2 to 60 s (44 examples). PMID:28695736

Integrated control system and method

DOEpatents

Wang, Paul Sai Keat; Baldwin, Darryl; Kim, Myoungjin

2013-10-29

An integrated control system for use with an engine connected to a generator providing electrical power to a switchgear is disclosed. The engine receives gas produced by a gasifier. The control system includes an electronic controller associated with the gasifier, engine, generator, and switchgear. A gas flow sensor monitors a gas flow from the gasifier to the engine through an engine gas control valve and provides a gas flow signal to the electronic controller. A gas oversupply sensor monitors a gas oversupply from the gasifier and provides an oversupply signal indicative of gas not provided to the engine. A power output sensor monitors a power output of the switchgear and provide a power output signal. The electronic controller changes gas production of the gasifier and the power output rating of the switchgear based on the gas flow signal, the oversupply signal, and the power output signal.

Competing Pathways in the photo- Proton-Coupled Electron Transfer Reduction of fac -[Re(bpy)(CO) 3 (4,4'-bpy] +* by Hydroquinone

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

Stewart, David J.; Brennaman, M. Kyle; Bettis, Stephanie E.

2011-08-04

The emitting metal-to-ligand charge transfer (MLCT) excited state of fac-[Re{sup I}(bpy)(CO)₃(4,4'-bpy)] + (1) (bpy is 2,2'-bipyridine, 4,4'-bpy is 4,4'-bipyridine), [Re II(bpy –•)(CO)₃(4,4'-bpy)] +*, is reductively quenched by 1,4-hydroquinone (H₂Q) in CH₃CN at 23 ± 2 °C by competing pathways to give a common electron–proton-transfer intermediate. In one pathway, electron transfer (ET) quenching occurs to give Re{sup I}(bpy –•)(CO)₃(4,4'-bpy)]⁰ with k = (1.8 ± 0.2) × 10⁹ M –1 s –1, followed by proton transfer from H₂Q to give [Re I(bpy)(CO)₃(4,4'-bpyH •)] +. Protonation triggers intramolecular bpy –•→ 4,4'-bpyH{sup +} electron transfer. In the second pathway, preassociationmore » occurs between the ground state and H₂Q at high concentrations. Subsequent Re → bpy MLCT excitation of the adduct is followed by electron–proton transfer from H₂Q in concert with intramolecular bpy –•→ 4,4'-bpyH + electron transfer to give [Re I(bpy)(CO)₃(4,4'-bpyH •)] + with k = (1.0 ± 0.4) × 10⁹ s –1 in 3:1 CH₃CN/H₂O.« less

­Understanding Information Flow Interaction along Separable Causal Paths in Environmental Signals

NASA Astrophysics Data System (ADS)

Jiang, P.; Kumar, P.

2017-12-01

Multivariate environmental signals reflect the outcome of complex inter-dependencies, such as those in ecohydrologic systems. Transfer entropy and information partitioning approaches have been used to characterize such dependencies. However, these approaches capture net information flow occurring through a multitude of pathways involved in the interaction and as a result mask our ability to discern the causal interaction within an interested subsystem through specific pathways. We build on recent developments of momentary information transfer along causal paths proposed by Runge [2015] to develop a framework for quantifying information decomposition along separable causal paths. Momentary information transfer along causal paths captures the amount of information flow between any two variables lagged at two specific points in time. Our approach expands this concept to characterize the causal interaction in terms of synergistic, unique and redundant information flow through separable causal paths. Multivariate analysis using this novel approach reveals precise understanding of causality and feedback. We illustrate our approach with synthetic and observed time series data. We believe the proposed framework helps better delineate the internal structure of complex systems in geoscience where huge amounts of observational datasets exist, and it will also help the modeling community by providing a new way to look at the complexity of real and modeled systems. Runge, Jakob. "Quantifying information transfer and mediation along causal pathways in complex systems." Physical Review E 92.6 (2015): 062829.

Multiscale interaction between a large scale magnetic island and small scale turbulence

NASA Astrophysics Data System (ADS)

Choi, M. J.; Kim, J.; Kwon, J.-M.; Park, H. K.; In, Y.; Lee, W.; Lee, K. D.; Yun, G. S.; Lee, J.; Kim, M.; Ko, W.-H.; Lee, J. H.; Park, Y. S.; Na, Y.-S.; Luhmann, N. C., Jr.; Park, B. H.

2017-12-01

Multiscale interaction between the magnetic island and turbulence has been demonstrated through simultaneous two-dimensional measurements of turbulence and temperature and flow profiles. The magnetic island and turbulence can mutually interact via coupling between the electron temperature (T e ) gradient, the T e turbulence, and the poloidal flow. The T e gradient altered by the magnetic island steepens outside and flattens inside the island. The T e turbulence can appear in increased T e gradient regions. The combined effects of the T e gradient and the poloidal flow shear determines the two-dimensional distribution of the T e turbulence. When the poloidal vortex flow forms, it can maintain the steepest T e gradient and the magnetic island acts more like an electron heat transport barrier. Interestingly, when the T e gradient, the T e turbulence, and the vortex flow shear increase beyond critical levels, the magnetic island turns into a fast electron heat transport channel, which directly leads to the minor disruption.

Code System to Calculate Tornado-Induced Flow Material Transport.

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

ANDRAE, R. W.

1999-11-18

Version: 00 TORAC models tornado-induced flows, pressures, and material transport within structures. Its use is directed toward nuclear fuel cycle facilities and their primary release pathway, the ventilation system. However, it is applicable to other structures and can model other airflow pathways within a facility. In a nuclear facility, this network system could include process cells, canyons, laboratory offices, corridors, and offgas systems. TORAC predicts flow through a network system that also includes ventilation system components such as filters, dampers, ducts, and blowers. These ventilation system components are connected to the rooms and corridors of the facility to form amore » complete network for moving air through the structure and, perhaps, maintaining pressure levels in certain areas. The material transport capability in TORAC is very basic and includes convection, depletion, entrainment, and filtration of material.« less

Physiological functions of the water-water cycle (Mehler reaction) and the cyclic electron flow around PSI in rice leaves.

PubMed

Makino, Amane; Miyake, Chikahiro; Yokota, Akiho

2002-09-01

Changes in chlorophyll fluorescence, P700(+)-absorbance and gas exchange during the induction phase and steady state of photosynthesis were simultaneously examined in rice (Oryza sativa L.), including the rbcS antisense plants. The quantum yield of photosystem II (PhiPSII) increased more rapidly than CO(2) assimilation in 20% O(2). This rapid increase in PhiPSII resulted from the electron flux through the water-water cycle (WWC) because of its dependency on O(2). The electron flux of WWC reached a maximum just after illumination, and rapidly generated non-photochemical quenching (NPQ). With increasing CO(2) assimilation, the electron flux of WWC and NPQ decreased. In 2% O(2), WWC scarcely operated and PhiPSI was always higher than PhiPSII. This suggested that cyclic electron flow around PSI resulted in the formation of NPQ, which remained at higher levels in 2% O(2). The electron flux of WWC in the rbcS antisense plants was lower, but these plants always showed a higher NPQ. This was also caused by the operation of the cyclic electron flow around PSI because of a higher ratio of PhiPSI/PhiPSII, irrespective of O(2) concentration. The results indicate that WWC functions as a starter of photosynthesis by generating DeltapH across thylakoid membranes for NPQ formation, supplying ATP for carbon assimilation. However, WWC does not act to maintain a high NPQ, and PhiPSII is down-regulated by DeltapH generated via the cyclic electron flow around PSI.

An acoustic sensor for monitoring airflow in pediatric tracheostomy patients.

PubMed

Ruscher, Thomas; Wicks Phd, Alexandrina; Muelenaer Md, Andre

2012-01-01

Without proper monitoring, patients with artificial airways in the trachea are at high risk for complications or death. Despite routine maintenance of the tube, dislodged or copious mucus can obstruct the airway. Young children ( 3yrs) have difficulty tending to their own tubes and are particularly vulnerable to blockages. They require external respiratory sensors. In a hospital environment, ventilators, end-tidal CO2 monitors, thermistors, and other auxiliary equipment provide sufficient monitoring of respiration. However, outpatient monitoring methods, such as thoracic impedance and pulse oximetry, are indirect and prone to false positives. Desensitization of caregivers to frequent false alarms has been cited in medical literature as a contributing factor in cases of child death. Ultrasonic time-of-flight (TOF) is a technique used in specialized industrial applications to non-invasively measure liquid and gas flow. Two transducers are oriented at a diagonal across a flow channel. Velocity measurement is accomplished by detecting slight variations in transit time of contra-propagating acoustic signals with a directional component parallel to air flow. Due to the symmetry of acoustic pathway between sensors, velocity measurements are immune to partial fouling in the tube from mucus, saliva, and condensation. A first generation proof of concept prototype was constructed to evaluate the ultrasonic TOF technique for medical tracheostomy monitoring. After successful performance, a second generation prototype was designed with a smaller form factor and more advanced electronics. This prototype was tested and found to measure inspired volume with a root-mean-square error < 2% during initial trials.

Process optimization for microcystin-LR degradation by Response Surface Methodology and mechanism analysis in gas-liquid hybrid discharge system.

PubMed

Zhang, Yi; Wei, Hanyu; Xin, Qing; Wang, Mingang; Wang, Qi; Wang, Qiang; Cong, Yanqing

2016-12-01

A gas-liquid hybrid discharge system was applied to microcystin-LR (MC-LR) degradation. MC-LR degradation was completed after 1 min under a pulsed high voltage of 16 kV, gas-liquid interface gap of 10 mm and oxygen flow rate of 160 L/h. The Box-Behnken Design was proposed in Response Surface Methodology to evaluate the influence of pulsed high voltage, electrode distance and oxygen flow rate on MC-LR removal efficiency. Multiple regression analysis, focused on multivariable factors, was employed and a reduced cubic model was developed. The ANOVA analysis shows that the model is significant and the model prediction on MC-LR removal was also validated with experimental data. The optimum conditions for the process are obtained at pulsed voltage of 16 kV, gas-liquid interface gap of 10 mm and oxygen flow rate of 120 L/h with ta removal efficiency of MC-LR of 96.6%. The addition of catalysts (TiO 2 or Fe 2+ ) in the gas-liquid hybrid discharge system was found to enhance the removal of MC-LR. The intermediates of MC-LR degradation were analyzed by liquid chromatography/mass spectrometry. The degradation pathway proposed envisaged the oxidation of hydroxyl radicals and ozone, and attack of high-energy electrons on the unsaturated double bonds of Adda and Mdha, with MC-LR finally decomposing into small molecular products. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nocardia cyriacigeogica from Bovine Mastitis Induced In vitro Apoptosis of Bovine Mammary Epithelial Cells via Activation of Mitochondrial-Caspase Pathway.

PubMed

Chen, Wei; Liu, Yongxia; Zhang, Limei; Gu, Xiaolong; Liu, Gang; Shahid, Muhammad; Gao, Jian; Ali, Tariq; Han, Bo

2017-01-01

Nocardia is one of the causing agents of bovine mastitis and increasing prevalence of nocardial mastitis in shape of serious outbreaks has been reported from many countries. However, the mechanisms by which this pathogen damages the bovine mammary epithelial cells (bMECs) is not yet studied. Therefore, this study was designed with the aim to evaluate the apoptotic effects elicited by Nocardia and to investigate the pathway by which the Nocardia induce apoptosis in bMECs. Clinical Nocardia cyriacigeorgica strain from bovine mastitis was used to infect the bMECs for different time intervals, viz . 1, 3, 6, 12, and 18 h, and then the induced effects on bMECs were studied using adhesion and invasion assays, release of lactate dehydrogenase (LDH), apoptosis analysis by annexin V and propidium iodide (PI) double staining, morphological, and ultrastructural observations under scanning electron microscope (SEM) and transmission electron microscope (TEM), mitochondrial transmembrane potential (ΔΨm) assay using flow cytometry, and the protein quantification of mitochondrial cytochrome c and caspase-9 and caspase-3 by western blotting. The results of this study showed that N. cyriacigeorgica possessed the abilities of adhesion and invasion to bMECs. N. cyriacigeorgica was found to collapse mitochondrial transmembrane potential, significantly ( p < 0.05) release mitochondrial cytochrome c and ultimately induce cell apoptosis. Additionally, it promoted casepase-9 ( p < 0.01) and casepase-3 ( p < 0.05) levels, significantly ( p < 0.01) increased the release of LDH and promoted DNA fragmentation which further confirmed the apoptosis. Furthermore, N. cyriacigeorgica induced apoptosis/necrosis manifested specific ultrastructure features under TEM, such as swollen endoplasmic reticulum, cristae degeneration, and swelling of mitochondria, vesicle formation on the cell surface, rupturing of cell membrane and nuclear membrane, clumping, fragmentation, and margination of chromatin. The present study is the first comprehensive insight into patho-morphological ultrastructural features of apoptosis/necrosis induced by N. cyriacigeorgica , which concluded that the clinical N. cyriacigeorgica induced apoptotic changes in the bMECs through mitochondrial-caspase dependent apoptotic pathway.

Effect of electronic excitation on high-temperature flows behind strong shock waves

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

Istomin, V. A.; Kustova, E. V.

2014-12-09

In the present paper, a strongly non-equilibrium one-dimensional steady-state flow behind the plane shock wave is studied. We consider a high-temperature chemically reacting five-component ionized mixture of nitrogen species (N{sub 2}/N{sub 2}{sup 2}/N/N{sup +}/e{sup −}) taking into account electronic degrees of freedom in N and N{sup +} (170 and 625 electronic energy levels respectively), and electronic-rotational-vibrational modes in N{sub 2} and N{sub 2}{sup +} (5 and 7 electronic terms). Non-equilibrium reactions of ionization, dissociation, recombination and charge-transfer are included to the kinetic scheme. The system of governing equations is written under the assumption that translation and internal energy relaxation ismore » fast whereas chemical reactions and ionization proceed on the macroscopic gas-dynamics time-scale. The developed model is applied to simulate the flow behind a plane shock wave under initial conditions characteristic for the spacecraft re-entry from an interplanetary flight (Hermes and Fire II experiments). Fluid-dynamic parameters behind the shock wave as well as transport coefficients and the heat flux are calculated for the (N{sub 2}/N{sub 2}{sup +}/N/N{sup +}/e{sup −}) mixture. The effect of electronic excitation on kinetics, dynamics and heat transfer is analyzed. Whereas the contribution of electronic degrees of freedom to the flow macroparameters is negligible, their influence on the heat flux is found to be important under conditions of Hermes re-entry.« less

Bio-medical flow sensor. [intrvenous procedures

NASA Technical Reports Server (NTRS)

Winkler, H. E. (Inventor)

1981-01-01

A bio-medical flow sensor including a packageable unit of a bottle, tubing and hypodermic needle which can be pre-sterilized and is disposable. The tubing has spaced apart tubular metal segments. The temperature of the metal segments and fluid flow therein is sensed by thermistors and at a downstream location heat is input by a resistor to the metal segment by a control electronics. The fluids flow and the electrical power required for the resisto to maintain a constant temperature differential between the tubular metal segments is a measurable function of fluid flow through the tubing. The differential temperature measurement is made in a control electronics and also can be used to control a flow control valve or pump on the tubing to maintain a constant flow in the tubing and to shut off the tubing when air is present in the tubing.

Thomson scattering measurements from asymmetric interpenetrating plasma flows

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

Ross, J. S., E-mail: ross36@llnl.gov; Moody, J. D.; Fiuza, F.

2014-11-15

Imaging Thomson scattering measurements of collective ion-acoustic fluctuations have been utilized to determine ion temperature and density from laser produced counter-streaming asymmetric flows. Two foils are heated with 8 laser beams each, 500 J per beam, at the Omega Laser facility. Measurements are made 4 mm from the foil surface using a 60 J 2ω probe laser with a 200 ps pulse length. Measuring the electron density and temperature from the electron-plasma fluctuations constrains the fit of the multi-ion species, asymmetric flows theoretical form factor for the ion feature such that the ion temperatures, ion densities, and flow velocities formore » each plasma flow are determined.« less

Cross-flow electrochemical reactor cells, cross-flow reactors, and use of cross-flow reactors for oxidation reactions

DOEpatents

Balachandran, Uthamalingam; Poeppel, Roger B.; Kleefisch, Mark S.; Kobylinski, Thaddeus P.; Udovich, Carl A.

1994-01-01

This invention discloses cross-flow electrochemical reactor cells containing oxygen permeable materials which have both electron conductivity and oxygen ion conductivity, cross-flow reactors, and electrochemical processes using cross-flow reactor cells having oxygen permeable monolithic cores to control and facilitate transport of oxygen from an oxygen-containing gas stream to oxidation reactions of organic compounds in another gas stream. These cross-flow electrochemical reactors comprise a hollow ceramic blade positioned across a gas stream flow or a stack of crossed hollow ceramic blades containing a channel or channels for flow of gas streams. Each channel has at least one channel wall disposed between a channel and a portion of an outer surface of the ceramic blade, or a common wall with adjacent blades in a stack comprising a gas-impervious mixed metal oxide material of a perovskite structure having electron conductivity and oxygen ion conductivity. The invention includes reactors comprising first and second zones seprated by gas-impervious mixed metal oxide material material having electron conductivity and oxygen ion conductivity. Prefered gas-impervious materials comprise at least one mixed metal oxide having a perovskite structure or perovskite-like structure. The invention includes, also, oxidation processes controlled by using these electrochemical reactors, and these reactions do not require an external source of electrical potential or any external electric circuit for oxidation to proceed.

Go big or die out: Bifurcation and bimodality in submarine sediment flow behaviour

NASA Astrophysics Data System (ADS)

Talling, P.; Paull, C. K.; Lintern, G.; Gwiazda, R.; Cartigny, M.; Hughes Clarke, J. E.; Xu, J.; Clare, M. A.; Parsons, D. R.; Simmons, S.; Maier, K. L.; Gales, J. A.; Hage, S.; McGann, M.; Pope, E.; Rosenberger, K. J.; Stacey, C.; Barry, J.; Lundsten, E. M.; Anderson, K.; O'Reilly, T. C.; Chapplow, N.; Vendettuoli, D.

2017-12-01

Submarine flows of sediment (turbidity currents) flush globally significant volumes of sediment and organic carbon into deep-sea basins. These flows create the largest sediment accumulations on Earth, which hold valuable oil and gas reserves. These flows affect global carbon burial, how deep-sea ecosystems function, and pose a hazard to offshore infrastructure. Only river systems transport such large amounts of sediment across such long distances. However, there are remarkably few direct measurements from active submarine flows, which is a stark contrast to >1 million direct observations from rivers. Here we present unusually detailed information on frequency, power and runout distance of multiple submarine flows at two contrasting locations. The first data set comes from Monterey Canyon, offshore California, which is fed by littoral cells. The second site is a river-fed delta in Bute Inlet, British Columbia. In both cases, the timing and runout distance of submarine flows was documented using instruments on multiple moorings placed along the 50-km long flow pathway. A striking observation is that flow behaviour and runout is strongly bimodal in both locations. Flows tend to either dissipate rapidly, or runout through the entire mooring arrays. We thus test whether i) the character of short or long runout flows can be distinguished at the first mooring and ii) whether long and short runout flows have different triggers. It has been proposed that submarine flows have two modes of behaviour; either eroding and accelerating, or depositing and dissipating. These field data support such a view of bifurcation and bimodality in flow behaviour. However, some short runout flows resemble their longer runout cousins at the first mooring, and there is no clear relationship between flow trigger and runout. Thus, some flows reach a point where their character is no longer dependent on their initial trigger or initial structure, but on factors acting along the flow pathway.

Plasma wake field XUV radiation source

DOEpatents

Prono, Daniel S.; Jones, Michael E.

1997-01-01

A XUV radiation source uses an interaction of electron beam pulses with a gas to create a plasma radiator. A flowing gas system (10) defines a circulation loop (12) with a device (14), such as a high pressure pump or the like, for circulating the gas. A nozzle or jet (16) produces a sonic atmospheric pressure flow and increases the density of the gas for interacting with an electron beam. An electron beam is formed by a conventional radio frequency (rf) accelerator (26) and electron pulses are conventionally formed by a beam buncher (28). The rf energy is thus converted to electron beam energy, the beam energy is used to create and then thermalize an atmospheric density flowing gas to a fully ionized plasma by interaction of beam pulses with the plasma wake field, and the energetic plasma then loses energy by line radiation at XUV wavelengths Collection and focusing optics (18) are used to collect XUV radiation emitted as line radiation when the high energy density plasma loses energy that was transferred from the electron beam pulses to the plasma.

Evolutionary sheath structure in magnetized collisionless plasma with electron inertia

NASA Astrophysics Data System (ADS)

Gohain, M.; Karmakar, P. K.

2017-09-01

A classical hydrodynamic model is methodologically formulated to see the equilibrium properties of a planar plasma sheath in two-component magnetized bounded plasma. It incorporates the weak but finite electron inertia instead of asymptotically inertialess electrons. The effects of the externally applied oblique (relative to the bulk plasma flow) magnetic field are judiciously accented. It is, for the sake of simplicity, assumed that the relevant physical parameters (plasma density, electrostatic potential, and flow velocity) vary only in a direction normal to the confining wall boundary. It is noticed for the first time that the derived Bohm condition for sheath formation is modified conjointly by the electron inertia, magnetic field, and field orientation. It is manifested that the electron inertia in the presence of plasma gyrokinetic effects slightly enhances the ion Mach threshold value (typically, M i0 ≥ 1.139) toward the sheath entrance. This flow supercriticality is in contrast with the heuristic formalism ( M i0 ≥ 1) for the zero-inertia electrons. A numerical illustrative scheme on the parametric sheath features on diverse nontrivial apposite arguments is constructed alongside ameliorative scope.

Estimating pathway-specific contributions to biodegradation in aquifers based on dual isotope analysis: theoretical analysis and reactive transport simulations.

PubMed

Centler, Florian; Heße, Falk; Thullner, Martin

2013-09-01

At field sites with varying redox conditions, different redox-specific microbial degradation pathways contribute to total contaminant degradation. The identification of pathway-specific contributions to total contaminant removal is of high practical relevance, yet difficult to achieve with current methods. Current stable-isotope-fractionation-based techniques focus on the identification of dominant biodegradation pathways under constant environmental conditions. We present an approach based on dual stable isotope data to estimate the individual contributions of two redox-specific pathways. We apply this approach to carbon and hydrogen isotope data obtained from reactive transport simulations of an organic contaminant plume in a two-dimensional aquifer cross section to test the applicability of the method. To take aspects typically encountered at field sites into account, additional simulations addressed the effects of transverse mixing, diffusion-induced stable-isotope fractionation, heterogeneities in the flow field, and mixing in sampling wells on isotope-based estimates for aerobic and anaerobic pathway contributions to total contaminant biodegradation. Results confirm the general applicability of the presented estimation method which is most accurate along the plume core and less accurate towards the fringe where flow paths receive contaminant mass and associated isotope signatures from the core by transverse dispersion. The presented method complements the stable-isotope-fractionation-based analysis toolbox. At field sites with varying redox conditions, it provides a means to identify the relative importance of individual, redox-specific degradation pathways. © 2013.

Identification of the alternative terminal oxidase of higher plant mitochondria

PubMed Central

Elthon, Thomas E.; McIntosh, Lee

1987-01-01

In addition to cytochrome oxidase, plant mitochondria have a second terminal oxidase called the alternative oxidase. The alternative oxidase is of great interest in that energy is not conserved when electrons flow through it. The potential energy of the system is thus lost as heat, and, in plants with high levels of the alternative oxidase, this results in thermogenesis. We have purified the alternative oxidase from mitochondria of the thermogenic spadix of Sauromatum guttatum and have identified its polypeptide constituents by using polyclonal antibodies. A 166-fold purification was achieved through a combination of cation-exchange (carboxymethyl-Sepharose) and hydrophobic-interaction (phenyl-Sepharose) chromatography. Polyclonal antibodies raised to the CM-Sepharose fractions readily immunoprecipitated alternative oxidase activity and immunoprecipitated four of the proteins that copurify with the activity. These proteins have apparent molecular masses of 37, 36, 35.5, and 35 kDa. Polyclonal antibodies raised individually to the 37-, 36-, and 35.5- plus 35-kDa proteins cross-reacted with all of these proteins, indicating the presence of common antigenic sites. The 37-kDa protein appears to be constitutive in Sauromatum, whereas expression of the 36- and 35-kDa proteins was correlated with presence of alternative pathway activity. The 35.5-kDa protein appears with loss of alternative pathway activity during senescence, indicating that this protein may be a degradation product of the 36-kDa protein. Binding of anti-36-kDa protein antibodies to total mitochondrial protein blots of five plant species indicated that similar proteins were always present when alternative pathway activity was observed. Images PMID:16593898

Jolkinolide B induces apoptosis in MCF-7 cells through inhibition of the PI3K/Akt/mTOR signaling pathway.

PubMed

Xu, Hui-Yu; Chen, Zhi-Wei; Hou, Jin-Cai; Du, Feng-Xia; Liu, Ji-Cheng

2013-01-01

The aim of this study was to explore the molecular mechanisms of jolkinolide B (JB), which is extracted from the root of Euphorbia fischeriana Steud. In this study, we found that JB, a diterpenoid from the traditional Chinese medicinal herb, strongly inhibited the PI3K/Akt/mTOR signaling pathway. Furthermore, we evaluated the effects of JB on the proliferation and apoptosis of MCF-7 human breast cancer cells. Our results showed significant induction of apoptosis in MCF-7 cells incubated with JB. The viability of the MCF-7 cells was assessed by MTT assay. Flow cytometry was used to detect apoptosis and cell cycle analysis. Transmission electron microscopy (TEM) analysis was used to observe cell morphology. MCF-7 cells were subcutaneously inoculated into nude mice to study the in vivo antitumor effects of JB. The growth of MCF-7 cells was inhibited and arrested in the S phase by JB. The data showed significantly decreased tumor volume and weight in nude mice inoculated with MCF-7 cells. In addition, treatment with JB was able to induce downregulation of cyclinD1, cyclinE, mTOR, p-PI3K and p-Akt, and upregulation of PTEN and p-eIF4E. Collectively, JB-induced apoptosis of MCF-7 cells occurs through the PI3K/Akt/mTOR signaling pathway. Furthermore, the PI3K/Akt signaling cascade plays a role in the induction of apoptosis in JB-treated cells. These observations suggest that JB may have therapeutic applications in the treatment of cancer.

Chitosan-coated doxorubicin nano-particles drug delivery system inhibits cell growth of liver cancer via p53/PRC1 pathway.

PubMed

Ye, Bai-Liang; Zheng, Ru; Ruan, Xiao-Jiao; Zheng, Zhi-Hai; Cai, Hua-Jie

2018-01-01

Nano-particles have been widely used in target-specific drug delivery system and showed advantages in cancers treatment. This study aims to evaluate the effect of chitosan coated doxorubicin nano-particles drug delivery system in liver cancer. The chitosan nano-particles were prepared by using the ionic gelation method. The characterizations of the nano-particles were determined by transmission electron microscopy. The cytotoxicity was detected by MTT assay, and the endocytosis, cell apoptosis and cell cycle were examined by flow cytometry. The protein level was analyzed with western blot. The dual luciferase reporter assay was performed to assess the interaction between p53 and the promoter of PRC1, and chromatin immune-precipitation was used to verify the binding between them. The FA-CS-DOX nano-particles were irregular and spherical particles around 30-40 nm, with uniform size and no adhesion. No significant difference was noted in doxorubicin release rate between CS-DOX and FA-CS-DOX. FA-CS-DOX nano-particles showed stronger cytotoxicity than CS-DOX. FA-CS-DOX nano-particles promoted the apoptosis and arrested cell cycle at G2/M phase, and they up-regulated p53. FA-CS-DOX nano-particles inhibited cell survival through p53/PRC1 pathway. Chitosan-coated doxorubicin nano-particles drug delivery system inhibits cell growth of liver cancer by promoting apoptosis and arresting cell cycle at G2/M phase through p53/PRC1 pathway. Copyright © 2017 Elsevier Inc. All rights reserved.

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

Validation of Multitemperature Nozzle Flow Code

NASA Technical Reports Server (NTRS)

Park, Chul; Lee, Seung -Ho.

1994-01-01

A computer code nozzle in n-temperatures (NOZNT), which calculates one-dimensional flows of partially dissociated and ionized air in an expanding nozzle, is tested against three existing sets of experimental data taken in arcjet wind tunnels. The code accounts for the differences among various temperatures, i.e., translational-rotational temperature, vibrational temperatures of individual molecular species, and electron-electronic temperature, and the effects of impurities. The experimental data considered are (1) the spectroscopic emission data; (2) electron beam data on vibrational temperature; and (3) mass-spectrometric species concentration data. It is shown that the impurities are inconsequential for the arcjet flows, and the NOZNT code is validated by numerically reproducing the experimental data.

Quasi-exospheric heat flux of solar-wind electrons

NASA Technical Reports Server (NTRS)

Eviatar, A.; Schultz, M.

1975-01-01

Density, bulk-velocity, and heat-flow moments are calculated for truncated Maxwellian distributions representing the cool and hot populations of solar-wind electrons, as realized at the base of a hypothetical exosphere. The electrostatic potential is thus calculated by requiring charge quasi-neutrality and the absence of electrical current. Plasma-kinetic coupling of the cool-electron and proton bulk velocities leads to an increase in the electrostatic potential and a decrease in the heat-flow moment.

Nitrogen Cycle Modeling: a Mechanistic Estimate of N-losses From Agricultural Fields Over the Seasonal Time Period

NASA Astrophysics Data System (ADS)

Maggi, F.; Gu, C.; Venterea, R.; Riley, W.; Oldenburg, C.

2007-12-01

The biogeochemical cycle of nitrogen and production of NO, N2O, and CO2 gas and NO2- and NO3- ions in nutrient-enriched agricultural fields is mediated by soil microbial activity, the hydrological cycle, plant dynamics, and climatic forcing. Understanding how NO, N2O, CO2 gases and NO2- and NO3- ions are released from agricultural fields to the environment is a key factor in controlling the green-house effect and water contamination, and assumes ever greater importance in view of the foreseen increase in biofuel, food, and fiber production. To address these issues we have developed a mechanistic model (TOUGHREACT-N) for various nitrification and denitrification pathways, multiple microbial biomass dynamics, heat and water flows, and various chemical reactions at local and kinetic equilibrium. The soil column is represented in a 1D framework, with hydraulic properties described by a water tension-saturation model. Biotic and abiotic reactions are assumed to follow Michaelis-Menten kinetics, while a consortium of several micro-organismal strains is assumed to follow multiple Monod growth kinetics accounting for electron donor, electron acceptor, and inhibitor concentrations. Water flow is modeled with the Darcy-Richards equation, while nutrient transport is modeled by Fickian advective and diffusive processes in both gaseous and liquid phases. Heat flow is modeled with the Fourier equation. Plant dynamics is taken into account by coupling TOUGHREACT-N with CERES to determine water and nutrient uptake, and soil carbon accumulation. TOUGHREACT-N was calibrated against field measurements to assess pathways of N losses following fertilization. A good agreement between field observations and model predictions was found. We identified two dominant time scales in the system response that depended on plants dynamics. Before plants have substantial impact on soil nutrients and moisture content, N losses are characterized by rapid increases as a function of water application rate and fertilizer amount and application depth. Under reference fertilization and irrigation practices, approximately 1.64% and 1.61% of the total applied N is lost as N-NO(g) and N-N2O(g), respectively, while losses of N-N2(g), N-NO2-, and N-NO3- where several orders of magnitude smaller. When plants grow, pulses in N losses became smoother due to nutrient and water uptake. Contrarily to predictions of non- mechanistic, coarse-scale models (e.g., CASA, CENTURY) N losses are predominantly non-linearly increasing with fertilizer and water application amount, and with fertilizer application depth, thus invoking a revision of long- term estimates of nitrogen and carbon balances at global scales

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

Ivarson, Kristine A.; Miller, Charles W.; Arola, Craig C.

Groundwater contamination by hexavalent chromium and other nuclear reactor operation-related contaminants has resulted in the need for groundwater remedial actions within the Hanford Site reactor areas (the Hanford Site 100 Area). The large geographic extent of the resultant contaminant plumes requires an extensive level of understanding of the aquifer structure, characteristics, and configuration to support assessment and design of remedial alternatives within the former 100-D, 100-H, and 100-K reactor areas. The authors have prepared two- and three-dimensional depictions of the key subsurface geologic structures at two Hanford Site reactor operable units (100-K and 100-D/H). These depictions, prepared using commercial-off-the-shelf (COTS)more » visualization software, provide a basis for expanding the understanding of groundwater contaminant migration pathways, including identification of geologically-defined preferential groundwater flow pathways. These identified preferential flow pathways support the conceptual site model and help explain both historical and current contaminant distribution and transport. (authors)« less

CHARACTERIZING THE CONFORMATIONAL AND ELECTRONIC PROPERTIES OF CONAZOLE FUNGICIDES

EPA Science Inventory

Conazole fungicides have important environmental and human health considerations including chemical reactivity and transformation pathways. The electronic and conformational properties of an organic molecule determines in conjunction with solvent properties, its chemical reacti...

Mechanical stretching stimulates collagen synthesis via down-regulating SO2/AAT1 pathway

PubMed Central

Liu, Jia; Yu, Wen; Liu, Yan; Chen, Selena; Huang, Yaqian; Li, Xiaohui; Liu, Cuiping; Zhang, Yanqiu; Li, Zhenzhen; Du, Jie; Tang, Chaoshu; Du, Junbao; Jin, Hongfang

2016-01-01

The aim of the study was to investigate the role of endogenous sulfur dioxide (SO2)/ aspartate aminotransferase 1 (AAT1) pathway in stretch-induced excessive collagen expression and its mechanism. The mechanical stretch downregulated SO2/AAT1 pathway and increased collagen I and III protein expression. Importantly, AAT1 overexpression blocked the increase in collagen I and III expression, transforming growth factor-β1 (TGF- β1) expression and phosphorylation of Smad2/3 induced by stretch, but AAT1 knockdown mimicked the increase in collagen I and III expression, TGF- β1 expression and phosphorylation of Smad2/3 induced by stretch. Mechanistically, SB431542, a TGF-β1/Smad2/3 inhibitor, eliminated excessive collagen I and III accumulation induced by AAT1 knockdown, stretch or stretch plus AAT1 knockdown. In a rat model of high pulmonary blood flow-induced pulmonary vascular collagen accumulation, AAT1 expression and SO2 content in lung tissues of rat were reduced in shunt rats with high pulmonary blood flow. Supplement of SO2 derivatives inhibited activation of TGF- β1/Smad2/3 pathway and alleviated the excessive collagen accumulation in lung tissues of shunt rats. The results suggested that deficiency of endogenous SO2/AAT1 pathway mediated mechanical stretch-stimulated abnormal collagen accumulation via TGF-β1/Smad2/3 pathway. PMID:26880260

Textile Inspired Lithium-Oxygen Battery Cathode with Decoupled Oxygen and Electrolyte Pathways.

PubMed

Xu, Shaomao; Yao, Yonggang; Guo, Yuanyuan; Zeng, Xiaoqiao; Lacey, Steven D; Song, Huiyu; Chen, Chaoji; Li, Yiju; Dai, Jiaqi; Wang, Yanbin; Chen, Yanan; Liu, Boyang; Fu, Kun; Amine, Khalil; Lu, Jun; Hu, Liangbing

2018-01-01

The lithium-air (Li-O 2 ) battery has been deemed one of the most promising next-generation energy-storage devices due to its ultrahigh energy density. However, in conventional porous carbon-air cathodes, the oxygen gas and electrolyte often compete for transport pathways, which limit battery performance. Here, a novel textile-based air cathode is developed with a triple-phase structure to improve overall battery performance. The hierarchical structure of the conductive textile network leads to decoupled pathways for oxygen gas and electrolyte: oxygen flows through the woven mesh while the electrolyte diffuses along the textile fibers. Due to noncompetitive transport, the textile-based Li-O 2 cathode exhibits a high discharge capacity of 8.6 mAh cm -2 , a low overpotential of 1.15 V, and stable operation exceeding 50 cycles. The textile-based structure can be applied to a range of applications (fuel cells, water splitting, and redox flow batteries) that involve multiple phase reactions. The reported decoupled transport pathway design also spurs potential toward flexible/wearable Li-O 2 batteries. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A model of the saturation of coupled electron and ion scale gyrokinetic turbulence

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

Staebler, Gary M.; Howard, Nathan T.; Candy, Jeffrey M.

A new paradigm of zonal flow mixing as the mechanism by which zonal E × B fluctuations impact the saturation of gyrokinetic turbulence has recently been deduced from the nonlinear 2D spectrum of electric potential fluctuations in gyrokinetic simulations. These state of the art simulations span the physical scales of both ion and electron turbulence. It was found that the zonal flow mixing rate, rather than zonal flow shearing rate, competes with linear growth at both electron and ion scales. A model for saturation of the turbulence by the zonal flow mixing was developed and applied to the quasilinear trappedmore » gyro-Landau fluid transport model (TGLF). The first validation tests of the new saturation model are reported in this paper with data from L-mode and high-β p regime discharges from the DIII-D tokamak. Lastly, the shortfall in the predicted L-mode edge electron energy transport is improved with the new saturation model for these discharges but additional multiscale simulations are required in order to verify the safety factor and collisionality dependencies found in the modeling.« less

A model of the saturation of coupled electron and ion scale gyrokinetic turbulence

DOE PAGES

Staebler, Gary M.; Howard, Nathan T.; Candy, Jeffrey M.; ...

2017-05-09

A new paradigm of zonal flow mixing as the mechanism by which zonal E × B fluctuations impact the saturation of gyrokinetic turbulence has recently been deduced from the nonlinear 2D spectrum of electric potential fluctuations in gyrokinetic simulations. These state of the art simulations span the physical scales of both ion and electron turbulence. It was found that the zonal flow mixing rate, rather than zonal flow shearing rate, competes with linear growth at both electron and ion scales. A model for saturation of the turbulence by the zonal flow mixing was developed and applied to the quasilinear trappedmore » gyro-Landau fluid transport model (TGLF). The first validation tests of the new saturation model are reported in this paper with data from L-mode and high-β p regime discharges from the DIII-D tokamak. Lastly, the shortfall in the predicted L-mode edge electron energy transport is improved with the new saturation model for these discharges but additional multiscale simulations are required in order to verify the safety factor and collisionality dependencies found in the modeling.« less

Kinetic and radiative power from optically thin accretion flows

NASA Astrophysics Data System (ADS)

Sądowski, Aleksander; Gaspari, Massimo

2017-06-01

We perform a set of general relativistic, radiative, magneto-hydrodynamical simulations (GR-RMHD) to study the transition from radiatively inefficient to efficient state of accretion on a non-rotating black hole. We study ion to electron temperature ratios ranging from TI/Te = 10 to 100, and simulate flows corresponding to accretion rates as low as 10^{-6}\\dot{M}_Edd, and as high as 10^{-2}\\dot{M}_Edd. We have found that the radiative output of accretion flows increases with accretion rate, and that the transition occurs earlier for hotter electrons (lower TI/Te ratio). At the same time, the mechanical efficiency hardly changes and accounts to ≈3 per cent of the accreted rest mass energy flux, even at the highest simulated accretion rates. This is particularly important for the mechanical active galactic nuclei (AGN) feedback regulating massive galaxies, groups and clusters. Comparison with recent observations of radiative and mechanical AGN luminosities suggests that the ion to electron temperature ratio in the inner, collisionless accretion flow should fall within 10 < TI/Te < 30, I.e. the electron temperature should be several percent of the ion temperature.

Photochemical Synthesis of Complex Carbazoles: Evaluation of Electronic Effects in Both UV- and Visible-Light Methods in Continuous Flow.

PubMed

Hernandez-Perez, Augusto C; Caron, Antoine; Collins, Shawn K

2015-11-09

An evaluation of both a visible-light- and UV-light-mediated synthesis of carbazoles from various triarylamines with differing electronic properties under continuous-flow conditions has been conducted. In general, triarylamines bearing electron-rich groups tend to produce higher yields than triarylamines possessing electron-withdrawing groups. The incorporation of nitrogen-based heterocycles, as well as halogen-containing arenes in carbazole skeletons, was well tolerated, and often synthetically useful complementarity was observed between the UV-light and visible-light (photoredox) methods. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Activation of somatosensory afferents elicit changes in vaginal blood flow and the urethrogenital reflex via autonomic efferents.

PubMed

Cai, R S; Alexander, M Sipski; Marson, L

2008-09-01

We examined the effects of pudendal sensory nerve stimulation and urethral distention on vaginal blood flow and the urethrogenital reflex, and the relationship between somatic and autonomic pathways regulating sexual responses. Distention of the urethra and stimulation of the pudendal sensory nerve were used to evoke changes in vaginal blood flow (laser Doppler perfusion monitoring) and pudendal motor nerve activity in anesthetized, spinally transected female rats. Bilateral cuts of either the pelvic or hypogastric nerve or both autonomic nerves were made, and blood flow and pudendal nerve responses were reexamined. Stimulation of the pudendal sensory nerve or urethral distention elicited consistent increases in vaginal blood flow and rhythmic firing of the pudendal motor nerve. Bilateral cuts of the pelvic plus hypogastric nerves significantly reduced vaginal blood flow responses without altering pudendal motor nerve responses. Pelvic nerve cuts also significantly reduced vaginal blood flow responses. In contrast, hypogastric nerve cuts did not significantly change vaginal blood flow. Bilateral cuts of the pudendal sensory nerve blocked pudendal motor nerve responses but stimulation of the central end evoked vaginal blood flow and pudendal motor nerve responses. Stimulation of the sensory branch of the pudendal nerve elicits vasodilatation of the vagina. The likely mechanism is via activation of spinal pathways that in turn activate pelvic nerve efferents to produced changes in vaginal blood flow. Climatic-like responses (firing of the pudendal motor nerve) occur in response to stimulation of the pudendal sensory nerve and do not require intact pelvic or hypogastric nerves.

Matrix-specific protein kinase A signaling regulates p21 activated kinase activation by flow in endothelial cells

PubMed Central

Funk, Steven Daniel; Yurdagul, Arif; Green, Jonette M.; Jhaveri, Krishna A.; Schwartz, Martin Alexander; Orr, A. Wayne

2010-01-01

Rationale Atherosclerosis is initiated by blood flow patterns that activate inflammatory pathways in endothelial cells. Activation of inflammatory signaling by fluid shear stress is highly dependent on the composition of the subendothelial extracellular matrix. The basement membrane proteins laminin and collagen found in normal vessels suppress flow-induced p21 activated kinase (PAK) and NF-κB activation. By contrast, the provisional matrix proteins fibronectin and fibrinogen found in wounded or inflamed vessels support flow-induced PAK and NF-κB activation. PAK mediates both flow-induced permeability and matrix-specific activation of NF-κB. Objective To elucidate the mechanisms regulating matrix-specific PAK activation. Methods and Results We now show that matrix composition does not affect the upstream pathway by which flow activates PAK (integrin activation, Rac). Instead basement membrane proteins enhance flow-induced protein kinase A (PKA) activation, which suppresses PAK. Inhibiting PKA restored flow-induced PAK and NF-κB activation in cells on basement membrane proteins, whereas stimulating PKA inhibited flow-induced activation of inflammatory signaling in cells on fibronectin. PKA suppressed inflammatory signaling through PAK inhibition. Activating PKA by injection of the PGI2 analog iloprost reduced PAK activation and inflammatory gene expression at sites of disturbed flow in vivo, whereas inhibiting PKA by PKI injection enhanced PAK activation and inflammatory gene expression. Inhibiting PAK prevented the enhancement of inflammatory gene expression by PKI. Conclusions Basement membrane proteins inhibit inflammatory signaling in endothelial cells via PKA-dependent inhibition of PAK. PMID:20224042

Electron attachment-induced DNA single-strand breaks at the pyrimidine sites

PubMed Central

Gu, Jiande; Wang, Jing; Leszczynski, Jerzy

2010-01-01

To elucidate the contribution of pyrimidine in DNA strand breaks caused by low-energy electrons (LEEs), theoretical investigations of the LEE attachment-induced C3′–O3′, and C5′–O5′ σ bond as well as N-glycosidic bond breaking of 2′-deoxycytidine-3′,5′-diphosphate and 2′-deoxythymidine-3′,5′-diphosphate were performed using the B3LYP/DZP++ approach. The base-centered radical anions are electronically stable enough to assure that either the C–O or glycosidic bond breaking processes might compete with the electron detachment and yield corresponding radical fragments and anions. In the gas phase, the computed glycosidic bond breaking activation energy (24.1 kcal/mol) excludes the base release pathway. The low-energy barrier for the C3′–O3′ σ bond cleavage process (∼6.0 kcal/mol for both cytidine and thymidine) suggests that this reaction pathway is the most favorable one as compared to other possible pathways. On the other hand, the relatively low activation energy barrier (∼14 kcal/mol) for the C5′–O5′ σ bond cleavage process indicates that this bond breaking pathway could be possible, especially when the incident electrons have relatively high energy (a few electronvolts). The presence of the polarizable medium greatly increases the activation energies of either C–O σ bond cleavage processes or the N-glycosidic bond breaking process. The only possible pathway that dominates the LEE-induced DNA single strands in the presence of the polarizable surroundings (such as in an aqueous solution) is the C3′–O3′ σ bond cleavage (the relatively low activation energy barrier, ∼13.4 kcal/mol, has been predicted through a polarizable continuum model investigation). The qualitative agreement between the ratio for the bond breaks of C5′–O5′, C3′–O3′ and N-glycosidic bonds observed in the experiment of oligonucleotide tetramer CGAT and the theoretical sequence of the bond breaking reaction pathways have been found. This consistency between the theoretical predictions and the experimental observations provides strong supportive evidences for the base-centered radical anion mechanism of the LEE-induced single-strand bond breaking around the pyrimidine sites of the DNA single strands. PMID:20430827

Traction Drive Inverter Cooling with Submerged Liquid Jet Impingement on Microfinned Enhanced Surfaces (Presentation)

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

Waye, S.; Narumanchi, S.; Moreno, G.

Jet impingement is one means to improve thermal management for power electronics in electric-drive traction vehicles. Jet impingement on microfin-enhanced surfaces further augments heat transfer and thermal performance. A channel flow heat exchanger from a commercial inverter was characterized as a baseline system for comparison with two new prototype designs using liquid jet impingement on plain and microfinned enhanced surfaces. The submerged jets can target areas with the highest heat flux to provide local cooling, such as areas under insulated-gate bipolar transistors and diode devices. Low power experiments, where four diodes were powered, dissipated 105 W of heat and weremore » used to validate computational fluid dynamics modeling of the baseline and prototype designs. Experiments and modeling used typical automotive flow rates using water-ethylene glycol as a coolant (50%-50% by volume). The computational fluid dynamics model was used to predict full inverter power heat dissipation. The channel flow and jet impingement configurations were tested at full inverter power of 40 to 100 kW (output power) on a dynamometer, translating to an approximate heat dissipation of 1 to 2 kW. With jet impingement, the cold plate material is not critical for the thermal pathway. A high-temperature plastic was used that could eventually be injection molded or formed, with the jets formed from a basic aluminum plate with orifices acting as nozzles. Long-term reliability of the jet nozzles and impingement on enhanced surfaces was examined. For jet impingement on microfinned surfaces, thermal performance increased 17%. Along with a weight reduction of approximately 3 kg, the specific power (kW/kg) increased by 36%, with an increase in power density (kW/L) of 12% compared with the baseline channel flow configuration.« less

Reaction pathways of producing and losing particles in atmospheric pressure methane nanosecond pulsed needle-plane discharge plasma

NASA Astrophysics Data System (ADS)

Zhao, Yuefeng; Wang, Chao; Li, Li; Wang, Lijuan; Pan, Jie

2018-03-01

In this work, a two-dimensional fluid model is built up to numerically investigate the reaction pathways of producing and losing particles in atmospheric pressure methane nanosecond pulsed needle-plane discharge plasma. The calculation results indicate that the electron collisions with CH4 are the key pathways to produce the neutral particles CH2 and CH as well as the charged particles e and CH3+. CH3, H2, H, C2H2, and C2H4 primarily result from the reactions between the neutral particles and CH4. The charge transfer reactions are the significant pathways to produce CH4+, C2H2+, and C2H4+. As to the neutral species CH and H and the charged species CH3+, the reactions between themselves and CH4 contribute to substantial losses of these particles. The ways responsible for losing CH3, H2, C2H2, and C2H4 are CH3 + H → CH4, H2 + CH → CH2 + H, CH4+ + C2H2 → C2H2+ + CH4, and CH4+ + C2H4 → C2H4+ + CH4, respectively. Both electrons and C2H4+ are consumed by the dissociative electron-ion recombination reactions. The essential reaction pathways of losing CH4+ and C2H2+ are the charge transfer reactions.

Influence of the variation potential on photosynthetic flows of light energy and electrons in pea.

PubMed

Sukhova, Ekaterina; Mudrilov, Maxim; Vodeneev, Vladimir; Sukhov, Vladimir

2018-05-01

Local damage (mainly burning, heating, and mechanical wounding) induces propagation of electrical signals, namely, variation potentials, which are important signals during the life of plants that regulate different physiological processes, including photosynthesis. It is known that the variation potential decreases the rate of CO 2 assimilation by the Calvin-Benson cycle; however, its influence on light reactions has been poorly investigated. The aim of our work was to investigate the influence of the variation potential on the light energy flow that is absorbed, trapped and dissipated per active reaction centre in photosystem II and on the flow of electrons through the chloroplast electron transport chain. We analysed chlorophyll fluorescence in pea leaves using JIP-test and PAM-fluorometry; we also investigated delayed fluorescence. The electrical signals were registered using extracellular electrodes. We showed that the burning-induced variation potential stimulated a nonphotochemical loss of energy in photosystem II under dark conditions. It was also shown that the variation potential gradually increased the flow of light energy absorbed, trapped and dissipated by photosystem II. These changes were likely caused by an increase in the fraction of absorbed light distributed to photosystem II. In addition, the variation potential induced a transient increase in electron flow through the photosynthetic electron transport chain. Some probable mechanisms for the influence of the variation potential on the light reactions of photosynthesis (including the potential role of intracellular pH decrease) are discussed in the work.

Evidence for a Hydrogenosomal-Type Anaerobic ATP Generation Pathway in Acanthamoeba castellanii

PubMed Central

Gray, Michael W.; Roger, Andrew J.

2013-01-01

Diverse, distantly-related eukaryotic lineages have adapted to low-oxygen environments, and possess mitochondrion-related organelles that have lost the capacity to generate adenosine triphosphate (ATP) through oxidative phosphorylation. A subset of these organelles, hydrogenosomes, has acquired a set of characteristic ATP generation enzymes commonly found in anaerobic bacteria. The recipient of these enzymes could not have survived prior to their acquisition had it not still possessed the electron transport chain present in the ancestral mitochondrion. In the divergence of modern hydrogenosomes from mitochondria, a transitional organelle must therefore have existed that possessed both an electron transport chain and an anaerobic ATP generation pathway. Here, we report a modern analog of this organelle in the habitually aerobic opportunistic pathogen, Acanthamoeba castellanii. This organism possesses a complete set of enzymes comprising a hydrogenosome-like ATP generation pathway, each of which is predicted to be targeted to mitochondria. We have experimentally confirmed the mitochondrial localizations of key components of this pathway using tandem mass spectrometry. This evidence is the first supported by localization and proteome data of a mitochondrion possessing both an electron transport chain and hydrogenosome-like energy metabolism enzymes. Our work provides insight into the first steps that might have occurred in the course of the emergence of modern hydrogenosomes. PMID:24086244

Mechanotransduction signaling in podocytes from fluid flow shear stress.

PubMed

Srivastava, Tarak; Dai, Hongying; Heruth, Daniel P; Alon, Uri S; Garola, Robert E; Zhou, Jianping; Duncan, R Scott; El-Meanawy, Ashraf; McCarthy, Ellen T; Sharma, Ram; Johnson, Mark L; Savin, Virginia J; Sharma, Mukut

2018-01-01

Recently, we and others have found that hyperfiltration-associated increase in biomechanical forces, namely, tensile stress and fluid flow shear stress (FFSS), can directly and distinctly alter podocyte structure and function. The ultrafiltrate flow over the major processes and cell body generates FFSS to podocytes. Our previous work suggests that the cyclooxygenase-2 (COX-2)-PGE 2 -PGE 2 receptor 2 (EP2) axis plays an important role in mechanoperception of FFSS in podocytes. To address mechanotransduction of the perceived stimulus through EP2, cultured podocytes were exposed to FFSS (2 dyn/cm 2 ) for 2 h. Total RNA from cells at the end of FFSS treatment, 2-h post-FFSS, and 24-h post-FFSS was used for whole exon array analysis. Differentially regulated genes ( P < 0.01) were analyzed using bioinformatics tools Enrichr and Ingenuity Pathway Analysis to predict pathways/molecules. Candidate pathways were validated using Western blot analysis and then further confirmed to be resulting from a direct effect of PGE 2 on podocytes. Results show that FFSS-induced mechanotransduction as well as exogenous PGE 2 activate the Akt-GSK3β-β-catenin (Ser552) and MAPK/ERK but not the cAMP-PKA signal transduction cascades. These pathways are reportedly associated with FFSS-induced and EP2-mediated signaling in other epithelial cells as well. The current regimen for treating hyperfiltration-mediated injury largely depends on targeting the renin-angiotensin-aldosterone system. The present study identifies specific transduction mechanisms and provides novel information on the direct effect of FFSS on podocytes. These results suggest that targeting EP2-mediated signaling pathways holds therapeutic significance for delaying progression of chronic kidney disease secondary to hyperfiltration.

Human cerebral venous outflow pathway depends on posture and central venous pressure

PubMed Central

Gisolf, J; van Lieshout, J J; van Heusden, K; Pott, F; Stok, W J; Karemaker, J M

2004-01-01

Internal jugular veins are the major cerebral venous outflow pathway in supine humans. In upright humans the positioning of these veins above heart level causes them to collapse. An alternative cerebral outflow pathway is the vertebral venous plexus. We set out to determine the effect of posture and central venous pressure (CVP) on the distribution of cerebral outflow over the internal jugular veins and the vertebral plexus, using a mathematical model. Input to the model was a data set of beat-to-beat cerebral blood flow velocity and CVP measurements in 10 healthy subjects, during baseline rest and a Valsalva manoeuvre in the supine and standing position. The model, consisting of 2 jugular veins, each a chain of 10 units containing nonlinear resistances and capacitors, and a vertebral plexus containing a resistance, showed blood flow mainly through the internal jugular veins in the supine position, but mainly through the vertebral plexus in the upright position. A Valsalva manoeuvre while standing completely re-opened the jugular veins. Results of ultrasound imaging of the right internal jugular vein cross-sectional area at the level of the laryngeal prominence in six healthy subjects, before and during a Valsalva manoeuvre in both body positions, correlate highly with model simulation of the jugular cross-sectional area (R2 = 0.97). The results suggest that the cerebral venous flow distribution depends on posture and CVP: in supine humans the internal jugular veins are the primary pathway. The internal jugular veins are collapsed in the standing position and blood is shunted to an alternative venous pathway, but a marked increase in CVP while standing completely re-opens the jugular veins. PMID:15284348

A novel algorithm for delineating wetland depressions and mapping surface hydrologic flow pathways using LiDAR data

EPA Science Inventory

In traditional watershed delineation and topographic modeling, surface depressions are generally treated as spurious features and simply removed from a digital elevation model (DEM) to enforce flow continuity of water across the topographic surface to the watershed outlets. In re...

Evaluation of existing and modified wetland equations in the SWAT model

USDA-ARS?s Scientific Manuscript database

The drainage significantly alters flow and nutrient pathways in small watersheds and reliable simulation at this scale is needed for effective planning of nutrient reduction strategies. The Soil and Water Assessment Tool (SWAT) has been widely utilized for prediction of flow and nutrient loads, but...

Changes in migration mode of brine and supercritical CO2 in imbibition process under steady flow state of very slow fluid velocities

NASA Astrophysics Data System (ADS)

Kogure, Tetsuya; Zhang, Yi; Nishizawa, Osamu; Xue, Ziqiu

2018-05-01

Relative permeability curves and flow mechanisms of CO2 and brine in Berea sandstone were investigated during a two-phase flow imbibition process, where CO2 saturation in the rock decreased from 55 per cent to 9 per cent by stepwise decrease of CO2/brine injection ratios. Total fluid flow velocity was 4.25 × 10-6 m/s, corresponding to the capillary number of order ˜10-8 for CO2 flow. The relative permeability curves showed a slight hysteresis compared to those during the drainage process. Local CO2 saturation and the differential pressure showed temporal fluctuations when the average differential pressure showed constant values or very small trends. The fluctuations in local CO2 saturation correlate with local porosity distributions. The differential pressure between the inlet and outlet ends showed the largest fluctuation when the CO2/brine ratio equals to one. A final brine-only injection resulted in more CO2 trapped within low porosity zones. These results suggest important roles of ganglion dynamics in the low flow rate ranges, where fluid pathways undergo repetitive brine snap-off and coalescence of CO2 ganglia that causes morphological changes in distributions of CO2 pathways.

Use of navigation channels by Lake Sturgeon: Does channelization increase vulnerability of fish to ship strikes?

PubMed

Hondorp, Darryl W; Bennion, David H; Roseman, Edward F; Holbrook, Christopher M; Boase, James C; Chiotti, Justin A; Thomas, Michael V; Wills, Todd C; Drouin, Richard G; Kessel, Steven T; Krueger, Charles C

2017-01-01

Channelization for navigation and flood control has altered the hydrology and bathymetry of many large rivers with unknown consequences for fish species that undergo riverine migrations. In this study, we investigated whether altered flow distributions and bathymetry associated with channelization attracted migrating Lake Sturgeon (Acipenser fulvescens) into commercial navigation channels, potentially increasing their exposure to ship strikes. To address this question, we quantified and compared Lake Sturgeon selection for navigation channels vs. alternative pathways in two multi-channel rivers differentially affected by channelization, but free of barriers to sturgeon movement. Acoustic telemetry was used to quantify Lake Sturgeon movements. Under the assumption that Lake Sturgeon navigate by following primary flow paths, acoustic-tagged Lake Sturgeon in the more-channelized lower Detroit River were expected to choose navigation channels over alternative pathways and to exhibit greater selection for navigation channels than conspecifics in the less-channelized lower St. Clair River. Consistent with these predictions, acoustic-tagged Lake Sturgeon in the more-channelized lower Detroit River selected the higher-flow and deeper navigation channels over alternative migration pathways, whereas in the less-channelized lower St. Clair River, individuals primarily used pathways alternative to navigation channels. Lake Sturgeon selection for navigation channels as migratory pathways also was significantly higher in the more-channelized lower Detroit River than in the less-channelized lower St. Clair River. We speculated that use of navigation channels over alternative pathways would increase the spatial overlap of commercial vessels and migrating Lake Sturgeon, potentially enhancing their vulnerability to ship strikes. Results of our study thus demonstrated an association between channelization and the path use of migrating Lake Sturgeon that could prove important for predicting sturgeon-vessel interactions in navigable rivers as well as for understanding how fish interact with their habitat in landscapes altered by human activity.

Use of navigation channels by Lake Sturgeon: Does channelization increase vulnerability of fish to ship strikes?

PubMed Central

Bennion, David H.; Roseman, Edward F.; Holbrook, Christopher M.; Boase, James C.; Chiotti, Justin A.; Thomas, Michael V.; Wills, Todd C.; Drouin, Richard G.; Kessel, Steven T.; Krueger, Charles C.

2017-01-01

Channelization for navigation and flood control has altered the hydrology and bathymetry of many large rivers with unknown consequences for fish species that undergo riverine migrations. In this study, we investigated whether altered flow distributions and bathymetry associated with channelization attracted migrating Lake Sturgeon (Acipenser fulvescens) into commercial navigation channels, potentially increasing their exposure to ship strikes. To address this question, we quantified and compared Lake Sturgeon selection for navigation channels vs. alternative pathways in two multi-channel rivers differentially affected by channelization, but free of barriers to sturgeon movement. Acoustic telemetry was used to quantify Lake Sturgeon movements. Under the assumption that Lake Sturgeon navigate by following primary flow paths, acoustic-tagged Lake Sturgeon in the more-channelized lower Detroit River were expected to choose navigation channels over alternative pathways and to exhibit greater selection for navigation channels than conspecifics in the less-channelized lower St. Clair River. Consistent with these predictions, acoustic-tagged Lake Sturgeon in the more-channelized lower Detroit River selected the higher-flow and deeper navigation channels over alternative migration pathways, whereas in the less-channelized lower St. Clair River, individuals primarily used pathways alternative to navigation channels. Lake Sturgeon selection for navigation channels as migratory pathways also was significantly higher in the more-channelized lower Detroit River than in the less-channelized lower St. Clair River. We speculated that use of navigation channels over alternative pathways would increase the spatial overlap of commercial vessels and migrating Lake Sturgeon, potentially enhancing their vulnerability to ship strikes. Results of our study thus demonstrated an association between channelization and the path use of migrating Lake Sturgeon that could prove important for predicting sturgeon-vessel interactions in navigable rivers as well as for understanding how fish interact with their habitat in landscapes altered by human activity. PMID:28678798

On the Electron Diffusion Region in Asymmetric Reconnection with a Guide Magnetic Field

NASA Technical Reports Server (NTRS)

Hesse, Michael; Liu, Yi-Hsin; Chen, Li-Jen; Bessho, Naoki; Kuznetsova, Masha; Birn, Joachim; Burch, James L.

2016-01-01

Particle-in-cell simulations in a 2.5-D geometry and analytical theory are employed to study the electron diffusion region in asymmetric reconnection with a guide magnetic field. The analysis presented here demonstrates that similar to the case without guide field, in-plane flow stagnation and null of the in-plane magnetic field are well separated. In addition, it is shown that the electric field at the local magnetic X point is again dominated by inertial effects, whereas it remains dominated by nongyrotropic pressure effects at the in-plane flow stagnation point. A comparison between local electron Larmor radii and the magnetic gradient scale lengths predicts that distribution should become nongyrotropic in a region enveloping both field reversal and flow stagnation points. This prediction is verified by an analysis of modeled electron distributions, which show clear evidence of mixing in the critical region.

Validation of multi-temperature nozzle flow code NOZNT

NASA Technical Reports Server (NTRS)

Park, Chul; Lee, Seung-Ho

1993-01-01

A computer code NOZNT (Nozzle in n-Temperatures), which calculates one-dimensional flows of partially dissociated and ionized air in an expanding nozzle, is tested against five existing sets of experimental data. The code accounts for: a) the differences among various temperatures, i.e., translational-rotational temperature, vibrational temperatures of individual molecular species, and electron-electronic temperature, b) radiative cooling, and c) the effects of impurities. The experimental data considered are: 1) the sodium line reversal and 2) the electron temperature and density data, both obtained in a shock tunnel, and 3) the spectroscopic emission data, 4) electron beam data on vibrational temperature, and 5) mass-spectrometric species concentration data, all obtained in arc-jet wind tunnels. It is shown that the impurities are most likely responsible for the observed phenomena in shock tunnels. For the arc-jet flows, impurities are inconsequential and the NOZNT code is validated by numerically reproducing the experimental data.

O/S-1/ interactions - The product channels. [collisional electron quenching and chemical reaction pathway frequencies

NASA Technical Reports Server (NTRS)

Slanger, T. G.; Black, G.

1978-01-01

The first measurements are reported of the reaction pathways for the interaction between oxygen atoms in the 4.19 eV S-1 state, and four molecules, N2O, CO2, H2O, and NO. Distinction is made between three possible paths - quenching to O(D-1), quenching to O(P-3), and chemical reaction. With N2O, the most reasonable interpretation of the data indicates that there no reaction, in sharp contrast with the interaction between O(D-1) and N2O, which proceeds entirely by reaction. Similarly, there is no reaction with CO2. With H2O, the reactive pathway is the dominant one, although electronic quenching is not negligible. With NO, O(D-1) is the preferred product.

Quantum decoherence in electronic current flowing through carbon nanotubes induced by thermal atomic vibrations

NASA Astrophysics Data System (ADS)

Ishizeki, Keisuke; Sasaoka, Kenji; Konabe, Satoru; Souma, Satofumi; Yamamoto, Takahiro

2018-06-01

We theoretically investigate quantum decoherence in electronic currents flowing through metallic carbon nanotubes caused by thermal atomic vibrations using the time-dependent Schrödinger equation for an open system. We reveal that the quantum coherence of conduction electrons decays exponentially with tube length at a fixed temperature, and that the decay rate increases with temperature. We also find that the phase relaxation length due to the thermal atomic vibrations is inversely proportional to temperature.

Quantum Computational Studies of Electron Transfer in Respiratory Complex III and its Application for Designing New Mitocan Drugs

NASA Astrophysics Data System (ADS)

Hagras, Muhammad Ahmed

Electron transfer occurs in many biological systems which are imperative to sustain life; oxidative phosphorylation in prokaryotes and eukaryotes, and photophosphorylation in photosynthetic and plant cells are well-balanced and complementary processes. Investigating electron transfer in those natural systems provides detailed knowledge of the atomistic events that lead eventually to production of ATP, or harvesting light energy. Ubiquinol:cytochrome c oxidoreductase complex (also known as bc 1 complex, or respiratory complex III) is a middle player in the electron transport proton pumping orchestra, located in the inner-mitochondrial membrane in eukaryotes or plasma membrane in prokaryotes, which converts the free energy of redox reactions to electrochemical proton gradient across the membrane, following the fundamental chemiosmotic principle discovered by Peter Mitchell 1. In humans, the malfunctioned bc1 complex plays a major role in many neurodegenerative diseases, stress-induced aging, and cancer development, because it produces most of the reactive oxygen species, which are also involved in cellular signaling 2. The mitochondrial bc1 complex has an intertwined dimeric structure comprised of 11 subunits in each monomer, but only three of them have catalytic function, and those are the only domains found in bacterial bc1 complex. The core subunits include: Rieske domain, which incorporates iron-sulfur cluster [2Fe-2S]; trans-membrane cytochrome b domain, incorporating low-potential heme group (heme b L) and high-potential heme group (heme b H); and cytochrome c1 domain, containing heme c1 group and two separate binding sites, Qo (or QP) site where the hydrophobic electron carrier ubihydroquinol QH2 is oxidized, and Qi (or QN) site where ubiquinone molecule Q is reduced 3. Electrons and protons in the bc1 complex flow according to the proton-motive Q-cycle proposed by Mitchell, which includes a unique electron flow bifurcation at the Qo site. At this site, one electron of a bound QH2 molecule transfers to [2Fe-2S] cluster of the Rieske domain, docked at the proximal docking site, and another electron transfers to heme b L , which subsequently passes it to heme bH , and finally to Q or SQ molecule bound at the Qi-site 4. Rieske domain undergoes a domain movement 22 A to bind at the distal docking site, where [2Fe-2S] cluster passes its electron to heme c1, which in turn passes it to heme c of the water-soluble cytochrome c carrier 3c, 5 (which shuttles it to cytochrome c oxidase, complex IV). In the current compiled work presented in the subsequent chapters, we deployed a stacking tiers hierarchy where each chapter's work presents a foundation for the next one. In chapter 1, we first present different methods to calculate tunneling currents in proteins including a new derivation method for the inter-atomic tunneling current method. In addition, we show the results of the inter-atomic tunneling current theory on models based on heme bL-heme bH redox pair system in bc1 complex. Afterwards, in chapter 2, we examine the electron tunneling pathways 6 between different intra-monomeric and inter-monomeric redox centers of bc1 complex, including its electron carriers - ubiquinol, ubiquinone, and cytochrome c molecules, using the well-studied coarse-grained interatomic method of the tunneling current theory 7. Going through the different tunneling pathways in bc1 complex, we discovered a pair of internal switches that modulate the electron transfer rate which we discuss in full details in chapter 3. Motivated by the discovery of those internal switches, we discuss in chapter 4 the discovery of a new binding pocket (designated as NonQ-site or NQ-site for short) in bc 1 complex which is located at the opposite side of the enzyme with respect to Qo site. In contrast to Qo site, however, the NQ-site penetrates deeply in the cytochrome b domain and reaches very closely the LH region. Hence the NQ-site provides a suitable binding pocket for ligands that can influence the orientation of Phe90 residue, and hence modulate the corresponding ET rate between heme b L and heme bH. Finally we present in chapter 5 our unique integrated software package (called Electron Tunneling in Proteins Program or ETP) which provides an environment with different capabilities such as tunneling current calculation, semi-empirical quantum mechanical calculation and molecular modeling simulation for calculation and analysis of electron transfer reactions in proteins.

Characterization of cell death caused by diplodiatoxin and dipmatol, toxic metabolites of Stenocarpella maydis.

PubMed

Masango, Mxolisi G; Ellis, Charlotte E; Botha, Christo J

2015-08-01

Diplodiosis, a neuromycotoxicosis of cattle and sheep grazing on mouldy cobs infected by Stenocarpella maydis, is considered the last major veterinary mycotoxicosis for which the causative mycotoxin is still unknown. The current study was aimed at characterizing the cell death observed in mouse neuroblastoma (Neuro-2a), Chinese hamster ovary (CHO-K1) and Madin-Darby bovine kidney (MDBK) cell lines exposed to the S. maydis metabolites (i.e. diplodiatoxin and dipmatol) by investigating the roles of necrosis and apoptosis. Necrosis was investigated using the lactate dehydrogenase (LDH) leakage and propidium iodide (PI) flow cytometry assays and apoptosis was evaluated using the caspase-3/7 and Annexin V flow cytometry assays. In addition, transmission electron microscopy (TEM) was used to correlate the cell death pathways observed in this study with their typical morphologies. Both diplodiatoxin and dipmatol (750 μM) induced necrosis and caspase-dependent apoptosis in Neuro-2a, CHO-K1 and MDBK cells. Ultrastructurally, the two mycotoxins induced mitochondrial damage, cytoplasmic vacuolation and nuclear fragmentation in the three cell lines. These findings have laid a foundation for future studies aimed at elucidating in detail the mechanism of action of the S. maydis metabolites. Copyright © 2015 Elsevier Ltd. All rights reserved.

On understanding nuclear reaction network flows with branchings on directed graphs

NASA Astrophysics Data System (ADS)

Meyer, Bradley S.

2018-04-01

Nuclear reaction network flow diagrams are useful for understanding which reactions are governing the abundance changes at a particular time during nucleosynthesis. This is especially true when the flows are largely unidirectional, such as during the s-process of nucleosynthesis. In explosive nucleosynthesis, when reaction flows are large, and when forward reactions are nearly balanced by their reverses, reaction flows no longer give a clear picture of the abundance evolution in the network. This paper presents a way of understanding network evolution in terms of sums of branchings on a directed graph, which extends the concept of reaction flows to allow for multiple reaction pathways.

A Proteomic View at the Biochemistry of Syntrophic Butyrate Oxidation in Syntrophomonas wolfei

PubMed Central

Schmidt, Alexander; Müller, Nicolai; Schink, Bernhard; Schleheck, David

2013-01-01

In syntrophic conversion of butyrate to methane and CO2, butyrate is oxidized to acetate by secondary fermenting bacteria such as Syntrophomonas wolfei in close cooperation with methanogenic partner organisms, e.g., Methanospirillum hungatei. This process involves an energetically unfavourable shift of electrons from the level of butyryl-CoA oxidation to the substantially lower redox potential of proton and/or CO2 reduction, in order to transfer these electrons to the methanogenic partner via hydrogen and/or formate. In the present study, all prominent membrane-bound and soluble proteins expressed in S. wolfei specifically during syntrophic growth with butyrate, in comparison to pure-culture growth with crotonate, were examined by one- and two-dimensional gel electrophoresis, and identified by peptide fingerprinting-mass spectrometry. A membrane-bound, externally oriented, quinone-linked formate dehydrogenase complex was expressed at high level specifically during syntrophic butyrate oxidation, comprising a selenocystein-linked catalytic subunit with a membrane-translocation pathway signal (TAT), a membrane-bound iron-sulfur subunit, and a membrane-bound cytochrome. Soluble hydrogenases were expressed at high levels specifically during growth with crotonate. The results were confirmed by native protein gel electrophoresis, by formate dehydrogenase and hydrogenase-activity staining, and by analysis of formate dehydrogenase and hydrogenase activities in intact cells and cell extracts. Furthermore, constitutive expression of a membrane-bound, internally oriented iron-sulfur oxidoreductase (DUF224) was confirmed, together with expression of soluble electron-transfer flavoproteins (EtfAB) and two previously identified butyryl-CoA dehydrogenases. Our findings allow to depict an electron flow scheme for syntrophic butyrate oxidation in S. wolfei. Electrons derived from butyryl-CoA are transferred through a membrane-bound EtfAB:quinone oxidoreductase (DUF224) to a menaquinone cycle and further via a b-type cytochrome to an externally oriented formate dehydrogenase. Hence, an ATP hydrolysis-driven proton-motive force across the cytoplasmatic membrane would provide the energy input for the electron potential shift necessary for formate formation. PMID:23468890

Biochemistry, physiology and biotechnology of sulfate-reducing bacteria.

PubMed

Barton, Larry L; Fauque, Guy D

2009-01-01

Chemolithotrophic bacteria that use sulfate as terminal electron acceptor (sulfate-reducing bacteria) constitute a unique physiological group of microorganisms that couple anaerobic electron transport to ATP synthesis. These bacteria (220 species of 60 genera) can use a large variety of compounds as electron donors and to mediate electron flow they have a vast array of proteins with redox active metal groups. This chapter deals with the distribution in the environment and the major physiological and metabolic characteristics of sulfate-reducing bacteria (SRB). This chapter presents our current knowledge of soluble electron transfer proteins and transmembrane redox complexes that are playing an essential role in the dissimilatory sulfate reduction pathway of SRB of the genus Desulfovibrio. Environmentally important activities displayed by SRB are a consequence of the unique electron transport components or the production of high levels of H(2)S. The capability of SRB to utilize hydrocarbons in pure cultures and consortia has resulted in using these bacteria for bioremediation of BTEX (benzene, toluene, ethylbenzene and xylene) compounds in contaminated soils. Specific strains of SRB are capable of reducing 3-chlorobenzoate, chloroethenes, or nitroaromatic compounds and this has resulted in proposals to use SRB for bioremediation of environments containing trinitrotoluene and polychloroethenes. Since SRB have displayed dissimilatory reduction of U(VI) and Cr(VI), several biotechnology procedures have been proposed for using SRB in bioremediation of toxic metals. Additional non-specific metal reductase activity has resulted in using SRB for recovery of precious metals (e.g. platinum, palladium and gold) from waste streams. Since bacterially produced sulfide contributes to the souring of oil fields, corrosion of concrete, and discoloration of stonework is a serious problem, there is considerable interest in controlling the sulfidogenic activity of the SRB. The production of biosulfide by SRB has led to immobilization of toxic metals and reduction of textile dyes, although the process remains unresolved, SRB play a role in anaerobic methane oxidation which not only contributes to carbon cycle activities but also depletes an important industrial energy reserve.

Role of the ring current in the dynamics of fluctuating electron and ion flows in the low-latitude magnetosphere

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

Shyutte, N.M.; Izhovkina, N.I.

1987-11-01

Electron and ion flows with fluctuating energy spectra show up on the low L-shells. The authors have discovered that these flows show up less frequently as the absolute value of D/sub st/ increases (for D/sub st/ < 0). Their results are based on data from Kosmos-900. Our results are based on data from Kosmos-900. Their estimates indicate that one of the reasons for this phenomenon may be strong nonlinear diffusion of charged particle flows in VLF waves in the waveguide channels which have been detected at the boundary of the plasmasphere

A Model of Titan-like Chemistry to Connect Experiments and Cassini Observations

NASA Astrophysics Data System (ADS)

Raymond, Alexander W.; Sciamma-O’Brien, Ella; Salama, Farid; Mazur, Eric

2018-02-01

A numerical model is presented for interpreting the chemical pathways that lead to the experimental mass spectra acquired in the Titan Haze Simulation (THS) laboratory experiments and for comparing the electron density and temperature of the THS plasma to observations made at Titan by the Cassini spacecraft. The THS plasma is a pulsed glow-discharge experiment designed to simulate the reaction of N2/CH4-dominated gas in Titan's upper atmosphere. The transient, one-dimensional model of THS chemistry tracks the evolution of more than 120 species in the direction of the plasma flow. As the minor species C2H2 and C2H4 are added to the N2/CH4-based mixture, the model correctly predicts the emergence of reaction products with up to five carbon atoms in relative abundances that agree well with measured mass spectra. Chemical growth in Titan's upper atmosphere transpires through ion–neutral and neutral–neutral chemistry, and the main reactions involving a series of known atmospheric species are retrieved from the calculation. The model indicates that the electron density and chemistry are steady during more than 99% of the 300 μs long discharge pulse. The model also suggests that the THS ionization fraction and electron temperature are comparable to those measured in Titan's upper atmosphere. These findings reaffirm that the THS plasma is a controlled analog environment for studying the first and intermediate steps of chemistry in Titan's upper atmosphere.

Modeling of nitrous oxide production by autotrophic ammonia-oxidizing bacteria with multiple production pathways.

PubMed

Ni, Bing-Jie; Peng, Lai; Law, Yingyu; Guo, Jianhua; Yuan, Zhiguo

2014-04-01

Autotrophic ammonia oxidizing bacteria (AOB) have been recognized as a major contributor to N2O production in wastewater treatment systems. However, so far N2O models have been proposed based on a single N2O production pathway by AOB, and there is still a lack of effective approach for the integration of these models. In this work, an integrated mathematical model that considers multiple production pathways is developed to describe N2O production by AOB. The pathways considered include the nitrifier denitrification pathway (N2O as the final product of AOB denitrification with NO2(-) as the terminal electron acceptor) and the hydroxylamine (NH2OH) pathway (N2O as a byproduct of incomplete oxidation of NH2OH to NO2(-)). In this model, the oxidation and reduction processes are modeled separately, with intracellular electron carriers introduced to link the two types of processes. The model is calibrated and validated using experimental data obtained with two independent nitrifying cultures. The model satisfactorily describes the N2O data from both systems. The model also predicts shifts of the dominating pathway at various dissolved oxygen (DO) and nitrite levels, consistent with previous hypotheses. This unified model is expected to enhance our ability to predict N2O production by AOB in wastewater treatment systems under varying operational conditions.

Proton gradient regulation 5 supports linear electron flow to oxidize photosystem I.

PubMed

Takagi, Daisuke; Miyake, Chikahiro

2018-03-31

In higher plants, light drives the linear photosynthetic electron transport reaction from H 2 O to electron sinks, which is called as linear electron flow (LEF). LEF activity should be regulated depending on electron sinks; otherwise excess electrons accumulate in the thylakoid membranes and stimulate reactive oxygen species (ROS) production in photosystem I (PSI), which causes oxidative damage to PSI. To prevent ROS production in PSI, PSI should be oxidized during photosynthesis, and PROTON GRADIENT REGULATION 5 (PGR5) and PGR like 1 (PGRL1) are important to oxidized PSI. PGR5 and PGRL1 are recognized as a component of ferredoxin-dependent cyclic electron flow around PSI (Fd-CEF-PSI), however there is no direct evidence for the significant operation of Fd-CEF-PSI during photosynthesis in wild-type (WT) plants. Thus, electron distribution by PGR5 and PGRL1 between Fd-CEF-PSI and LEF is still elusive. Here, we show direct evidence that Fd-CEF-PSI activity is minor during steady state photosynthesis by measuring the Fd redox state in vivo in Arabidopsis thaliana. We found that Fd oxidation rate is determined by LEF activity during steady state photosynthesis in WT. On the other hand, pgr5 and pgrl1 showed lower electron transport efficiency from PSI to electron sinks through Fd during steady state photosynthesis. These results demonstrate that electrons are exclusively consumed in electron sinks through Fd, and the phenotypes of pgr5 and pgrl1 are likely caused by the disturbance of the LEF between PSI and electron sinks. We suggest that PGR5 and PGRL1 modulate the LEF according to electron sink activities around PSI. This article is protected by copyright. All rights reserved.

TGLF Recalibration for ITER Standard Case Parameters FY2015: Theory and Simulation Performance Target Final Report

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

Candy, J.

2015-12-01

This work was motivated by the observation, as early as 2008, that GYRO simulations of some ITER operating scenarios exhibited nonlinear zonal-flow generation large enough to effectively quench turbulence inside r /a ~ 0.5. This observation of flow-dominated, low-transport states persisted even as more accurate and comprehensive predictions of ITER profiles were made using the state-of-the-art TGLF transport model. This core stabilization is in stark contrast to GYRO-TGLF comparisons for modern-day tokamaks, for which GYRO and TGLF are typically in very close agreement. So, we began to suspect that TGLF needed to be generalized to include the effect of zonal-flowmore » stabilization in order to be more accurate for the conditions of reactor simulations. While the precise cause of the GYRO-TGLF discrepancy for ITER parameters was not known, it was speculated that closeness to threshold in the absence of driven rotation, as well as electromagnetic stabilization, created conditions more sensitive the self-generated zonal-flow stabilization than in modern tokamaks. Need for nonlinear zonal-flow stabilization: To explore the inclusion of a zonal-flow stabilization mechanism in TGLF, we started with a nominal ITER profile predicted by TGLF, and then performed linear and nonlinear GYRO simulations to characterize the behavior at and slightly above the nominal temperature gradients for finite levels of energy transport. Then, we ran TGLF on these cases to see where the discrepancies were largest. The predicted ITER profiles were indeed near to the TGLF threshold over most of the plasma core in the hybrid discharge studied (weak magnetic shear, q > 1). Scanning temperature gradients above the TGLF power balance values also showed that TGLF overpredicted the electron energy transport in the low-collisionality ITER plasma. At first (in Q3), a model of only the zonal-flow stabilization (Dimits shift) was attempted. Although we were able to construct an ad hoc model of the zonal flows that fit the GYRO simulations, the parameters of the model had to be tuned to each case. A physics basis for the zonal flow model was lacking. Electron energy transport at short wavelength: A secondary issue – the high-k electron energy flux – was initially assumed to be independent of the zonal flow effect. However, detailed studies of the fluctuation spectra from recent multiscale (electron and ion scale) GYRO simulations provided a critical new insight into the role of zonal flows. The multiscale simulations suggested that advection by the zonal flows strongly suppressed electron-scale turbulence. Radial shear of the zonal E×B fluctuation could not compete with the large electron-scale linear growth rate, but the k x-mixing rate of the E×B advection could. This insight led to a preliminary new model for the way zonal flows saturate both electron- and ion-scale turbulence. It was also discovered that the strength of the zonal E×B velocity could be computed from the linear growth rate spectrum. The new saturation model (SAT1), which replaces the original model (SAT0), was fit to the multiscale GYRO simulations as well as the ion-scale GYRO simulations used to calibrate the original SAT0 model. Thus, SAT1 captures the physics of both multiscale electron transport and zonal-flow stabilization. In future work, the SAT1 model will require significant further testing and (expensive) calibration with nonlinear multiscale gyrokinetic simulations over a wider variety of plasma conditions – certainly more than the small set of scans about a single C-Mod L-mode discharge. We believe the SAT1 model holds great promise as a physics-based model of the multiscale turbulent transport in fusion devices. Correction to ITER performance predictions: Finally, the impact of the SAT1model on the ITER hybrid case is mixed. Without the electron-scale contribution to the fluxes, the Dimits shift makes a significant improvement in the predicted fusion power as originally posited. Alas, including the high-k electron transport reduces the improvement, yielding a modest net increase in predicted fusion power compared to the TGLF prediction with the original SAT0 model.« less

Shear flow driven tripolar vortices in a nonuniform electron-ion magnetoplasma with non-Maxwellian electrons

NASA Astrophysics Data System (ADS)

Masood, W.; Mirza, Arshad M.

2014-04-01

A set of nonlinear equations governing the dynamics of finite amplitude drift-ion acoustic-waves is derived for sheared ion flows parallel and perpendicular to the ambient magnetic field in the presence of Cairns and Kappa distributed electrons. It is shown that stationary solution of the nonlinear equations can be represented in the form of a tripolar vortex for specific profiles of the equilibrium sheared flows. The tripolar vortices are, however, observed to form on a scale of the order of ion Larmor radius ρ i which is calculated to be around a Kilometer for the plasma parameters found in the Saturn's E-ring. The relevance of the present investigation in planetary environments is also pointed out.

Disentangling nutrient concentrations trends in transfer pathways of agricultural watersheds

NASA Astrophysics Data System (ADS)

Mellander, P. E.; Jordan, P.

2017-12-01

Targeted schemes designed to attenuate agricultural pollution to water are needed to reach goals of sustainable food production. Such approaches require insight into temporal and spatial variability in the most representative flows and active pollution transfer pathways. Interpreting changes in total stream flow can be misleading since some changes may only be apparent in specific pathways. The aim of this study was to investigate changing land use pressures on water quality. The objectives were to assess intra-annual and inter-annual changes in phosphorus (P) and nitrogen (N) concentrations and loads in apportioned pathways. Pathways were separated using hydrograph and loadograph separation techniques on a seven-year dataset of sub-hourly river discharge and concentrations of NO3-N, reactive P and total P in two intensively managed agricultural watersheds of contrasting hydrology in Ireland. Active transfer pathways were dictated by soil drainage. There were intra-annual variability in both P and N concentrations in different pathways and loads, and these had the largest influence of all-year baseflow (BF) concentrations and summer quickflow (QF) concentrations. Nutrient loss responded to seasonality in the river discharge in all pathways in both watersheds and was mostly transport limited. In both watersheds there were inter-annual trends in P concentration in some pathways and seasons that did not correspond to the trend of total river P concentration. The response in stream water quality to management, mitigation measures and changes in weather may be hidden by counteracting responses in different pathways. The hydrology had a major impact on seasonal changes in N and P loss. By apportioning different transfer pathways more information on the temporal and site-specific nature of nutrient transfer was provided. BF and QF pathways largely contributed to the river P concentrations in summer while all pathways contributed to the P and N loads in wintertime. The data indicated that increasing trends in river P concentrations were mostly linked to trends in BF concentration in both catchment types. This may be explained by increased point source influence, increased vertical transfer through increased soil P loading, or decreased stream bed attenuation. Each will require different policy considerations.

Transfer of the cytochrome P450-dependent dhurrin pathway from Sorghum bicolor into Nicotiana tabacum chloroplasts for light-driven synthesis

PubMed Central

Gnanasekaran, Thiyagarajan; Karcher, Daniel; Nielsen, Agnieszka Zygadlo; Martens, Helle Juel; Ruf, Stephanie; Kroop, Xenia; Olsen, Carl Erik; Motawie, Mohammed Saddik; Pribil, Mathias; Møller, Birger Lindberg; Bock, Ralph; Jensen, Poul Erik

2016-01-01

Plant chloroplasts are light-driven cell factories that have great potential to act as a chassis for metabolic engineering applications. Using plant chloroplasts, we demonstrate how photosynthetic reducing power can drive a metabolic pathway to synthesise a bio-active natural product. For this purpose, we stably engineered the dhurrin pathway from Sorghum bicolor into the chloroplasts of Nicotiana tabacum (tobacco). Dhurrin is a cyanogenic glucoside and its synthesis from the amino acid tyrosine is catalysed by two membrane-bound cytochrome P450 enzymes (CYP79A1 and CYP71E1) and a soluble glucosyltransferase (UGT85B1), and is dependent on electron transfer from a P450 oxidoreductase. The entire pathway was introduced into the chloroplast by integrating CYP79A1, CYP71E1, and UGT85B1 into a neutral site of the N. tabacum chloroplast genome. The two P450s and the UGT85B1 were functional when expressed in the chloroplasts and converted endogenous tyrosine into dhurrin using electrons derived directly from the photosynthetic electron transport chain, without the need for the presence of an NADPH-dependent P450 oxidoreductase. The dhurrin produced in the engineered plants amounted to 0.1–0.2% of leaf dry weight compared to 6% in sorghum. The results obtained pave the way for plant P450s involved in the synthesis of economically important compounds to be engineered into the thylakoid membrane of chloroplasts, and demonstrate that their full catalytic cycle can be driven directly by photosynthesis-derived electrons. PMID:26969746

Root carbon flow from an invasive plant to belowground foodwebs

Treesearch

Mark A. Bradford; Michael S. Strickland; Jayna L. DeVore; John C. Maerz

2012-01-01

Aims Soil foodwebs are based on plant production. This production enters belowground foodwebs via numerous pathways, with root pathways likely dominating supply. Indeed, root exudation may fuel 30–50 % of belowground activity with photosynthate fixed only hours earlier. Yet we have limited knowledge of root fluxes of recent-photosynthate from invasive plants to...

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.

Commonalities and differences in plants deficient in autophagy and alternative pathways of respiration on response to extended darkness.

PubMed

Barros, Jessica A S; Cavalcanti, João Henrique F; Medeiros, David B; Nunes-Nesi, Adriano; Avin-Wittenberg, Tamar; Fernie, Alisdair R; Araújo, Wagner L

2017-11-02

Autophagy is a highly conserved cellular mechanism in eukaryotes allowing the degradation of cell constituents. It is of crucial significance in both cellular homeostasis and nutrient recycling. During energy limited conditions plant cells can metabolize alternative respiratory substrates, such as amino acids, providing electrons to the mitochondrial metabolism via the tricarboxylic acid (TCA) cycle or electron transfer flavoprotein/ electron transfer flavoprotein ubiquinone oxidoreductase (ETF/ETFQO) system. Our recent study reveals the importance of autophagy in the supply of amino acids to provide energy through alternative pathways of respiration during carbon starvation. This fact apart, autophagy seems to have more generalized effects related not only to amino acid catabolism but also to metabolism in general. By further comparing the metabolic data obtained with atg mutants with those of mutants involved in the alternative pathways of respiration, we observed clear differences between these mutants, pointing out additional effects of the autophagy deficiency on metabolism of Arabidopsis leaves. Collectively, our data point to an interdependence between mitochondrial metabolism and autophagy and suggest an exquisite regulation of primary metabolism under low energetic conditions.

A study of information management in the patient surgical pathway in NHSScotland.

PubMed

Bouamrane, Matt-Mouley; Mair, Frances S

2013-01-01

We conducted a study of information management processes across the patient surgical pathway in NHSScotland. While the majority of general practitioners (GPs) consider electronic medical records systems as an essential and integral part of their work during the patient consultation, many were not fully satisfied with the functionalities of these systems. A majority of GPs considered that the national eReferral system streamlined referral processes. Almost all GPs reported marked variability in the quality of discharge information. Preoperative processes vary significantly across Scotland, with most services using paper-based systems. Insufficient use is made of information provided through the patient electronic referral leading to a considerable duplication of tasks already performed in primary care. Three health-boards have implemented electronic preoperative information systems. These have transformed clinical practices and facilitated communication and information-sharing among the multi-disciplinary team and within the health-boards. Substantial progress has been made towards improving information transfer and sharing within the surgical pathway in recent years. However, there remains scope for further improvements at the interface between services.

Transforming exoelectrogens for biotechnology using synthetic biology.

PubMed

TerAvest, Michaela A; Ajo-Franklin, Caroline M

2016-04-01

Extracellular electron transfer pathways allow certain bacteria to transfer energy between intracellular chemical energy stores and extracellular solids through redox reactions. Microorganisms containing these pathways, exoelectrogens, are a critical part of microbial electrochemical technologies that aim to impact applications in bioenergy, biosensing, and biocomputing. However, there are not yet any examples of economically viable microbial electrochemical technologies due to the limitations of naturally occurring exoelectrogens. Here we first briefly summarize recent discoveries in understanding extracellular electron transfer pathways, then review in-depth the creation of customized and novel exoelectrogens for biotechnological applications. We analyze engineering efforts to increase current production in native exoelectrogens, which reveals that modulating certain processes within extracellular electron transfer are more effective than others. We also review efforts to create new exoelectrogens and highlight common challenges in this work. Lastly, we summarize work utilizing engineered exoelectrogens for biotechnological applications and the key obstacles to their future development. Fueled by the development of genetic tools, these approaches will continue to expand and genetically modified organisms will continue to improve the outlook for microbial electrochemical technologies. © 2015 Wiley Periodicals, Inc.

Non-isomorphic radial wavenumber dependencies of residual zonal flows in ion and electron Larmor radius scales, and effects of initial parallel flow and electromagnetic potentials in a circular tokamak

NASA Astrophysics Data System (ADS)

Yamagishi, Osamu

2018-04-01

Radial wavenumber dependencies of the residual zonal potential for E × B flow in a circular, large aspect ratio tokamak is investigated by means of the collisionless gyrokinetic simulations of Rosenbluth-Hinton (RH) test and the semi-analytic approach using an analytic solution of the gyrokinetic equation Rosenbluth and Hinton (1998 Phys. Rev. Lett. 80 724). By increasing the radial wavenumber from an ion Larmor radius scale {k}r{ρ }i≲ 1 to an electron Larmor radius scale {k}r{ρ }e≲ 1, the well-known level ˜ O[1/(1+1.6{q}2/\\sqrt{r/{R}0})] is retained, while the level remains O(1) when the wavenumber is decreased from the electron to the ion Larmor radius scale, if physically same adiabatic assumption is presumed for species other than the main species that is treated kinetically. The conclusion is not modified by treating both species kinetically, so that in the intermediate scale between the ion and electron Larmor radius scale it seems difficult to determine the level uniquely. The toroidal momentum conservation property in the RH test is also investigated by including an initial parallel flow in addition to the perpendicular flow. It is shown that by taking a balance between the initial parallel flow and perpendicular flows which include both E × B flow and diamagnetic flow in the initial condition, the mechanical toroidal angular momentum is approximately conserved despite the toroidal symmetry breaking due to the finite radial wavenumber zonal modes. Effect of electromagnetic potentials is also investigated. When the electromagnetic potentials are applied initially, fast oscillations which are faster than the geodesic acoustic modes are introduced in the decay phase of the zonal modes. Although the residual level in the long time limit is not modified, this can make the time required to reach the stationary zonal flows longer and may weaken the effectiveness of the turbulent transport suppression by the zonal flows.

Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens

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

Feist, AM; Nagarajan, H; Rotaru, AE

2014-04-24

Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO2 fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically withmore » formate and Fe(III) was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III), nitrate, and fumarate) by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species. Author Summary The ability of microorganisms to exchange electrons directly with their environment has large implications for our knowledge of industrial and environmental processes. For decades, it has been known that microbes can use electrodes as electron acceptors in microbial fuel cell settings. Geobacter metallireducens has been one of the model organisms for characterizing microbe-electrode interactions as well as environmental processes such as bioremediation. Here, we significantly expand the knowledge of metabolism and energetics of this model organism by employing constraint-based metabolic modeling. Through this analysis, we build the metabolic pathways necessary for carbon fixation, a desirable property for industrial chemical production. We further discover a novel growth condition which enables the characterization of autotrophic (i.e., carbon-fixing) metabolism in Geobacter. Importantly, our systems-level modeling approach helped elucidate the key metabolic pathways and the energetic cost associated with extracellular electron transfer. This model can be applied to characterize and engineer the metabolism and electron transfer capabilities of Geobacter for biotechnological applications.« less

Stormwater infiltration and the 'urban karst' - A review

NASA Astrophysics Data System (ADS)

Bonneau, Jeremie; Fletcher, Tim D.; Costelloe, Justin F.; Burns, Matthew J.

2017-09-01

The covering of native soils with impervious surfaces (e.g. roofs, roads, and pavement) prevents infiltration of rainfall into the ground, resulting in increased surface runoff and decreased groundwater recharge. When this excess water is managed using stormwater drainage systems, flow and water quality regimes of urban streams are severely altered, leading to the degradation of their ecosystems. Urban streams restoration requires alternative approaches towards stormwater management, which aim to restore the flow regime towards pre-development conditions. The practice of stormwater infiltration-achieved using a range of stormwater source-control measures (SCMs)-is central to restoring baseflow. Despite this, little is known about what happens to the infiltrated water. Current knowledge about the impact of stormwater infiltration on flow regimes was reviewed. Infiltration systems were found to be efficient at attenuating high-flow hydrology (reducing peak magnitudes and frequencies) at a range of scales (parcel, streetscape, catchment). Several modelling studies predict a positive impact of stormwater infiltration on baseflow, and empirical evidence is emerging, but the fate of infiltrated stormwater remains unclear. It is not known how infiltrated water travels along the subsurface pathways that characterise the urban environment, in particular the 'urban karst', which results from networks of human-made subsurface pathways, e.g. stormwater and sanitary sewer pipes and associated high permeability trenches. Seepage of groundwater into and around such pipes is possible, meaning some infiltrated stormwater could travel along artificial pathways. The catchment-scale ability of infiltration systems to restore groundwater recharge and baseflow is thus ambiguous. Further understanding of the fate of infiltrated stormwater is required to ensure infiltration systems deliver optimal outcomes for waterway flow regimes.

The Use of Chemical Probes for the Characterization of the Predominant Abiotic Reductants in Anaerobic Sediments

EPA Science Inventory

Identifying the predominant chemical reductants and pathways for electron transfer in anaerobic systems is paramount to the development of environmental fate models that incorporate pathways for abiotic reductive transformations. Currently, such models do not exist. In this chapt...

Early time evolution of a chemically produced electron depletion

NASA Technical Reports Server (NTRS)

Scales, W. A.; Bernhardt, P. A.; Ganguli, G.

1995-01-01

The early time evolution of an ionospheric electron depletion produced by a radially expanding electron attachment chemical release is studied with a two-dimensional simulation model. The model includes electron attachment chemistry, incorporates fluid electrons, particle ions and neutrals, and considers the evolution in a plane perpendicular to the geomagnetic field for a low beta plasma. Timescales considered are of the order of or less than the cyclotron period of the negative ions that result as a by-product of the electron attacment reaction. This corresponds to time periods of tenths of seconds during recent experiemts. Simulation results show that a highly sheared azimuthal electron flow velocity develops in the radially expanding depletion boundary. This sheared electron flow velocity and the steep density gradients in the boundary give rise to small-scale irregulatities in the form of electron density cavities and spikes. The nonlinear evolution of these irregularities results in trapping and ultimately turbulent heating of the negative ions.

Plasma Relaxation and Topological Aspects in Electron Magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Shivamoggi, Bhimsen

2016-10-01

Parker's formulation of isotopological plasma relaxation process toward minimum magnetics energy states in magnetohydrodynamics (MHD) is extended to electron MHD (EMHD). The lower bound on magnetic energy in EMHD is determined by both the magnetic field and the electron vorticity field topologies, and is shown to be reduced further in EMHD by an amount proportional to the sum of total electron-flow kinetic energy and total electron-flow enstrophy. The EMHD Beltrami condition becomes equivalent to the potential vorticity conservation equation in two-dimensional (2D) hydrodynamics, and the torsion coefficient and turns out to be proportional to potential vorticity. The winding pattern of the magnetic field lines appears to evolve therefore in the same way as potential vorticity lines in 2D hydrodynamics.

Plasma relaxation and topological aspects in electron magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Shivamoggi, B. K.

2016-07-01

Parker's formulation of isotopological plasma relaxation process toward minimum magnetics energy states in magnetohydrodynamics (MHD) is extended to electron MHD (EMHD). The lower bound on magnetic energy in EMHD is determined by both the magnetic field and the electron vorticity field topologies, and is shown to be reduced further in EMHD by an amount proportional to the sum of total electron-flow kinetic energy and total electron-flow enstrophy. The EMHD Beltrami condition becomes equivalent to the potential vorticity conservation equation in two-dimensional (2D) hydrodynamics, and the torsion coefficient α turns out to be proportional to potential vorticity. The winding pattern of the magnetic field lines appears to evolve, therefore, in the same way as potential vorticity lines in 2D hydrodynamics.

Nutrient enrichment reduces constraints on material flows in a detritus-based food web

Treesearch

Wyatt F. Cross; Bruce Wallace; Amy D. Rosemond

2007-01-01

Most aquatic and terrestrial ecosystems are experiencing increased nutrient availability, which is affecting their structure and function. By altering community composition and productivity of consumers, enrichment can indirectly cause changes in the pathways and magnitude of material flows in food webs. These changes, in turn, have major consequences for material...

Impacts of the Conversion of Forest to Arable Land and Long Term Agriculture Practices on the Water Pathways in Southern Brazil

NASA Astrophysics Data System (ADS)

Robinet, J.; Minella, J. P. G.; Schlesner, A.; Lücke, A.; Ameijeiras-Marino, Y.; Opfergelt, S.; Vanderborght, J.; Gerard, G.

2017-12-01

Changes in runoff pathways affect many environmental processes. Land use change (LUC), and more specifically forest conversion to arable land, is one of the controls of water fluxes at the hillslope or catchment scale. Still, the long term effects of forest conversion and agricultural activities in (sub-) tropical environments have been relatively understudied. Our objective was therefore to study the impact of deforestation and land degradation through agriculture on runoff pathways. We selected two small catchments with contrasting land use (agriculture vs. natural forest) in a subtropical region in the south of Brazil. Stream-, pore-, subsurface- and rainwater were monitored, sampled and analyzed for Dissolve Silicon concentration (DSi) and δ18O isotopic signature. Both forested and agricultural catchments were highly responsive to rainfall event and only 2 runoff components contributed to the stream discharge were identified: baseflow and peak flow components. The δ18O peak flow signal in the agricultural catchment was closely related to the δ18O rainfall signal. In the forested catchment, the δ18O peak flow signal was similar to a seasonally averaged signal. This suggested that most peak flow was derived from current rainfall events in the agricultural catchment, while being derived from a mixed reservoir in the forested one. The DSi of the peak flow was low in both catchments. Hence, the mixing in the forested catchment cannot have taken place in the soil matrix as the soil pore water contained high DSi concentrations. Instead, the mixing must have taken place in a reservoir with a relatively short residence time and isolated, to some extent, from the soil matrix. The dense channel network left by decayed roots in the forest soil above a clay-rich water-impeding B horizon is the most likely candidate and this was confirmed by visual observations. Contributions of other, deeper reservoirs are unlikely given the quick response time of the catchment. Dissolved fluxes at the catchment scale are therefore less likely to be strongly affected by the change in water pathways as, in both catchments, the peak flow component had low solute concentrations. Land use change effects on dissolved loads are likely to be more impacted by the change in water balance caused by forest removal, which leads to a higher water surplus.

Using New Theory and Experimental Methods to Understand the Relative Controls of Storage, Antecedent Conditions and Precipitation Intensity on Transit Time Distributions through a Sloping Soil Lysimeter

NASA Astrophysics Data System (ADS)

Kim, M.; Pangle, L. A.; Cardoso, C.; Lora, M.; Wang, Y.; Harman, C. J.; Troch, P. A. A.

2014-12-01

Transit time distributions (TTD) are an efficient way of characterizing transport through the complex flow dynamics of a hydrologic system, and can serve as a basis for spatially-integrated solute transport modeling. Recently there has been progress in the development of a theory of time-variable TTDs that captures the effect of temporal variability in the timing of fluxes as well as changes in flow pathways. Furthermore, a new formulation of this theory allows the essential transport properties of a system to be parameterized by a physically meaningful time-variable probability distribution, the Ω function. This distribution determines how the age distribution of water in storage is sampled by the outflow. The form of the Ω function varies if the flow pathways change, but is not determined by the timing of fluxes (unlike the TTD). In this study, we use this theory to characterize transport by transient flows through a homogeneously packed 1 m3 sloping soil lysimeter. The transit time distribution associated with each of four irrigation periods (repeated daily for 24 days) are compared to examine the significance of changes in the Ω function due to variations in total storage, antecedent conditions, and precipitation intensity. We observe both the time-variable TTD and the Ω function experimentally by applying the PERTH method (Harman and Kim, 2014, GRL, 41, 1567-1575). The method allows us to observe multiple overlapping time-variable TTD in controlled experiments using only two conservative tracers. We hypothesize that both the TTD and the Ω function will vary in time, even in this small scale, because water will take different flow pathways depending on the initial state of the lysimeter and irrigation intensity. However, based on primarily modeling, we conjecture that major variability in the Ω function will be limited to a period during and immediately after each irrigation. We anticipate the Ω function is almost time-invariant (or scales simply with total storage) during the recession period because flow pathways are stable during this period. This is one of the first experimental studies of this type, and the results offer insights into solute transport in transient, variably-saturated systems.

STEP-TRAMM - A modeling interface for simulating localized rainfall induced shallow landslides and debris flow runout pathways

NASA Astrophysics Data System (ADS)

von Ruette, Jonas; Lehmann, Peter; Fan, Linfeng; Bickel, Samuel; Or, Dani

2017-04-01

Landslides and subsequent debris-flows initiated by rainfall represent a ubiquitous natural hazard in steep mountainous regions. We integrated a landslide hydro-mechanical triggering model and associated debris flow runout pathways with a graphical user interface (GUI) to represent these natural hazards in a wide range of catchments over the globe. The STEP-TRAMM GUI provides process-based locations and sizes of landslides patterns using digital elevation models (DEM) from SRTM database (30 m resolution) linked with soil maps from global database SoilGrids (250 m resolution) and satellite based information on rainfall statistics for the selected region. In a preprocessing step STEP-TRAMM models soil depth distribution and complements soil information that jointly capture key hydrological and mechanical properties relevant to local soil failure representation. In the presentation we will discuss feature of this publicly available platform and compare landslide and debris flow patterns for different regions considering representative intense rainfall events. Model outcomes will be compared for different spatial and temporal resolutions to test applicability of web-based information on elevation and rainfall for hazard assessment.

Diversity and degradation mechanism of an anaerobic bacterial community treating phenolic wastewater with sulfate as an electron acceptor.

PubMed

Guo, X J; Lu, Z Y; Wang, P; Li, H; Huang, Z Z; Lin, K F; Liu, Y D

2015-10-01

Petrochemical wastewater often contains high concentrations of phenol and sulfate that must be properly treated to meet discharge standards. This study acclimated anaerobic-activated sludge to treat saline phenolic wastewater with sulfate reduction and clarified the diversity and degradation mechanism of the microbial community. The active sludge in an upflow anaerobic sludge blanket (UASB) reactor could remove 90 % of phenol and maintain the effluent concentration of SO4 (2-) below 400 mg/L. Cloning and sequencing showed that Clostridium spp. and Desulfotomaculum spp. were major phenol-degrading bacteria. Phenol was probably degraded through the carboxylation pathway and sulfate reduction catalyzed by adenosine-5'-phosphosulfate (APS) reductase and dissimilatory sulfite reductase (DSR). A real-time polymerase chain reaction (RT-PCR) showed that as phenol concentration increased, the quantities of 16S rRNA gene, dsrB, and mcrA in the sludge all decreased. The relative abundance of dsrB dropped to 12.46 %, while that of mcrA increased to 56.18 %. The change in the electron flow ratio suggested that the chemical oxygen demand (COD) was removed mainly by sulfate-reducing bacteria under a phenol concentration of 420 mg/L, whereas it was removed mainly by methanogens above 630 mg/L.

The Kinetic Reaction Mechanism of the Vibrio cholerae Sodium-dependent NADH Dehydrogenase*♦

PubMed Central

Tuz, Karina; Mezic, Katherine G.; Xu, Tianhao; Barquera, Blanca; Juárez, Oscar

2015-01-01

The sodium-dependent NADH dehydrogenase (Na+-NQR) is the main ion transporter in Vibrio cholerae. Its activity is linked to the operation of the respiratory chain and is essential for the development of the pathogenic phenotype. Previous studies have described different aspects of the enzyme, including the electron transfer pathways, sodium pumping structures, cofactor and subunit composition, among others. However, the mechanism of the enzyme remains to be completely elucidated. In this work, we have studied the kinetic mechanism of Na+-NQR with the use of steady state kinetics and stopped flow analysis. Na+-NQR follows a hexa-uni ping-pong mechanism, in which NADH acts as the first substrate, reacts with the enzyme, and the oxidized NAD leaves the catalytic site. In this conformation, the enzyme is able to capture two sodium ions and transport them to the external side of the membrane. In the last step, ubiquinone is bound and reduced, and ubiquinol is released. Our data also demonstrate that the catalytic cycle involves two redox states, the three- and five-electron reduced forms. A model that gathers all available information is proposed to explain the kinetic mechanism of Na+-NQR. This model provides a background to understand the current structural and functional information. PMID:26004776

A Generalized Electron Heat Flow Relation and its Connection to the Thermal Force and the Solar Wind Parallel Electric Field

NASA Astrophysics Data System (ADS)

Scudder, J. D.

2017-12-01

Enroute to a new formulation of the heat law for the solar wind plasma the role of the invariably neglected, but omnipresent, thermal force for the multi-fluid physics of the corona and solar wind expansion will be discussed. This force (a) controls the size of the collisional ion electron energy exchange, favoring the thermal vs supra thermal electrons; (b) occurs whenever heat flux occurs; (c) remains after the electron and ion fluids come to a no slip, zero parallel current, equilibrium; (d) enhances the equilibrium parallel electric field; but (e) has a size that is theoretically independent of the electron collision frequency - allowing its importance to persist far up into the corona where collisions are invariably ignored in first approximation. The constituent parts of the thermal force allow the derivation of a new generalized electron heat flow relation that will be presented. It depends on the separate field aligned divergences of electron and ion pressures and the gradients of the ion gravitational potential and parallel flow energies and is based upon a multi-component electron distribution function. The new terms in this heat law explicitly incorporate the astrophysical context of gradients, acceleration and external forces that make demands on the parallel electric field and quasi-neutrality; essentially all of these effects are missing in traditional formulations.

Kinetic studies of the yeast His-Asp phosphorelay signaling pathway

PubMed Central

Kaserer, Alla O.; Andi, Babak; Cook, Paul F.; West, Ann H.

2010-01-01

For both prokaryotic and eukaryotic His-Asp phosphorelay signaling pathways, the rates of protein phosphorylation and dephosphorylation determine the stimulus-to-response time frame. Thus, kinetic studies of phosphoryl group transfer between signaling partners are important for gaining a full understanding of how the system is regulated. In many cases, the phosphotransfer reactions are too fast for rates to be determined by manual experimentation. Rapid quench flow techniques thus provide a powerful method for studying rapid reactions that occur in the millisecond time frame. In this chapter, we describe experimental design and procedures for kinetic characterization of the yeast SLN1-YPD1-SSK1 osmoregulatory phosphorelay system using a rapid quench flow kinetic instrument. PMID:20946842

Urine collection device

NASA Technical Reports Server (NTRS)

Michaud, R. B. (Inventor)

1981-01-01

A urine collection device for females is described. It is comprised of a collection element defining a urine collection chamber and an inlet opening into the chamber and is adapted to be disposed in surrounding relation to the urethral opening of the user. A drainage conduit is connected to the collection element in communication with the chamber whereby the chamber and conduit together comprise a urine flow pathway for carrying urine generally away from the inlet. A first body of wicking material is mounted adjacent the collection element and extends at least partially into the flow pathway. The device preferably also comprise a vaginal insert element including a seal portion for preventing the entry of urine into the vagina.

40 CFR 89.419 - Dilute gaseous exhaust sampling and analytical system description.

Code of Federal Regulations, 2014 CFR

2014-07-01

... requirements are as follows: (1) This sampling system requires the use of a PDP-CVS and a heat exchanger or a CFV-CVS with either a heat exchanger or electronic flow compensation. Figure 2 in appendix A to this..., either a heat exchanger or electronic flow compensation is required (see Figure 3 in appendix A to this...

40 CFR 89.419 - Dilute gaseous exhaust sampling and analytical system description.

Code of Federal Regulations, 2012 CFR

2012-07-01

... requirements are as follows: (1) This sampling system requires the use of a PDP-CVS and a heat exchanger or a CFV-CVS with either a heat exchanger or electronic flow compensation. Figure 2 in appendix A to this..., either a heat exchanger or electronic flow compensation is required (see Figure 3 in appendix A to this...

40 CFR 89.419 - Dilute gaseous exhaust sampling and analytical system description.

Code of Federal Regulations, 2013 CFR

2013-07-01

... requirements are as follows: (1) This sampling system requires the use of a PDP-CVS and a heat exchanger or a CFV-CVS with either a heat exchanger or electronic flow compensation. Figure 2 in appendix A to this..., either a heat exchanger or electronic flow compensation is required (see Figure 3 in appendix A to this...

Contamination and Micropropulsion Technology

DTIC Science & Technology

2012-07-01

23, 027101 (2011) Evaluation of active flow control applied to wind turbine blade section J. Renewable Sustainable Energy 2, 063101 (2010) Effect...field lines at high latitudes where solar wind electrons can readily access the upper atmosphere. The electron energy distribution in the auroral... slip behavior of n-hexadecane in large amplitude oscillatory shear flow via nonequilibrium molecular dynamic simulation J. Chem. Phys. 136, 104904

40 CFR 89.419 - Dilute gaseous exhaust sampling and analytical system description.

Code of Federal Regulations, 2011 CFR

2011-07-01

... requirements are as follows: (1) This sampling system requires the use of a PDP-CVS and a heat exchanger or a CFV-CVS with either a heat exchanger or electronic flow compensation. Figure 2 in appendix A to this..., either a heat exchanger or electronic flow compensation is required (see Figure 3 in appendix A to this...

Paper to Electronic Questionnaires: Effects on Structured Questionnaire Forms

NASA Technical Reports Server (NTRS)

Trujillo, Anna C.

2009-01-01

With the use of computers, paper questionnaires are being replaced by electronic questionnaires. The formats of traditional paper questionnaires have been found to effect a subject's rating. Consequently, the transition from paper to electronic format can subtly change results. The research presented begins to determine how electronic questionnaire formats change subjective ratings. For formats where subjects used a flow chart to arrive at their rating, starting at the worst and middle ratings of the flow charts were the most accurate but subjects took slightly more time to arrive at their answers. Except for the electronic paper format, starting at the worst rating was the most preferred. The paper and electronic paper versions had the worst accuracy. Therefore, for flowchart type of questionnaires, flowcharts should start at the worst rating and work their way up to better ratings.

Plastic protein microarray to investigate the molecular pathways of magnetic nanoparticle-induced nanotoxicity

NASA Astrophysics Data System (ADS)

Liu, Yingshuai; Li, Xuelian; Bao, Shujuan; Lu, Zhisong; Li, Qing; Li, Chang Ming

2013-05-01

Superparamagnetic iron oxide nanoparticles (SPIONs) (about 15 nm) were synthesized via a hydrothermal method and characterized by field emission scanning electron microscopy, transmission electron microscopy, dynamic light scattering, x-ray diffraction, and vibrating sample magnetometer. The molecular pathways of SPIONs-induced nanotoxicity was further investigated by protein microarrays on a plastic substrate from evaluation of cell viability, reactive oxygen species (ROS) generation and cell apoptosis. The experimental results reveal that 50 μg ml-1 or higher levels of SPIONs cause significant loss of cell viability, considerable generation of ROS and cell apoptosis. It is proposed that high level SPIONs could induce cell apoptosis via a mitochondria-mediated intrinsic pathway by activation of caspase 9 and caspase 3, an increase of the Bax/Bcl-2 ratio, and down-regulation of HSP70 and HSP90 survivor factors.

Performance of a restrictive flow device and an electronic syringe driver for continuous subcutaneous infusion.

PubMed

Capes, D; Martin, K; Underwood, R

1997-10-01

The aim of this study was to investigate the flow performance of the mechanical Springfusor 30 short model and the electronic Graseby MS16A. Flow rate was measured gravimetrically in a temperature-controlled cabinet. There was no statistically significant difference between the Graseby and Springfusor syringe drivers in the flow rate error at 25 degrees C. The percentage of flow rates within +/-20% accuracy during a 35-min periods at 25 degrees C was significantly less with the Graseby, being 91.9% compared with 100% for the Springfusor. Only 58.2% of flow rates with the Graseby were within the manufacturer claimed accuracy of +/-5%. The flow rate of the Springfusor was affected by temperature; at 30 degrees C the mean flow rate was 10.8% greater than at 25 degrees C. These results indicate that the Springfusor 30 had less flow rate variation than the Graseby MS16A. However, this would not be expected to cause noticeable clinical effects when used for opioid infusion in palliative care.

Hydrological Controls on Nutrient Concentrations and Fluxes in Agricultural Catchments

NASA Astrophysics Data System (ADS)

Petry, J.; Soulsby, C.

2002-12-01

This investigation into diffuse agricultural pollution and the hydrological controls that exert a strong influence on both nutrient concentrations and fluxes, was conducted in an intensively farmed lowland catchment in north-east Scotland. The study focuses on spatial and seasonal variations in nutrient concentrations and fluxes at the catchment scale, over a 15-month period. The water quality of the 14.5 km2 Newmills Burn catchment has relatively high nutrient levels with mean concentrations of NO3-N and NH3-N at 6.09 mg/l and 0.28 mg/l respectively. Average PO4-P concentrations are 0.06 mg/l. Over short timescales nutrient concentrations and fluxes are greatest during storm events when PO4-P and NH3-N are mobilised by overland flow in riparian areas, where soils have been compacted by livestock or machinery. Delivery of deeper soil water in subsurface storm flow, facilitated by agricultural under-drainage, produces a marked increase in NO3-N (6.9 mg/l) concentrations on the hydrograph recession limb. A more detailed insight into the catchment response to storm events, and in particular the response of the hydrological pathways which provide the main sources of runoff during storm events, was gained by sampling stream water at 2-hourly intervals during 5 events. End Member Mixing Analysis (EMMA) was carried out using event specific end-member chemistries to differentiate three catchment-scale hydrological pathways (overland flow, subsurface storm flow, groundwater flow) on the basis of observed Si and NO3-N concentrations in sampled source waters. Results show that overland flow generally dominates the storm peak and provides the main flow path by which P is transferred to stream channels during storm events, whilst subsurface storm flows usually dominate the storm hydrograph volumetrically and route NO3-rich soil water to the stream. The study shows that altering hydrological pathways in a catchment can have implications for nutrient management. Whilst buffer strips can reduce the delivery of NH3-N and PO4-P by overland flow to stream channels during storm events, the management of N-rich storm runoff as NO3 via sub-surface drains would require significant interference with the drainage network. This could have a negative impact on agricultural production in the catchment.

Elucidating the role of methyl viologen as a scavenger of photoactivated electrons from photosystem I under aerobic and anaerobic conditions.

PubMed

Bennett, Tyler; Niroomand, Hanieh; Pamu, Ravi; Ivanov, Ilia; Mukherjee, Dibyendu; Khomami, Bamin

2016-03-28

We present detailed electrochemical investigations into the role of dissolved O2 in electrolyte solutions in scavenging photoactivated electrons from a uniform photosystem I (PS I) monolayer assembled on alkanethiolate SAM (self-assembled monolayer)/Au surfaces while using methyl viologen (MV(2+)) as the redox mediator. To this end, we report results for direct measurements of light induced photocurrent from uniform monolayer assemblies of PS I on C9 alkanethiolate SAM/Au surfaces. These measurements, apart from demonstrating the ability of dissolved O2 in the electrolyte medium to act as an electron scavenger, also reveal its essential role in driving the solution-phase methyl viologen to initiate light-induced directional electron transfer from an electron donor surface (Au) via surface assembled PS I trimers. Specifically, our systematic electrochemical measurements have revealed that the dissolved O2 in aqueous electrolyte solutions form a complex intermediate species with MV that plays the essential role in mediating redox pathways for unidirectional electron transfer processes. This critical insight into the redox-mediated electron transfer pathways allows for rational design of electron scavengers through systematic tuning of mediator combinations that promote such intermediate formation. Our current findings facilitate the incorporation of PS I-based bio-hybrid constructs as photo-anodes in future photoelectrochemical cells and bio-electronic devices.

Role of the photosynthetic electron transfer chain in electrogenic activity of cyanobacteria.

PubMed

Pisciotta, John M; Zou, Yongjin; Baskakov, Ilia V

2011-07-01

Certain anaerobic bacteria, termed electrogens, produce an electric current when electrons from oxidized organic molecules are deposited to extracellular metal oxide acceptors. In these heterotrophic "metal breathers", the respiratory electron transport chain (R-ETC) works in concert with membrane-bound cytochrome oxidases to transfer electrons to the extracellular acceptors. The diversity of bacteria able to generate an electric current appears more widespread than previously thought, and aerobic phototrophs, including cyanobacteria, possess electrogenic activity. However, unlike heterotrophs, cyanobacteria electrogenic activity is light dependent, which suggests that a novel pathway could exist. To elucidate the electrogenic mechanism of cyanobacteria, the current studies used site-specific inhibitors to target components of the photosynthetic electron transport chain (P-ETC) and cytochrome oxidases. Here, we show that (1) P-ETC and, particularly, water photolysed by photosystem II (PSII) is the source of electrons discharged to the environment by illuminated cyanobacteria, and (2) water-derived electrons are transmitted from PSII to extracellular electron acceptors via plastoquinone and cytochrome bd quinol oxidase. Two cyanobacterial genera (Lyngbya and Nostoc) displayed very similar electrogenic responses when treated with P-ETC site-specific inhibitors, suggesting a conserved electrogenic pathway. We propose that in cyanobacteria, electrogenic activity may represent a form of overflow metabolism to protect cells under high-intensity light. This study offers insight into electron transfer between phototrophic microorganisms and the environment and expands our knowledge into biologically based mechanisms for harnessing solar energy.

40 CFR 86.314-79 - Fuel flow measurement specifications.

Code of Federal Regulations, 2010 CFR

2010-07-01

... percent of the measuring weight. (3) If the mass of fuel consumed is measured electronically (load cell... 40 Protection of Environment 18 2010-07-01 2010-07-01 false Fuel flow measurement specifications....314-79 Fuel flow measurement specifications. (a) The fuel flow rate measurement instrument must have a...

40 CFR 86.314-79 - Fuel flow measurement specifications.

Code of Federal Regulations, 2013 CFR

2013-07-01

... percent of the measuring weight. (3) If the mass of fuel consumed is measured electronically (load cell... 40 Protection of Environment 19 2013-07-01 2013-07-01 false Fuel flow measurement specifications....314-79 Fuel flow measurement specifications. (a) The fuel flow rate measurement instrument must have a...

40 CFR 86.314-79 - Fuel flow measurement specifications.

Code of Federal Regulations, 2012 CFR

2012-07-01

... percent of the measuring weight. (3) If the mass of fuel consumed is measured electronically (load cell... 40 Protection of Environment 19 2012-07-01 2012-07-01 false Fuel flow measurement specifications....314-79 Fuel flow measurement specifications. (a) The fuel flow rate measurement instrument must have a...

40 CFR 86.314-79 - Fuel flow measurement specifications.

Code of Federal Regulations, 2011 CFR

2011-07-01

... percent of the measuring weight. (3) If the mass of fuel consumed is measured electronically (load cell... 40 Protection of Environment 18 2011-07-01 2011-07-01 false Fuel flow measurement specifications....314-79 Fuel flow measurement specifications. (a) The fuel flow rate measurement instrument must have a...

High quality and uniformity GaN grown on 150 mm Si substrate using in-situ NH3 pulse flow cleaning process

NASA Astrophysics Data System (ADS)

Ji, Panfeng; Yang, Xuelin; Feng, Yuxia; Cheng, Jianpeng; Zhang, Jie; Hu, Anqi; Song, Chunyan; Wu, Shan; Shen, Jianfei; Tang, Jun; Tao, Chun; Pan, Yaobo; Wang, Xinqiang; Shen, Bo

2017-04-01

By using in-situ NH3 pulse flow cleaning method, we have achieved the repeated growth of high quality and uniformity GaN and AlGaN/GaN high electron mobility transistors (HEMTs) on 150 mm Si substrate. The two dimensional electron gas (2DEG) mobility is 2200 cm2/Vs with an electron density of 7.3 × 1012 cm-2. The sheet resistance is 305 ± 4 Ω/□ with ±1.3% variation. The achievement is attributed to the fact that this method can significantly remove the Al, Ga, etc. metal droplets coating on the post growth flow flange and reactor wall which are difficult to clean by normal bake process under H2 ambient.

Child-Langmuir flow in a planar diode filled with charged dust impurities

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

Tang Xiaoyan; Institut fuer Theoretische Physik IV, Fakultaet fuer Physik und Astronomie, Ruhr-Universitaet Bochum, D-44870 Bochum; Shukla, Padma Kant

The Child-Langmuir (CL) flow in a planar diode in the presence of stationary charged dust particles is studied. The limiting electron current density and other diode properties, such as the electrostatic potential, the electron flow speed, and the electron number density, are calculated analytically. A comparison of the results with the case without dust impurities reveals that the diode parameters mentioned above decrease with the increase of the dust charge density. Furthermore, it is found that the classical scaling of D{sup -2} (the gap spacing D) for the CL current density remains exactly valid, while the scaling of V{sup 3/2}more » (the applied gap voltage V) can be a good approximation for low applied gap voltage and for low dust charge density.« less

Short time effects of radiotherapy on lymphatic vessels and restorative lymphatic pathways: experimental approaches ina mouse model.

PubMed

Pastouret, F; Lievens, P; Leduc, O; Bourgeois, P; Tournel, K; Lamote, J; Zirak, C; Leduc, A

2014-06-01

Radiotherapy (RT) is an important component in the therapeutic approach to oncologic conditions. This study presents the investigative results on the impact of RT on lymphatic vessels and on the regenerative response of the lymphatic system in a mouse model. We first irradiated 3 groups of ten mice using brachytherapy in a single treatment of 20 Gy. We then performed morphological examination of the irradiated lymphatic vessels using an in vivo microscopic transillumination technique at 2, 4, and 6 weeks. Next we evaluated lymphatic flow using lymphoscintigraphy and in vivo microscopy at 6 to 11 weeks in: 10 additional mice following irradiation as above (IR), in 10 mice following incision of a lymphatic vessel (I), and in a non-treated control group of 10 mice (N). Intact lymphatic vessels were observed in all mice at 2, 4, and 8 weeks following the single dose of radiotherapy in the first group of mice and normal lymphatic flow was fully restored in the irradiated (IR) and incised (I) mice indicating that the reparative substitution lymphatic pathways are functioning normally. We found that following irradiation with one dose of 20 Gy, lymphatic vessels were not visibly damaged and also that lymphatic flow was consistently restored and substitutive lymphatic pathways formed.

Identification of critical paralog groups with indispensable roles in the regulation of signaling flow

PubMed Central

Modos, Dezso; Brooks, Johanne; Fazekas, David; Ari, Eszter; Vellai, Tibor; Csermely, Peter; Korcsmaros, Tamas; Lenti, Katalin

2016-01-01

Extensive cross-talk between signaling pathways is required to integrate the myriad of extracellular signal combinations at the cellular level. Gene duplication events may lead to the emergence of novel functions, leaving groups of similar genes - termed paralogs - in the genome. To distinguish critical paralog groups (CPGs) from other paralogs in human signaling networks, we developed a signaling network-based method using cross-talk annotation and tissue-specific signaling flow analysis. 75 CPGs were found with higher degree, betweenness centrality, closeness, and ‘bowtieness’ when compared to other paralogs or other proteins in the signaling network. CPGs had higher diversity in all these measures, with more varied biological functions and more specific post-transcriptional regulation than non-critical paralog groups (non-CPG). Using TGF-beta, Notch and MAPK pathways as examples, SMAD2/3, NOTCH1/2/3 and MEK3/6-p38 CPGs were found to regulate the signaling flow of their respective pathways. Additionally, CPGs showed a higher mutation rate in both inherited diseases and cancer, and were enriched in drug targets. In conclusion, the results revealed two distinct types of paralog groups in the signaling network: CPGs and non-CPGs. Thus highlighting the importance of CPGs as compared to non-CPGs in drug discovery and disease pathogenesis. PMID:27922122

In vitro metabolic engineering of bioelectricity generation by the complete oxidation of glucose.

PubMed

Zhu, Zhiguang; Zhang, Y-H Percival

2017-01-01

The direct generation of electricity from the most abundant renewable sugar, glucose, is an appealing alternative to the production of liquid biofuels and biohydrogen. However, enzyme-catalyzed bioelectricity generation from glucose suffers from low yields due to the incomplete oxidation of the six-carbon compound glucose via one or few enzymes. Here, we demonstrate a synthetic ATP- and CoA-free 12-enzyme pathway to implement the complete oxidation of glucose in vitro. This pathway is comprised of glucose phosphorylation via polyphosphate glucokinase, NADH generation catalyzed by glucose 6-phosphate dehydrogenase (G6PDH) and 6-phosphogluconate dehydrogenase (6PGDH), electron transfer from NADH to the anode, and glucose 6-phosphate regeneration via the non-oxidative pentose phosphate pathway and gluconeogenesis. The faraday efficiency from glucose to electrons via this pathway was as high as 98.8%, suggesting the generation of nearly 24 electrons per molecule of glucose. The generated current density was greatly increased from 2.8 to 6.9mAcm -2 by replacing a low-activity G6PDH with a high-activity G6PDH and introducing a new enzyme, 6-phosphogluconolactonase, between G6PDH and 6PGDH. These results suggest the great potential of high-yield bioelectricity generation through in vitro metabolic engineering. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans.

PubMed

Christel, Stephan; Fridlund, Jimmy; Buetti-Dinh, Antoine; Buck, Moritz; Watkin, Elizabeth L; Dopson, Mark

2016-04-01

Acidithiobacillus ferrivorans is an acidophile implicated in low-temperature biomining for the recovery of metals from sulfide minerals. Acidithiobacillus ferrivorans obtains its energy from the oxidation of inorganic sulfur compounds, and genes encoding several alternative pathways have been identified. Next-generation sequencing of At. ferrivorans RNA transcripts identified the genes coding for metabolic and electron transport proteins for energy conservation from tetrathionate as electron donor. RNA transcripts suggested that tetrathionate was hydrolyzed by the tetH1 gene product to form thiosulfate, elemental sulfur and sulfate. Despite two of the genes being truncated, RNA transcripts for the SoxXYZAB complex had higher levels than for thiosulfate quinone oxidoreductase (doxDAgenes). However, a lack of heme-binding sites in soxX suggested that DoxDA was responsible for thiosulfate metabolism. Higher RNA transcript counts also suggested that elemental sulfur was metabolized by heterodisulfide reductase (hdrgenes) rather than sulfur oxygenase reductase (sor). The sulfite produced as a product of heterodisulfide reductase was suggested to be oxidized by a pathway involving the sat gene product or abiotically react with elemental sulfur to form thiosulfate. Finally, several electron transport complexes were involved in energy conservation. This study has elucidated the previously unknown At. ferrivorans tetrathionate metabolic pathway that is important in biomining. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Information Flow in Interaction Networks II: Channels, Path Lengths, and Potentials

PubMed Central

Stojmirović, Aleksandar

2012-01-01

Abstract In our previous publication, a framework for information flow in interaction networks based on random walks with damping was formulated with two fundamental modes: emitting and absorbing. While many other network analysis methods based on random walks or equivalent notions have been developed before and after our earlier work, one can show that they can all be mapped to one of the two modes. In addition to these two fundamental modes, a major strength of our earlier formalism was its accommodation of context-specific directed information flow that yielded plausible and meaningful biological interpretation of protein functions and pathways. However, the directed flow from origins to destinations was induced via a potential function that was heuristic. Here, with a theoretically sound approach called the channel mode, we extend our earlier work for directed information flow. This is achieved by constructing a potential function facilitating a purely probabilistic interpretation of the channel mode. For each network node, the channel mode combines the solutions of emitting and absorbing modes in the same context, producing what we call a channel tensor. The entries of the channel tensor at each node can be interpreted as the amount of flow passing through that node from an origin to a destination. Similarly to our earlier model, the channel mode encompasses damping as a free parameter that controls the locality of information flow. Through examples involving the yeast pheromone response pathway, we illustrate the versatility and stability of our new framework. PMID:22409812

Aqueous pathways dominate permeation of solutes across Pisum sativum seed coats and mediate solute transport via diffusion and bulk flow of water.

PubMed

Niemann, Sylvia; Burghardt, Markus; Popp, Christian; Riederer, Markus

2013-05-01

The permeability of seed coats to solutes either of biological or anthropogenic origin plays a major role in germination, seedling growth and seed treatment by pesticides. An experimental set-up was designed for investigating the mechanisms of seed coat permeation, which allows steady-state experiments with isolated seed coats of Pisum sativum. Permeances were measured for a set of organic model compounds with different physicochemical properties and sizes. The results show that narrow aqueous pathways dominate the diffusion of solutes across pea seed coats, as indicated by a correlation of permeances with the molecular sizes of the compounds instead of their lipophilicity. Further indicators for an aqueous pathway are small size selectivity and a small effect of temperature on permeation. The application of an osmotic water potential gradient across isolated seed coats leads to an increase in solute transfer, indicating that the aqueous pathways form a water-filled continuum across the seed coat allowing the bulk flow of water. Thus, the uptake of organic solutes across pea testae has two components: (1) by diffusion and (2) by bulk water inflow, which, however, is relevant only during imbibition. © 2012 Blackwell Publishing Ltd.

Oscillations and patterns in a model of simultaneous CO and C2H2 oxidation and NO(x) reduction in a cross-flow reactor.

PubMed

Hadač, Otto; Kohout, Martin; Havlica, Jaromír; Schreiber, Igor

2015-03-07

A model describing simultaneous catalytic oxidation of CO and C2H2 and reduction of NOx in a cross-flow tubular reactor is explored with the aim of relating spatiotemporal patterns to specific pathways in the mechanism. For that purpose, a detailed mechanism proposed for three-way catalytic converters is split into two subsystems, (i) simultaneous oxidation of CO and C2H2, and (ii) oxidation of CO combined with NOx reduction. The ability of these two subsystems to display mechanism-specific dynamical effects is studied initially by neglecting transport phenomena and applying stoichiometric network and bifurcation analyses. We obtain inlet temperature - inlet oxygen concentration bifurcation diagrams, where each region possessing specific dynamics - oscillatory, bistable and excitable - is associated with a dominant reaction pathway. Next, the spatiotemporal behaviour due to reaction kinetics combined with transport processes is studied. The observed spatiotemporal patterns include phase waves, travelling fronts, pulse waves and spatiotemporal chaos. Although these types of pattern occur generally when the kinetic scheme possesses autocatalysis, we find that some of their properties depend on the underlying dominant reaction pathway. The relation of patterns to specific reaction pathways is discussed.

Visual-Cerebellar Pathways and Their Roles in the Control of Avian Flight.

PubMed

Wylie, Douglas R; Gutiérrez-Ibáñez, Cristián; Gaede, Andrea H; Altshuler, Douglas L; Iwaniuk, Andrew N

2018-01-01

In this paper, we review the connections and physiology of visual pathways to the cerebellum in birds and consider their role in flight. We emphasize that there are two visual pathways to the cerebellum. One is to the vestibulocerebellum (folia IXcd and X) that originates from two retinal-recipient nuclei that process optic flow: the nucleus of the basal optic root (nBOR) and the pretectal nucleus lentiformis mesencephali (LM). The second is to the oculomotor cerebellum (folia VI-VIII), which receives optic flow information, mainly from LM, but also local visual motion information from the optic tectum, and other visual information from the ventral lateral geniculate nucleus (Glv). The tectum, LM and Glv are all intimately connected with the pontine nuclei, which also project to the oculomotor cerebellum. We believe this rich integration of visual information in the cerebellum is important for analyzing motion parallax that occurs during flight. Finally, we extend upon a suggestion by Ibbotson (2017) that the hypertrophy that is observed in LM in hummingbirds might be due to an increase in the processing demands associated with the pathway to the oculomotor cerebellum as they fly through a cluttered environment while feeding.

Potential radiological impact of tornadoes on the safety of Nuclear Fuel Services' West Valley Fuel Reprocessing Plant. Volume I. Tornado effects on head-end cell airflow

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

Holloway, L.J.; Andrae, R.W.

1981-09-01

This report describes results of a parametric study of the impacts of a tornado-generated depressurization on airflow in the contaminated process cells within the presently inoperative Nuclear Fuel Services fuel reprocessing facility near West Valley, NY. The study involved the following tasks: (1) mathematical modeling of installed ventilation and abnormal exhaust pathways from the cells and prediction of tornado-induced airflows in these pathways; (2) mathematical modeling of individual cell flow characteristics and prediction of in-cell velocities induced by flows from step 1; and (3) evaluation of the results of steps 1 and 2 to determine whether any of the pathwaysmore » investigated have the potential for releasing quantities of radioactively contaminated air from the main process cells. The study has concluded that in the event of a tornado strike, certain pathways from the cells have the potential to release radioactive materials of the atmosphere. Determination of the quantities of radioactive material released from the cells through pathways identified in step 3 is presented in Part II of this report.« less