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Sample records for dna gate zipping

  1. DNA Methylation Influences Chlorogenic Acid Biosynthesis in Lonicera japonica by Mediating LjbZIP8 to Regulate Phenylalanine Ammonia-Lyase 2 Expression

    Directory of Open Access Journals (Sweden)

    Liangping Zha

    2017-07-01

    Full Text Available The content of active compounds differ in buds and flowers of Lonicera japonica (FLJ and L. japonica var. chinensis (rFLJ. Chlorogenic acid (CGAs were major active compounds of L. japonica and regarded as measurements for quality evaluation. However, little is known concerning the formation of active compounds at the molecular level. We quantified the major CGAs in FLJ and rFLJ, and found the concentrations of CGAs were higher in the buds of rFLJ than those of FLJ. Further analysis of CpG methylation of CGAs biosynthesis genes showed differences between FLJ and rFLJ in the 5′-UTR of phenylalanine ammonia-lyase 2 (PAL2. We identified 11 LjbZIP proteins and 24 rLjbZIP proteins with conserved basic leucine zipper domains, subcellular localization, and electrophoretic mobility shift assay showed that the transcription factor LjbZIP8 is a nuclear-localized protein that specifically binds to the G-box element of the LjPAL2 5′-UTR. Additionally, a transactivation assay and LjbZIP8 overexpression in transgenic tobacco indicated that LjbZIP8 could function as a repressor of transcription. Finally, treatment with 5-azacytidine decreased the transcription level of LjPAL2 and CGAs content in FLJ leaves. These results raise the possibility that DNA methylation might influence the recruitment of LjbZIP8, regulating PAL2 expression level and CGAs content in L. japonica.

  2. Direct observation of DNA translocation influenced by electrically gated nanopores

    Science.gov (United States)

    Ando, Genki; Moriya, Hiroki; Tsukahira, Kenta; Yano, Satoshi; Mitsui, Toshiyuki

    2012-02-01

    One of remarkable recent developments in the solid state nanopore based DNA analysis is adding the ability to control electric potential near nanopore as a gate electrode by patterning metal in or on nanopore. In this approach, better control of DNA translocations for example, slowing down the translocation speed might be expected. We have fabricated insulator-metal-insulator nanopores of rather large 100 nm pore in diameter. The 100 nm diameter pores allow us to observe the translocation of lambda-DNA molecules directly by means of fluorescence microscopy without heavy clogging of the DNA molecules into the pores. By controlling ?gate voltage? on metal relative to the cis and trans voltages, the translocation rates of DNA are able to change. Interestingly, applying pulse voltage to the gate metal near 100 ms to reverse the direction of the electric field near the cis side of nanopore reverses the direction of the DNA translocation instantaneously. This in fact provides us a new way to repeat translocation of the same DNA molecule. Furthermore, repeating the pulse tends to clear off the clogged DNA molecules in nanopore. We will present more details of these phenomena caused by the gate voltages.

  3. Thermal and electrochemical gate effects on DNA conductance

    International Nuclear Information System (INIS)

    Hihath, Joshua; Chen Fang; Zhang Peiming; Tao Nongjian

    2007-01-01

    In an attempt to understand the complexities of DNA charge transport we have used a scanning tunnelling microscope break junction to repeatedly form a large number of Au-DNA-Au junctions. The DNA is covalently bound to the Au electrodes via gold-thiol bonds, and all measurements are carried out in an aqueous buffer solution to maintain a biological conformation of the duplex. A statistical analysis is carried out to determine the conductance of a single DNA duplex. Previously, we have seen an algebraic dependence of the conductance on length, suggesting a hopping mechanism. To attempt to verify this as the conduction mechanism we have changed the solution temperature and applied an electrochemical gate to the molecular junction to help elucidate the charge transport properties. In an alternating GC sequence with a length of eight base pairs, neither the temperature nor the gate potential caused a significant change in the conductance within the available experimental window

  4. Thermal and electrochemical gate effects on DNA conductance

    Energy Technology Data Exchange (ETDEWEB)

    Hihath, Joshua [Department of Electrical Engineering and Center for Solid State Electronics Research, Arizona State University, Tempe, AZ 85287 (United States); Chen Fang [Department of Electrical Engineering and Center for Solid State Electronics Research, Arizona State University, Tempe, AZ 85287 (United States); Zhang Peiming [Center for Single Molecule Biophysics, Biodesign Institute, Arizona State University, Tempe, AZ 85287 (United States); Tao Nongjian [Department of Electrical Engineering and Center for Solid State Electronics Research, Arizona State University, Tempe, AZ 85287 (United States)

    2007-05-30

    In an attempt to understand the complexities of DNA charge transport we have used a scanning tunnelling microscope break junction to repeatedly form a large number of Au-DNA-Au junctions. The DNA is covalently bound to the Au electrodes via gold-thiol bonds, and all measurements are carried out in an aqueous buffer solution to maintain a biological conformation of the duplex. A statistical analysis is carried out to determine the conductance of a single DNA duplex. Previously, we have seen an algebraic dependence of the conductance on length, suggesting a hopping mechanism. To attempt to verify this as the conduction mechanism we have changed the solution temperature and applied an electrochemical gate to the molecular junction to help elucidate the charge transport properties. In an alternating GC sequence with a length of eight base pairs, neither the temperature nor the gate potential caused a significant change in the conductance within the available experimental window.

  5. Mechanosensing Potentials Gate Fuel Consumption in a Bipedal DNA Nanowalker

    Science.gov (United States)

    Tee, Shern Ren; Hu, Xinpeng; Loh, Iong Ying; Wang, Zhisong

    2018-03-01

    A bipedal DNA nanowalker was recently reported to convert chemical energy into directional motion autonomously and efficiently. To elucidate its chemomechanical coupling mechanisms, three-dimensional molecular modeling is used to obtain coarse-grained foot-track binding potentials of the DNA nanowalker via unbiased and biased sampling techniques (for the potentials' basin and high-energy edges, respectively). The binding state that is protected against fuel-induced dissociation responds asymmetrically to forward versus backward forces, unlike the unprotected state, demonstrating a mechanosensing capability to gate fuel binding. Despite complex DNA mechanics, the foot-track potential exhibits a surprisingly neat three-part profile, offering some general guidelines to rationally design efficient nanowalkers. Subsequent modeling of the bipedal walker attached to the track gives estimates of the free energy for each bipedal state, showing how the mechanosensing foot-track binding breaks the symmetry between the rear and front feet, enabling the rear foot to be selectively dissociated by fuel and generating efficient chemomechanical coupling.

  6. Construction of a fuzzy and all Boolean logic gates based on DNA

    DEFF Research Database (Denmark)

    M. Zadegan, Reza; Jepsen, Mette D E; Hildebrandt, Lasse

    2015-01-01

    to the operation of the six Boolean logic gates AND, NAND, OR, NOR, XOR, and XNOR. The logic gate complex is shown to work also when implemented in a three-dimensional DNA origami box structure, where it controlled the position of the lid in a closed or open position. Implementation of multiple microRNA sensitive...... DNA locks on one DNA origami box structure enabled fuzzy logical operation that allows biosensing of complex molecular signals. Integrating logic gates with DNA origami systems opens a vast avenue to applications in the fields of nanomedicine for diagnostics and therapeutics....

  7. Construction of a fuzzy and Boolean logic gates based on DNA.

    Science.gov (United States)

    Zadegan, Reza M; Jepsen, Mette D E; Hildebrandt, Lasse L; Birkedal, Victoria; Kjems, Jørgen

    2015-04-17

    Logic gates are devices that can perform logical operations by transforming a set of inputs into a predictable single detectable output. The hybridization properties, structure, and function of nucleic acids can be used to make DNA-based logic gates. These devices are important modules in molecular computing and biosensing. The ideal logic gate system should provide a wide selection of logical operations, and be integrable in multiple copies into more complex structures. Here we show the successful construction of a small DNA-based logic gate complex that produces fluorescent outputs corresponding to the operation of the six Boolean logic gates AND, NAND, OR, NOR, XOR, and XNOR. The logic gate complex is shown to work also when implemented in a three-dimensional DNA origami box structure, where it controlled the position of the lid in a closed or open position. Implementation of multiple microRNA sensitive DNA locks on one DNA origami box structure enabled fuzzy logical operation that allows biosensing of complex molecular signals. Integrating logic gates with DNA origami systems opens a vast avenue to applications in the fields of nanomedicine for diagnostics and therapeutics. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Bioelectronic Interface Connecting Reversible Logic Gates Based on Enzyme and DNA Reactions.

    Science.gov (United States)

    Guz, Nataliia; Fedotova, Tatiana A; Fratto, Brian E; Schlesinger, Orr; Alfonta, Lital; Kolpashchikov, Dmitry M; Katz, Evgeny

    2016-07-18

    It is believed that connecting biomolecular computation elements in complex networks of communicating molecules may eventually lead to a biocomputer that can be used for diagnostics and/or the cure of physiological and genetic disorders. Here, a bioelectronic interface based on biomolecule-modified electrodes has been designed to bridge reversible enzymatic logic gates with reversible DNA-based logic gates. The enzyme-based Fredkin gate with three input and three output signals was connected to the DNA-based Feynman gate with two input and two output signals-both representing logically reversible computing elements. In the reversible Fredkin gate, the routing of two data signals between two output channels was controlled by the control signal (third channel). The two data output signals generated by the Fredkin gate were directed toward two electrochemical flow cells, responding to the output signals by releasing DNA molecules that serve as the input signals for the next Feynman logic gate based on the DNA reacting cascade, producing, in turn, two final output signals. The Feynman gate operated as the controlled NOT gate (CNOT), where one of the input channels controlled a NOT operation on another channel. Both logic gates represented a highly sophisticated combination of input-controlled signal-routing logic operations, resulting in redirecting chemical signals in different channels and performing orchestrated computing processes. The biomolecular reaction cascade responsible for the signal processing was realized by moving the solution from one reacting cell to another, including the reacting flow cells and electrochemical flow cells, which were organized in a specific network mimicking electronic computing circuitries. The designed system represents the first example of high complexity biocomputing processes integrating enzyme and DNA reactions and performing logically reversible signal processing. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. VT ZIP Code Areas

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) A ZIP Code Tabulation Area (ZCTA) is a statistical geographic entity that approximates the delivery area for a U.S. Postal Service five-digit...

  10. The DNA binding properties of the parsley bZIP transcription factor CPRF4a are regulated by light.

    Science.gov (United States)

    Wellmer, F; Schäfer, E; Harter, K

    2001-03-02

    The common plant regulatory factors (CPRFs) from parsley are transcription factors with a basic leucine zipper motif that bind to cis-regulatory elements frequently found in promoters of light-regulated genes. Recent studies have revealed that certain CPRF proteins are regulated in response to light by changes in their expression level and in their intracellular localization. Here, we describe an additional mechanism contributing to the light-dependent regulation of CPRF proteins. We show that the DNA binding activity of the factor CPRF4a is modulated in a phosphorylation-dependent manner and that cytosolic components are involved in the regulation of this process. Moreover, we have identified a cytosolic kinase responsible for CPRF4a phosphorylation. Modification of recombinant CPRF4a by this kinase, however, is insufficient to cause a full activation of the factor, suggesting that additional modifications are required. Furthermore, we demonstrate that the DNA binding activity of the factor is modified upon light treatment. The results of additional irradiation experiments suggest that this photoresponse is controlled by different photoreceptor systems. We discuss the possible role of CPRF4a in light signal transduction as well as the emerging regulatory network controlling CPRF activities in parsley.

  11. Heterochiral Jun and Fos bZIP peptides form a coiled-coil heterodimer that is competent for DNA binding.

    Science.gov (United States)

    Kamada, Rui; Nakagawa, Natsumi; Oyama, Taiji; Sakaguchi, Kazuyasu

    2017-07-01

    Coiled coils, consisting of at least two α-helices, have important roles in the regulation of transcription, cell differentiation, and cell growth. Peptides composed of d-amino acids (d-peptides) have received great attention for their potential in biomedical applications, because they give large diversity for the design of peptidyl drug and are more resistant to proteolytic digestion than l-peptides. However, the interactions between l-peptides/l-protein and d-peptides in the formation of complex are poorly understood. In this study, stereoisomer-specific peptides were constructed corresponding to regions of the basic-leucine-zipper domains of Jun and Fos proteins. basic-leucine-zipper domains consist of an N-terminal basic domain, which is responsible for DNA binding, and a C-terminal domain that enables homodimerization or heterodimerization via formation of a coiled-coil. By combining peptides with different stereochemistries, the d-l heterochiral Jun-Fos heterodimer formation induced DNA binding by the basic domains of Jun-Fos. Our study provides new insight into the interaction between l-peptide and d-peptide enantiomers for developing d-peptide materials and drugs. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

  12. Self-Assembling Molecular Logic Gates Based on DNA Crossover Tiles.

    Science.gov (United States)

    Campbell, Eleanor A; Peterson, Evan; Kolpashchikov, Dmitry M

    2017-07-05

    DNA-based computational hardware has attracted ever-growing attention due to its potential to be useful in the analysis of complex mixtures of biological markers. Here we report the design of self-assembling logic gates that recognize DNA inputs and assemble into crossover tiles when the output signal is high; the crossover structures disassemble to form separate DNA stands when the output is low. The output signal can be conveniently detected by fluorescence using a molecular beacon probe as a reporter. AND, NOT, and OR logic gates were designed. We demonstrate that the gates can connect to each other to produce other logic functions. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Logic Gate Operation by DNA Translocation through Biological Nanopores.

    Directory of Open Access Journals (Sweden)

    Hiroki Yasuga

    Full Text Available Logical operations using biological molecules, such as DNA computing or programmable diagnosis using DNA, have recently received attention. Challenges remain with respect to the development of such systems, including label-free output detection and the rapidity of operation. Here, we propose integration of biological nanopores with DNA molecules for development of a logical operating system. We configured outputs "1" and "0" as single-stranded DNA (ssDNA that is or is not translocated through a nanopore; unlabeled DNA was detected electrically. A negative-AND (NAND operation was successfully conducted within approximately 10 min, which is rapid compared with previous studies using unlabeled DNA. In addition, this operation was executed in a four-droplet network. DNA molecules and associated information were transferred among droplets via biological nanopores. This system would facilitate linking of molecules and electronic interfaces. Thus, it could be applied to molecular robotics, genetic engineering, and even medical diagnosis and treatment.

  14. DNA motion induced by electrokinetic flow near an Au coated nanopore surface as voltage controlled gate.

    Science.gov (United States)

    Sugimoto, Manabu; Kato, Yuta; Ishida, Kentaro; Hyun, Changbae; Li, Jiali; Mitsui, Toshiyuki

    2015-02-13

    We used fluorescence microscopy to investigate the diffusion and drift motion of λ DNA molecules on an Au-coated membrane surface near nanopores, prior to their translocation through solid-state nanopores. With the capability of controlling electric potential at the Au surface as a gate voltage, Vgate, the motions of DNA molecules, which are presumably generated by electrokinetic flow, vary dramatically near the nanopores in our observations. We carefully investigate these DNA motions with different values of Vgate in order to alter the densities and polarities of the counterions, which are expected to change the flow speed or direction, respectively. Depending on Vgate, our observations have revealed the critical distance from a nanopore for DNA molecules to be attracted or repelled-DNA's anisotropic and unsteady drifting motions and accumulations of DNA molecules near the nanopore entrance. Further finite element method (FEM) numerical simulations indicate that the electrokinetic flow could qualitatively explain these unusual DNA motions near metal-collated gated nanopores. Finally, we demonstrate the possibility of controlling the speed and direction of DNA motion near or through a nanopore, as in the case of recapturing a single DNA molecule multiple times with alternating current voltages on the Vgate.

  15. Intelligent layered nanoflare: ``lab-on-a-nanoparticle'' for multiple DNA logic gate operations and efficient intracellular delivery

    Science.gov (United States)

    Yang, Bin; Zhang, Xiao-Bing; Kang, Li-Ping; Huang, Zhi-Mei; Shen, Guo-Li; Yu, Ru-Qin; Tan, Weihong

    2014-07-01

    DNA strand displacement cascades have been engineered to construct various fascinating DNA circuits. However, biological applications are limited by the insufficient cellular internalization of naked DNA structures, as well as the separated multicomponent feature. In this work, these problems are addressed by the development of a novel DNA nanodevice, termed intelligent layered nanoflare, which integrates DNA computing at the nanoscale, via the self-assembly of DNA flares on a single gold nanoparticle. As a ``lab-on-a-nanoparticle'', the intelligent layered nanoflare could be engineered to perform a variety of Boolean logic gate operations, including three basic logic gates, one three-input AND gate, and two complex logic operations, in a digital non-leaky way. In addition, the layered nanoflare can serve as a programmable strategy to sequentially tune the size of nanoparticles, as well as a new fingerprint spectrum technique for intelligent multiplex biosensing. More importantly, the nanoflare developed here can also act as a single entity for intracellular DNA logic gate delivery, without the need of commercial transfection agents or other auxiliary carriers. By incorporating DNA circuits on nanoparticles, the presented layered nanoflare will broaden the applications of DNA circuits in biological systems, and facilitate the development of DNA nanotechnology.DNA strand displacement cascades have been engineered to construct various fascinating DNA circuits. However, biological applications are limited by the insufficient cellular internalization of naked DNA structures, as well as the separated multicomponent feature. In this work, these problems are addressed by the development of a novel DNA nanodevice, termed intelligent layered nanoflare, which integrates DNA computing at the nanoscale, via the self-assembly of DNA flares on a single gold nanoparticle. As a ``lab-on-a-nanoparticle'', the intelligent layered nanoflare could be engineered to perform a variety of

  16. DNA-nucleobases: Gate Dielectric/Passivation Layer for Flexible GFET-based Sensor Applications (Postprint)

    Science.gov (United States)

    2015-09-24

    deposition of the gate dielectric layer used for making transistor devices. The approach was introducing a thin film of deoxyribonucleic acid (DNA...were investigated as well. This is an important first step to realizing high performance graphene-based transistors that have potential use in bio ...deposition; Sensors; Thin films ; 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT: SAR 18. NUMBER OF PAGES 9 19a. NAME OF

  17. Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly.

    Directory of Open Access Journals (Sweden)

    Andreas I Andreou

    Full Text Available Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile-simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation.

  18. The combination of gold nanorods and nanoparticles with DNA nanodevices for logic gates construction

    International Nuclear Information System (INIS)

    Yao, Dongbao; Song, Tingjie; Xiao, Shiyan; Huang, Fujian; Liang, Haojun; Zheng, Bin

    2015-01-01

    In this work, two DNA nanodevices were constructed utilizing a DNA strand displacement reaction. With the assistance of gold nanoparticles (AuNPs) and gold nanorods (AuNRs), the autonomous reactions can be reflected from the aggregation states of nanoparticles. By sequence design and the two non-overlapping double hump-like UV–vis spectral peaks of AuNPs and AuNRs, two logic gates with multiple inputs and outputs were successfully run with expected outcomes. This method not only shows how to achieve computing with multiple logic calculations but also has great potential for multiple targets detection. (paper)

  19. Logic gates and antisense DNA devices operating on a translator nucleic Acid scaffold.

    Science.gov (United States)

    Shlyahovsky, Bella; Li, Yang; Lioubashevski, Oleg; Elbaz, Johann; Willner, Itamar

    2009-07-28

    A series of logic gates, "AND", "OR", and "XOR", are designed using a DNA scaffold that includes four "footholds" on which the logic operations are activated. Two of the footholds represent input-recognition strands, and these are blocked by complementary nucleic acids, whereas the other two footholds are blocked by nucleic acids that include the horseradish peroxidase (HRP)-mimicking DNAzyme sequence. The logic gates are activated by either nucleic acid inputs that hybridize to the respective "footholds", or by low-molecular-weight inputs (adenosine monophosphate or cocaine) that yield the respective aptamer-substrate complexes. This results in the respective translocation of the blocking nucleic acids to the footholds carrying the HRP-mimicking DNAzyme sequence, and the concomitant release of the respective DNAzyme. The released product-strands then self-assemble into the hemin/G-quadruplex-HRP-mimicking DNAzyme that biocatalyzes the formation of a colored product and provides an output signal for the different logic gates. The principle of the logic operation is, then, implemented as a possible paradigm for future nanomedicine. The nucleic acid inputs that bind to the blocked footholds result in the translocation of the blocking nucleic acids to the respective footholds carrying the antithrombin aptamer. The released aptamer inhibits, then, the hydrolytic activity of thrombin. The system demonstrates the regulation of a biocatalytic reaction by a translator system activated on a DNA scaffold.

  20. Synthetic Ion Channels and DNA Logic Gates as Components of Molecular Robots.

    Science.gov (United States)

    Kawano, Ryuji

    2018-02-19

    A molecular robot is a next-generation biochemical machine that imitates the actions of microorganisms. It is made of biomaterials such as DNA, proteins, and lipids. Three prerequisites have been proposed for the construction of such a robot: sensors, intelligence, and actuators. This Minireview focuses on recent research on synthetic ion channels and DNA computing technologies, which are viewed as potential candidate components of molecular robots. Synthetic ion channels, which are embedded in artificial cell membranes (lipid bilayers), sense ambient ions or chemicals and import them. These artificial sensors are useful components for molecular robots with bodies consisting of a lipid bilayer because they enable the interface between the inside and outside of the molecular robot to function as gates. After the signal molecules arrive inside the molecular robot, they can operate DNA logic gates, which perform computations. These functions will be integrated into the intelligence and sensor sections of molecular robots. Soon, these molecular machines will be able to be assembled to operate as a mass microrobot and play an active role in environmental monitoring and in vivo diagnosis or therapy. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Tyramine Hydrochloride Based Label-Free System for Operating Various DNA Logic Gates and a DNA Caliper for Base Number Measurements.

    Science.gov (United States)

    Fan, Daoqing; Zhu, Xiaoqing; Dong, Shaojun; Wang, Erkang

    2017-07-05

    DNA is believed to be a promising candidate for molecular logic computation, and the fluorogenic/colorimetric substrates of G-quadruplex DNAzyme (G4zyme) are broadly used as label-free output reporters of DNA logic circuits. Herein, for the first time, tyramine-HCl (a fluorogenic substrate of G4zyme) is applied to DNA logic computation and a series of label-free DNA-input logic gates, including elementary AND, OR, and INHIBIT logic gates, as well as a two to one encoder, are constructed. Furthermore, a DNA caliper that can measure the base number of target DNA as low as three bases is also fabricated. This DNA caliper can also perform concatenated AND-AND logic computation to fulfil the requirements of sophisticated logic computing. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Zip Codes - MDC_WCSZipcode

    Data.gov (United States)

    NSGIC Local Govt | GIS Inventory — The WCSZipcode polygon feature class was created by Miami-Dade Enterprise Technology Department to be used in the WCS batch jobs to assign the actual zip code of...

  3. Allegheny County Zip Code Boundaries

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — This dataset demarcates the zip code boundaries that lie within Allegheny County.If viewing this description on the Western Pennsylvania Regional Data Center’s open...

  4. Functional Analysis of Maize Silk-Specific ZmbZIP25 Promoter

    Directory of Open Access Journals (Sweden)

    Wanying Li

    2018-03-01

    Full Text Available ZmbZIP25 (Zea mays bZIP (basic leucine zipper transcription factor 25 is a function-unknown protein that belongs to the D group of the bZIP transcription factor family. RNA-seq data showed that the expression of ZmbZIP25 was tissue-specific in maize silks, and this specificity was confirmed by RT-PCR (reverse transcription-polymerase chain reaction. In situ RNA hybridization showed that ZmbZIP25 was expressed exclusively in the xylem of maize silks. A 5′ RACE (rapid amplification of cDNA ends assay identified an adenine residue as the transcription start site of the ZmbZIP25 gene. To characterize this silk-specific promoter, we isolated and analyzed a 2450 bp (from −2083 to +367 and a 2600 bp sequence of ZmbZIP25 (from −2083 to +517, the transcription start site was denoted +1. Stable expression assays in Arabidopsis showed that the expression of the reporter gene GUS driven by the 2450 bp ZmbZIP25 5′-flanking fragment occurred exclusively in the papillae of Arabidopsis stigmas. Furthermore, transient expression assays in maize indicated that GUS and GFP expression driven by the 2450 bp ZmbZIP25 5′-flanking sequences occurred only in maize silks and not in other tissues. However, no GUS or GFP expression was driven by the 2600 bp ZmbZIP25 5′-flanking sequences in either stable or transient expression assays. A series of deletion analyses of the 2450 bp ZmbZIP25 5′-flanking sequence was performed in transgenic Arabidopsis plants, and probable elements prediction analysis revealed the possible presence of negative regulatory elements within the 161 bp region from −1117 to −957 that were responsible for the specificity of the ZmbZIP25 5′-flanking sequence.

  5. DNA and RNA sequencing by nanoscale reading through programmable electrophoresis and nanoelectrode-gated tunneling and dielectric detection

    Science.gov (United States)

    Lee, James W.; Thundat, Thomas G.

    2005-06-14

    An apparatus and method for performing nucleic acid (DNA and/or RNA) sequencing on a single molecule. The genetic sequence information is obtained by probing through a DNA or RNA molecule base by base at nanometer scale as though looking through a strip of movie film. This DNA sequencing nanotechnology has the theoretical capability of performing DNA sequencing at a maximal rate of about 1,000,000 bases per second. This enhanced performance is made possible by a series of innovations including: novel applications of a fine-tuned nanometer gap for passage of a single DNA or RNA molecule; thin layer microfluidics for sample loading and delivery; and programmable electric fields for precise control of DNA or RNA movement. Detection methods include nanoelectrode-gated tunneling current measurements, dielectric molecular characterization, and atomic force microscopy/electrostatic force microscopy (AFM/EFM) probing for nanoscale reading of the nucleic acid sequences.

  6. Changing Postal ZIP Code Boundaries

    Science.gov (United States)

    2006-06-23

    for distribution to a specific delivery post office, identified by the fourth and fifth digits. For example, the ZIP Code for Alturas , the county seat...distribution point for some California post offices such as Alturas , Cedarville (96104), Fort Bidwell (96112), and Likely (96116), distinguished by the

  7. GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping.

    Science.gov (United States)

    Alser, Mohammed; Hassan, Hasan; Xin, Hongyi; Ergin, Oguz; Mutlu, Onur; Alkan, Can

    2017-11-01

    High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -called short reads- that cause significant computational burden. To analyze the entire genome, each of the billions of short reads must be mapped to a reference genome based on the similarity between a read and 'candidate' locations in that reference genome. The similarity measurement, called alignment, formulated as an approximate string matching problem, is the computational bottleneck because: (i) it is implemented using quadratic-time dynamic programming algorithms and (ii) the majority of candidate locations in the reference genome do not align with a given read due to high dissimilarity. Calculating the alignment of such incorrect candidate locations consumes an overwhelming majority of a modern read mapper's execution time. Therefore, it is crucial to develop a fast and effective filter that can detect incorrect candidate locations and eliminate them before invoking computationally costly alignment algorithms. We propose GateKeeper, a new hardware accelerator that functions as a pre-alignment step that quickly filters out most incorrect candidate locations. GateKeeper is the first design to accelerate pre-alignment using Field-Programmable Gate Arrays (FPGAs), which can perform pre-alignment much faster than software. When implemented on a single FPGA chip, GateKeeper maintains high accuracy (on average >96%) while providing, on average, 90-fold and 130-fold speedup over the state-of-the-art software pre-alignment techniques, Adjacency Filter and Shifted Hamming Distance (SHD), respectively. The addition of GateKeeper as a pre-alignment step can reduce the verification time of the mrFAST mapper by a factor of 10. https://github.com/BilkentCompGen/GateKeeper. mohammedalser@bilkent.edu.tr or onur.mutlu@inf.ethz.ch or calkan@cs.bilkent.edu.tr. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press

  8. The steric gate amino acid tyrosine 112 is required for efficient mismatched-primer extension by human DNA polymerase kappa.

    Science.gov (United States)

    Niimi, Naoko; Sassa, Akira; Katafuchi, Atsushi; Grúz, Petr; Fujimoto, Hirofumi; Bonala, Radha-Rani; Johnson, Francis; Ohta, Toshihiro; Nohmi, Takehiko

    2009-05-26

    Human DNA is continuously damaged by exogenous and endogenous genotoxic insults. To counteract DNA damage and ensure the completion of DNA replication, cells possess specialized DNA polymerases (Pols) that bypass a variety of DNA lesions. Human DNA polymerase kappa (hPolkappa) is a member of the Y-family of DNA Pols and a direct counterpart of DinB in Escherichia coli. hPolkappa is characterized by its ability to bypass several DNA adducts [e.g., benzo[a]pyrene diolepoxide-N(2)-deoxyguanine (BPDE-N(2)-dG) and thymine glycol] and efficiently extend primers with mismatches at the termini. hPolkappa is structurally distinct from E. coli DinB in that it possesses an approximately 100-amino acid extension at the N-terminus. Here, we report that tyrosine 112 (Y112), the steric gate amino acid of hPolkappa, which distinguishes dNTPs from rNTPs by sensing the 2'-hydroxy group of incoming nucleotides, plays a crucial role in extension reactions with mismatched primer termini. When Y112 was replaced with alanine, the amino acid change severely reduced the catalytic constant, i.e., k(cat), of the extending mismatched primers and lowered the efficiency, i.e., k(cat)/K(m), of this process by approximately 400-fold compared with that of the wild-type enzyme. In contrast, the amino acid replacement did not reduce the insertion efficiency of dCMP opposite BPDE-N(2)-dG in template DNA, nor did it affect the ability of hPolkappa to bind strongly to template-primer DNA with BPDE-N(2)-dG/dCMP. We conclude that the steric gate of hPolkappa is a major fidelity factor that regulates extension reactions from mismatched primer termini.

  9. Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes.

    Directory of Open Access Journals (Sweden)

    Carola Engler

    Full Text Available We have developed a protocol to assemble in one step and one tube at least nine separate DNA fragments together into an acceptor vector, with 90% of recombinant clones obtained containing the desired construct. This protocol is based on the use of type IIs restriction enzymes and is performed by simply subjecting a mix of 10 undigested input plasmids (nine insert plasmids and the acceptor vector to a restriction-ligation and transforming the resulting mix in competent cells. The efficiency of this protocol allows generating libraries of recombinant genes by combining in one reaction several fragment sets prepared from different parental templates. As an example, we have applied this strategy for shuffling of trypsinogen from three parental templates (bovine cationic trypsinogen, bovine anionic trypsinogen and human cationic trypsinogen each divided in 9 separate modules. We show that one round of shuffling using the 27 trypsinogen entry plasmids can easily produce the 19,683 different possible combinations in one single restriction-ligation and that expression screening of a subset of the library allows identification of variants that can lead to higher expression levels of trypsin activity. This protocol, that we call 'Golden Gate shuffling', is robust, simple and efficient, can be performed with templates that have no homology, and can be combined with other shuffling protocols in order to introduce any variation in any part of a given gene.

  10. Compound list: rosiglitazone maleate [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available rosiglitazone maleate RGZ 00151 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LAT...EST/Human/in_vitro/rosiglitazone_maleate.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tg...gates/LATEST/Rat/in_vivo/Liver/Single/rosiglitazone_maleate.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscienc...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/rosiglitazone_maleate.Rat.in_vivo.Liver.Repeat.zip ...

  11. An intelligent 1:2 demultiplexer as an intracellular theranostic device based on DNA/Ag cluster-gated nanovehicles

    Science.gov (United States)

    Ran, Xiang; Wang, Zhenzhen; Ju, Enguo; Pu, Fang; Song, Yanqiu; Ren, Jinsong; Qu, Xiaogang

    2018-02-01

    The logic device demultiplexer can convey a single input signal into one of multiple output channels. The choice of the output channel is controlled by a selector. Several molecules and biomolecules have been used to mimic the function of a demultiplexer. However, the practical application of logic devices still remains a big challenge. Herein, we design and construct an intelligent 1:2 demultiplexer as a theranostic device based on azobenzene (azo)-modified and DNA/Ag cluster-gated nanovehicles. The configuration of azo and the conformation of the DNA ensemble can be regulated by light irradiation and pH, respectively. The demultiplexer which uses light as the input and acid as the selector can emit red fluorescence or a release drug under different conditions. Depending on different cells, the intelligent logic device can select the mode of cellular imaging in healthy cells or tumor therapy in tumor cells. The study incorporates the logic gate with the theranostic device, paving the way for tangible applications of logic gates in the future.

  12. Geant4-DNA coupling and validation in the GATE Monte Carlo platform for DNA molecules irradiation in a calculation grid environment

    International Nuclear Information System (INIS)

    Pham, Quang Trung

    2014-01-01

    The Monte Carlo simulation methods are successfully being used in various areas of medical physics but also at different scales, for example, from the radiation therapy treatment planning systems to the prediction of the effects of radiation in cancer cells. The Monte Carlo simulation platform GATE based on the Geant4 tool-kit offers features dedicated to simulations in medical physics (nuclear medicine and radiotherapy). For radiobiology applications, the Geant4-DNA physical models are implemented to track particles till very low energy (eV) and are adapted for estimation of micro-dosimetric quantities. In order to implement a multi-scale Monte Carlo platform, we first validated the physical models of Geant4-DNA, and integrated them into GATE. Finally, we validated this implementation in the context of radiation therapy and proton therapy. In order to validate the Geant4-DNA physical models, dose point kernels for monoenergetic electrons (10 keV to 100 keV) were simulated using the physical models of Geant4-DNA and were compared to those simulated with Geant4 Standard physical models and another Monte Carlo code EGSnrc. The range and the stopping powers of electrons (7.4 eV to 1 MeV) and protons (1 keV to 100 MeV) calculated with GATE/Geant4-DNA were then compared with literature. We proposed to simulate with the GATE platform the impact of clinical and preclinical beams on cellular DNA. We modeled a clinical proton beam of 193.1 MeV, 6 MeV clinical electron beam and a X-ray irradiator beam. The beams models were validated by comparing absorbed dose computed and measured in liquid water. Then, the beams were used to calculate the frequency of energy deposits in DNA represented by different geometries. First, the DNA molecule was represented by small cylinders: 2 nm x 2 nm (∼10 bp), 5 nm x 10 nm (nucleosome) and 25 nm x 25 nm (chromatin fiber). All these cylinders were placed randomly in a sphere of liquid water (500 nm radius). Then we reconstructed the DNA

  13. Two Cassava Basic Leucine Zipper (bZIP Transcription Factors (MebZIP3 and MebZIP5 Confer Disease Resistance against Cassava Bacterial Blight

    Directory of Open Access Journals (Sweden)

    Xiaolin Li

    2017-12-01

    Full Text Available Basic domain-leucine zipper (bZIP transcription factor, one type of conserved gene family, plays an important role in plant development and stress responses. Although 77 MebZIPs have been genome-wide identified in cassava, their in vivo roles remain unknown. In this study, we analyzed the expression pattern and the function of two MebZIPs (MebZIP3 and MebZIP5 in response to pathogen infection. Gene expression analysis indicated that MebZIP3 and MebZIP5 were commonly regulated by flg22, Xanthomonas axonopodis pv. manihotis (Xam, salicylic acid (SA, and hydrogen peroxide (H2O2. Subcellular localization analysis showed that MebZIP3 and MebZIP5 are specifically located in cell nucleus. Through overexpression in tobacco, we found that MebZIP3 and MebZIP5 conferred improved disease resistance against cassava bacterial blight, with more callose depositions. On the contrary, MebZIP3- and MebZIP5-silenced plants by virus-induced gene silencing (VIGS showed disease sensitive phenotype, lower transcript levels of defense-related genes and less callose depositions. Taken together, this study highlights the positive role of MebZIP3 and MebZIP5 in disease resistance against cassava bacterial blight for further utilization in genetic improvement of cassava disease resistance.

  14. Cloning and molecular analysis of HlbZip1 and HlbZip2 transcription factors putatively involved in the regulation of the lupulin metabolome in hop (Humulus lupulus L.).

    Science.gov (United States)

    Matousek, Jaroslav; Kocábek, Tomás; Patzak, Josef; Stehlík, Jan; Füssy, Zoltan; Krofta, Karel; Heyerick, Arne; Roldán-Ruiz, Isabel; Maloukh, Lina; De Keukeleire, Denis

    2010-01-27

    Hop (Humulus lupulus L.), the essential source of beer flavor is of interest from a medicinal perspective in view of its high content in health-beneficial terpenophenolics including prenylflavonoids. The dissection of biosynthetic pathway(s) of these compounds in lupulin glands, as well as its regulation by transcription factors (TFs), is important for efficient biotechnological manipulation of the hop metabolome. TFs of the bZIP class were preselected from the hop transcriptome using a cDNA-AFLP approach and cloned from a cDNA library based on glandular tissue-enriched hop cones. The cloned TFs HlbZIP1A and HlbZIP2 have predicted molecular masses of 27.4 and 34.2 kDa, respectively, and both are similar to the group A3 bZIP TFs according to the composition of characteristic domains. While HlbZIP1A is rather neutral (pI 6.42), HlbZIP2 is strongly basic (pI 8.51). A truncated variant of HlbZIP1 (HlbZIP1B), which is strongly basic but lacks the leucine zipper domain, has also been cloned from hop. Similar to the previously cloned HlMyb3 from hop, both bZIP TFs show a highly specific expression in lupulin glands, although low expression was observed also in other tissues including roots and immature pollen. Comparative functional analyses of HlbZip1A, HlbZip2, and subvariants of HlMyb3 were performed in a transient expression system using Nicotiana benthamiana leaf coinfiltration with Agrobacterium tumefaciens strains bearing hop TFs and selected promoters fused to the GUS reference gene. Both hop bZIP TFs and HlMyb3 mainly activated the promoters of chalcone synthase chs_H1 and the newly cloned O-methyl transferase 1 genes, while the response of the valerophenone synthase promoter to the cloned hop TFs was very low. These analyses also showed that the cloned bZIP TFs are not strictly G-box-specific. HPLC analysis of secondary metabolites in infiltrated Petunia hybrida showed that both hop bZIP TFs interfere with the accumulation and the composition of flavonol

  15. Isolation and characterization of a gene from Medicago sativa L., encoding a bZIP transcription factor.

    Science.gov (United States)

    Li, Yan; Sun, Yan; Yang, Qingchuan; Fang, Feng; Kang, Junmei; Zhang, Tiejun

    2013-02-01

    A full-length cDNA of 1,537 nucleotides was cloned from Medicago sativa L. cv. "Zhongmu No. 1" by rapid amplification of cDNA ends. It was designated as MsZIP, encoding a protein of 340 amino acids. The protein molecular weight was 36.43 kDa, and the theoretical isoelectric point was 5.72. The MsZIP preferentially localized in nucleus and have signal peptide. Blast analysis revealed that MsZIP shared the highest homology with some bZIP proteins of M. truncatula. The transcript of MsZIP was strongly enriched in leaf compared with root and stem of mature alfalfa plants. MsZIP was strongly induced by 15 % PEG6000 (polyethylene glycol), 50 μM abscisic acid, 200 mM NaCl, 70 μM gibberellic acid, 5 mM salicylic acid and 200 μM methyl jasmonate. Physiological resistance parameters were measured in the transgenic tobacco. Malondialdehyde content, relative water content, soluble sugar content, soluble protein content and proline content in transgenic tobacco increased compared with non-transgenic tobacco under salt stress or drought stress. The results showed that accumulation of the MsZIP protein in the vegetative tissues of transgenic plants enhanced their tolerance to osmotic pressure stress. These results demonstrate a role for the MsZIP protein in stress protection and suggest the potential of the MsZIP gene for genetic engineering of salt tolerance and drought tolerance.

  16. hZip2 and hZip3 zinc transporters are down regulated in human prostate adenocarcinomatous glands

    Directory of Open Access Journals (Sweden)

    Franklin Renty B

    2007-06-01

    Full Text Available Abstract Background The normal human prostate glandular epithelium has the unique function of accumulating high levels of zinc. In prostate cancer this capability is lost as an early event in the development of the malignant cells. The mechanism and factors responsible for the ability of the normal epithelial cells to accumulate zinc and the loss of this capability in the malignant cells need to be identified. We previously reported that Zip1 is an important zinc uptake transporter in prostate cells and is down regulated in the malignant cells in situ along with the depletion of zinc levels. In this report we investigated the expression of two other Zip family zinc transporters, Zip2 and Zip3 in malignant versus nonmalignant (normal and BPH glands. Zip2 and Zip3 relative protein levels were determined by immunohistochemistry analysis of human prostate tissue sections. Results Normal and BPH glandular epithelium consistently exhibited the strong presence of both Zip 2 and Zip3; whereas both transporters consistently were essentially non-detectable in the malignant glands. This represents the first report of the expression of Zip3 in human prostate tissue; and more importantly, reveals that ZiP2 and Zip3 are down regulated in malignant cells in situ as we also had demonstrated for Zip1. Zip2 and Zip3 transporter proteins were localized predominantly at the apical cell membrane, which is in contrast to the Zip1 localization at the basolateral membrane. Zip2 and Zip3 seemingly are associated with the re-uptake of zinc from prostatic fluid. Conclusion These results coupled with previous reports implicate Zip2 and Zip3 along with Zip1 as important zinc uptake transporters involved in the unique ability of prostate cells to accumulate high cellular zinc levels. Zip1 is important for the extraction of zinc from circulation as the primary source of cellular zinc. Zip 2 and Zip3 appear to be important for retention of the zinc in the cellular compartment

  17. Atractividad local en la bifurcación de zip Local atractivity in zip bifurcation

    Directory of Open Access Journals (Sweden)

    Carlos Mario Escobar–Callejas

    2010-12-01

    Full Text Available En el presente trabajo se estudia la atractividad local del segmento de equilibriosque se forma en el fenómeno de la bifurcación de zip para un sistematridimensional de ecuaciones diferenciales no lineales. Este trabajo puede serconsiderado como una generalización de un resultado de Farkas en bifurcaciónde zip de modelos en competición.In this paper the local segment attractiveness equilibrium that forms on the phenomenon of zip bifurcation for a three–dimensional system of differential equations nonlinear is studied. This work may be regarded as a generalization as a result on Farkas’s zip bifurcation in competition models.

  18. High-sensitivity assay for Hg (II) and Ag (I) ion detection: A new class of droplet digital PCR logic gates for an intelligent DNA calculator.

    Science.gov (United States)

    Cheng, Nan; Zhu, Pengyu; Xu, Yuancong; Huang, Kunlun; Luo, Yunbo; Yang, Zhansen; Xu, Wentao

    2016-10-15

    The first example of droplet digital PCR logic gates ("YES", "OR" and "AND") for Hg (II) and Ag (I) ion detection has been constructed based on two amplification events triggered by a metal-ion-mediated base mispairing (T-Hg(II)-T and C-Ag(I)-C). In this work, Hg(II) and Ag(I) were used as the input, and the "true" hierarchical colors or "false" green were the output. Through accurate molecular recognition and high sensitivity amplification, positive droplets were generated by droplet digital PCR and viewed as the basis of hierarchical digital signals. Based on this principle, YES gate for Hg(II) (or Ag(I)) detection, OR gate for Hg(II) or Ag(I) detection and AND gate for Hg(II) and Ag(I) detection were developed, and their sensitively and selectivity were reported. The results indicate that the ddPCR logic system developed based on the different indicators for Hg(II) and Ag(I) ions provides a useful strategy for developing advanced detection methods, which are promising for multiplex metal ion analysis and intelligent DNA calculator design applications. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Abscisic-acid-dependent basic leucine zipper (bZIP) transcription factors in plant abiotic stress.

    Science.gov (United States)

    Banerjee, Aditya; Roychoudhury, Aryadeep

    2017-01-01

    One of the major causes of significant crop loss throughout the world is the myriad of environmental stresses including drought, salinity, cold, heavy metal toxicity, and ultraviolet-B (UV-B) rays. Plants as sessile organisms have evolved various effective mechanism which enable them to withstand this plethora of stresses. Most of such regulatory mechanisms usually follow the abscisic-acid (ABA)-dependent pathway. In this review, we have primarily focussed on the basic leucine zipper (bZIP) transcription factors (TFs) activated by the ABA-mediated signalosome. Upon perception of ABA by specialized receptors, the signal is transduced via various groups of Ser/Thr kinases, which phosphorylate the bZIP TFs. Following such post-translational modification of TFs, they are activated so that they bind to specific cis-acting sequences called abscisic-acid-responsive elements (ABREs) or GC-rich coupling elements (CE), thereby influencing the expression of their target downstream genes. Several in silico techniques have been adopted so far to predict the structural features, recognize the regulatory modification sites, undergo phylogenetic analyses, and facilitate genome-wide survey of TF under multiple stresses. Current investigations on the epigenetic regulation that controls greater accessibility of the inducible regions of DNA of the target gene to the bZIP TFs exclusively under stress situations, along with the evolved stress memory responses via genomic imprinting mechanism, have been highlighted. The potentiality of overexpression of bZIP TFs, either in a homologous or in a heterologous background, in generating transgenic plants tolerant to various abiotic stressors have also been addressed by various groups. The present review will provide a coherent documentation on the functional characterization and regulation of bZIP TFs under multiple environmental stresses, with the major goal of generating multiple-stress-tolerant plant cultivars in near future.

  20. Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating.

    Science.gov (United States)

    Yoo, Jejoong; Aksimentiev, Aleksei

    2015-12-03

    DNA self-assembly has emerged as a new paradigm for design of biomimetic membrane channels. Several experimental groups have already demonstrated assembly and insertion of DNA channels into lipid bilayer membranes; however, the structure of the channels and their conductance mechanism have remained undetermined. Here, we report the results of molecular dynamics simulations that characterized the biophysical properties of the DNA membrane channels with atomic precision. We show that, while overall remaining stable, the local structure of the channels undergoes considerable fluctuations, departing from the idealized design. The transmembrane ionic current flows both through the central pore of the channel as well as along the DNA walls and through the gaps in the DNA structure. Surprisingly, we find that the conductance of DNA channels depend on the membrane tension, making them potentially suitable for force-sensing applications. Finally, we show that electro-osmosis governs the transport of druglike molecules through the DNA channels.

  1. Iron importers Zip8 and Zip14 are expressed in retina and regulated by retinal iron levels.

    Science.gov (United States)

    Sterling, Jacob; Guttha, Samyuktha; Song, Ying; Song, Delu; Hadziahmetovic, Majda; Dunaief, Joshua L

    2017-02-01

    Intracellular retinal iron accumulation has been implicated in the pathogenesis of age-related macular degeneration (AMD), the leading cause of irreversible blindness among individuals over the age of 50. Ceruloplasmin/hephaestin double knockout mice (Cp/Heph DKO) and hepcidin knockout mice (Hepc KO) accumulate retinal iron and model some features of AMD. Two canonical pathways govern cellular iron import - transferrin-bound iron import and non-transferrin bound iron import. In Cp/Heph DKO and Hepc KO iron-loaded retinas, transferrin-bound iron import is downregulated. Despite this effort to reduce cellular iron burden, iron continues to accumulate in these retinas in an age-dependent manner. Quantitative RT-PCR and Western analysis were used to quantify the expression of three ferrous iron importers, Dmt1, Zip8, and Zip14, in wild-type (Wt), Cp/Heph DKO, and Hepc KO retinas. Zip8 and Zip14 protein levels were analyzed using Western analysis in mice injected intravitreally with either apo- or holo-transferrin to elucidate one possible mechanism of Zip14 regulation in the retina. Both zip8 and zip14 were expressed in the mouse retina. Paradoxically, protein levels of non-transferrin bound iron importers were upregulated in both Cp/Heph DKO and Hepc KO retinas. Intravitreal holo-transferrin injection decreased Zip 14 protein levels. These data indicate that Zip8 and Zip14 may take up increasing amounts of non-transferrin bound iron in these two mouse models of retinal iron accumulation. Their upregulation in these already iron-loaded retinas suggests a vicious cycle leading to toxicity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Ultrasensitive in situ label-free DNA detection using a GaN nanowire-based extended-gate field-effect-transistor sensor.

    Science.gov (United States)

    Chen, Chin-Pei; Ganguly, Abhijit; Lu, Ching-Ying; Chen, Ting-Yu; Kuo, Chun-Chiang; Chen, Reui-San; Tu, Wen-Hsun; Fischer, Wolfgang B; Chen, Kuei-Hsien; Chen, Li-Chyong

    2011-03-15

    In this study, we have successfully demonstrated that a GaN nanowire (GaNNW) based extended-gate field-effect-transistor (EGFET) biosensor is capable of specific DNA sequence identification under label-free in situ conditions. Our approach shows excellent integration of the wide bandgap semiconducting nature of GaN, surface-sensitivity of the NW-structure, and high transducing performance of the EGFET-design. The simple sensor-architecture, by direct assembly of as-synthesized GaNNWs with a commercial FET device, can achieve an ultrahigh detection limit below attomolar level concentrations: about 3 orders of magnitude higher in resolution than that of other FET-based DNA-sensors. Comparative in situ studies on mismatches ("hotspot" mutations related to human p53 tumor-suppressor gene) and complementary targets reveal excellent selectivity and specificity of the sensor, even in the presence of noncomplementary DNA strands, suggesting the potential pragmatic application in complex clinical samples. In comparison with GaN thin film, NW-based EGFET exhibits excellent performance with about 2 orders higher sensitivity, over a wide detection range, 10(-19)-10(-6) M, reaching about a 6-orders lower detection limit. Investigations illustrate the unique and distinguished feature of nanomaterials. Detailed studies indicate a positive effect of energy band alignment at the biomaterials-semiconductor hybrid interface influencing the effective capacitance and carrier-mobility of the system.

  3. The transcription factor bZIP14 regulates the TCA cycle in the diatom Phaeodactylum tricornutum.

    Science.gov (United States)

    Matthijs, Michiel; Fabris, Michele; Obata, Toshihiro; Foubert, Imogen; Franco-Zorrilla, José Manuel; Solano, Roberto; Fernie, Alisdair R; Vyverman, Wim; Goossens, Alain

    2017-06-01

    Diatoms are amongst the most important marine microalgae in terms of biomass, but little is known concerning the molecular mechanisms that regulate their versatile metabolism. Here, the pennate diatom Phaeodactylum tricornutum was studied at the metabolite and transcriptome level during nitrogen starvation and following imposition of three other stresses that impede growth. The coordinated upregulation of the tricarboxylic acid (TCA) cycle during the nitrogen stress response was the most striking observation. Through co-expression analysis and DNA binding assays, the transcription factor bZIP14 was identified as a regulator of the TCA cycle, also beyond the nitrogen starvation response, namely in diurnal regulation. Accordingly, metabolic and transcriptional shifts were observed upon overexpression of bZIP14 in transformed P. tricornutum cells. Our data indicate that the TCA cycle is a tightly regulated and important hub for carbon reallocation in the diatom cell during nutrient starvation and that bZIP14 is a conserved regulator of this cycle. © 2017 The Authors.

  4. Plan Selections by ZIP Code in the Marketplace April 2015

    Data.gov (United States)

    U.S. Department of Health & Human Services — The dataset provides the total number of Qualified Health Plan selections by ZIP Code for the 37 states that use the HealthCare.gov platform, including the...

  5. Pan-Domain Analysis of ZIP Zinc Transporters

    Directory of Open Access Journals (Sweden)

    Laura E. Lehtovirta-Morley

    2017-12-01

    Full Text Available The ZIP (Zrt/Irt-like protein family of zinc transporters is found in all three domains of life. However, little is known about the phylogenetic relationship amongst ZIP transporters, their distribution, or their origin. Here we employed phylogenetic analysis to explore the evolution of ZIP transporters, with a focus on the major human fungal pathogen, Candida albicans. Pan-domain analysis of bacterial, archaeal, fungal, and human proteins revealed a complex relationship amongst the ZIP family members. Here we report (i a eukaryote-wide group of cellular zinc importers, (ii a fungal-specific group of zinc importers having genetic association with the fungal zincophore, and, (iii a pan-kingdom supercluster made up of two distinct subgroups with orthologues in bacterial, archaeal, and eukaryotic phyla.

  6. Archive of Census Related Products (ACRP): 1990 ZIP Equivalency Files

    Data.gov (United States)

    National Aeronautics and Space Administration — The 1990 Zip Equivalency Files portion of the Archive of Census Related Products (ACRP) contains population and housing data derived from the U.S. Census Bureau's...

  7. Linear gate

    International Nuclear Information System (INIS)

    Suwono.

    1978-01-01

    A linear gate providing a variable gate duration from 0,40μsec to 4μsec was developed. The electronic circuity consists of a linear circuit and an enable circuit. The input signal can be either unipolar or bipolar. If the input signal is bipolar, the negative portion will be filtered. The operation of the linear gate is controlled by the application of a positive enable pulse. (author)

  8. Overexpression of an EaZIP gene devoid of transit peptide sequence induced leaf variegation in tobacco.

    Directory of Open Access Journals (Sweden)

    Xiayu Guan

    Full Text Available Leaf variegation is an ornamental trait that is not only biologically but also economically important. In our previous study, a Mg-protoporphyrin IX monomethyl ester cyclase homologue, EaZIP (Epipremnum aureum leucine zipper was found to be associated with leaf variegation in Epipremnum aureum (Linden & Andre G.S. Bunting. The protein product of this nuclear-encoded gene is targeted back to chloroplast involving in chlorophyll biosynthesis. Based on a web-based homology analysis, the EaZIP was found to lack a chloroplast transit peptide (cTP sequence. In the present study, we tested if overexpression of the EaZIP cDNA with or without the cTP sequence could affect leaf variegation. Transgenic tobacco plants overexpressing EaZIP genes with (EaZIPwcTP and without (EaZIPwocTP cTP sequence were generated. Many plant lines harboring EaZIPwocTP showed variegated leaves, while none of the plant lines with EaZIPwcTP produced such a phenotype. Molecular analysis of T0 plants and selfed T1 progeny, as well as observations of tagged marker GFP (green fluorescent protein did not show any other difference in patterns of gene integrity and expression. Results from this study indicate that transgenic approach for expressing EaZIPwocTP could be a novel method of generating variegated plants even through the underlying mechanisms remain to be elucidated.

  9. A Ramie bZIP Transcription Factor BnbZIP2 Is Involved in Drought, Salt, and Heavy Metal Stress Response.

    Science.gov (United States)

    Huang, Chengjian; Zhou, Jinghua; Jie, Yucheng; Xing, Hucheng; Zhong, Yingli; Yu, Weilin; She, Wei; Ma, Yushen; Liu, Zehang; Zhang, Ying

    2016-12-01

    bZIP transcription factors play key roles in plant growth, development, and stress signaling. A bZIP gene BnbZIP2 (GenBank accession number: KP642148) was cloned from ramie. BnbZIP2 has a 1416 base pair open reading frame, encoding a 471 amino acid protein containing a characteristic bZIP domain and a leucine zipper. BnbZIP2 shares high sequence similarity with bZIP factors from other plants. The BnbZIP2 protein is localized to both nuclei and cytoplasm. Transcripts of BnbZIP2 were found in various tissues in ramie, with significantly higher levels in female and male flowers. Its expression was induced by drought, high salinity, and abscisic acid treatments. Analysis of the cis-elements in promoters of BnbZIP2 identified cis-acting elements involved in growth, developmental processes, and a variety of stress responses. Transgenic Arabidopsis plants' overexpression of BnbZIP2 exhibited more sensitivity to drought and heavy metal Cd stress during seed germination, whereas more tolerance to high-salinity stress than the wild type during both seed germination and plant development. Thus, BnbZIP2 may act as a positive regulator in plants' response to high-salinity stress and be an important candidate gene for molecular breeding of salt-tolerant plants.

  10. MEMS variable capacitance devices utilizing the substrate: II. Zipping varactors

    KAUST Repository

    Elshurafa, Amro M.

    2010-03-22

    This paper, the second and last in this series, introduces PolyMUMPS zipping varactors that exploit the substrate and provide a high tuning range and a high quality factor. Building on the important findings of part I of this paper, the substrate was utilized effectively once again in the design and fabrication of zipping varactors to attain devices with very good performance. Two zipping varactors are proposed, analysed theoretically, simulated, fabricated and tested successfully. The tuning range, quality factor and actuation voltage of those varactors are 4.5, 16.4, 55 V and 4.2, 17, 55 V respectively. Finally, and based on one of the proposed zipping varactors, a very large capacitance value varactor array, with a tuning range of 5.3, was designed and tested. To the best of our knowledge, these zipping varactors exhibit the best reported characteristics in PolyMUMPS to date within their category in terms of tuning range, quality factor, required actuation voltage and total area consumed. © 2010 IOP Publishing Ltd.

  11. Zipping dielectric elastomer actuators: characterization, design and modeling

    International Nuclear Information System (INIS)

    Maffli, L; Rosset, S; Shea, H R

    2013-01-01

    We report on miniature dielectric elastomer actuators (DEAs) operating in zipping mode with an analytical model that predicts their behavior. Electrostatic zipping is a well-known mechanism in silicon MEMS to obtain large deformations and forces at lower voltages than for parallel plate electrostatic actuation. We extend this concept to DEAs, which allows us to obtain much larger out-of-plane displacements compared to silicon thanks to the softness of the elastomer membrane. We study experimentally the effect of sidewall angles and elastomer prestretch on 2.3 mm diameter actuators with PDMS membranes. With 15° and 22.5° sidewall angles, the devices zip in a bistable manner down 300 μm to the bottom of the chambers. The highly tunable bistable behavior is controllable by both chamber geometry and membrane parameters. Other specific characteristics of zipping DEAs include well-controlled deflected shape, tunable displacement versus voltage characteristics to virtually any shape, including multi-stable modes, sealing of embedded holes or channels for valving action and the reduction of the operating voltage. These properties make zipping DEAs an excellent candidate for applications such as integrated microfluidics actuators or Braille displays. (paper)

  12. Expression analysis of OsbZIP transcription factors in resistance ...

    African Journals Online (AJOL)

    They have been shown to regulate diverse plant specific phenomena, including germination, floral induction and development, seed maturation, photomorphogenesis, biotic and abiotic stresses. Resistance response mediated by the rice blast resistance gene Pi36 is a typical signal transduction, in which 12 OsbZIP genes ...

  13. The Evolutionary unZIPping of a Dimerization Motif—A Comparison of ZIP and PrP Architectures

    Directory of Open Access Journals (Sweden)

    Jian Hu

    2017-12-01

    Full Text Available The cellular prion protein, notorious for its causative role in a range of fatal neurodegenerative diseases, evolved from a Zrt-/Irt-like Protein (ZIP zinc transporter approximately 500 million years ago. Whilst atomic structures for recombinant prion protein (PrP from various species have been available for some time, and are believed to stand for the structure of PrPC, the first structure of a ZIP zinc transporter ectodomain was reported only recently. Here, we compare this ectodomain structure to structures of recombinant PrP. A shared feature of both is a membrane-adjacent helix-turn-helix fold that is coded by a separate exon in the respective ZIP transporters and is stabilized by a disulfide bridge. A ‘CPALL’ amino acid motif within this cysteine-flanked core domain appears to be critical for dimerization and has undergone stepwise regression in fish and mammalian prion proteins. These insights are intriguing in the context of repeated observations of PrP dimers. Other structural elements of ZIP transporters and PrP are discussed with a view to distilling shared versus divergent biological functions.

  14. Gene family structure, expression and functional analysis of HD-Zip III genes in angiosperm and gymnosperm forest trees.

    Science.gov (United States)

    Côté, Caroline L; Boileau, Francis; Roy, Vicky; Ouellet, Mario; Levasseur, Caroline; Morency, Marie-Josée; Cooke, Janice E K; Séguin, Armand; MacKay, John J

    2010-12-11

    Class III Homeodomain Leucine Zipper (HD-Zip III) proteins have been implicated in the regulation of cambium identity, as well as primary and secondary vascular differentiation and patterning in herbaceous plants. They have been proposed to regulate wood formation but relatively little evidence is available to validate such a role. We characterised and compared HD-Zip III gene family in an angiosperm tree, Populus spp. (poplar), and the gymnosperm Picea glauca (white spruce), representing two highly evolutionarily divergent groups. Full-length cDNA sequences were isolated from poplar and white spruce. Phylogenetic reconstruction indicated that some of the gymnosperm sequences were derived from lineages that diverged earlier than angiosperm sequences, and seem to have been lost in angiosperm lineages. Transcript accumulation profiles were assessed by RT-qPCR on tissue panels from both species and in poplar trees in response to an inhibitor of polar auxin transport. The overall transcript profiles HD-Zip III complexes in white spruce and poplar exhibited substantial differences, reflecting their evolutionary history. Furthermore, two poplar sequences homologous to HD-Zip III genes involved in xylem development in Arabidopsis and Zinnia were over-expressed in poplar plants. PtaHB1 over-expression produced noticeable effects on petiole and primary shoot fibre development, suggesting that PtaHB1 is involved in primary xylem development. We also obtained evidence indicating that expression of PtaHB1 affected the transcriptome by altering the accumulation of 48 distinct transcripts, many of which are predicted to be involved in growth and cell wall synthesis. Most of them were down-regulated, as was the case for several of the poplar HD-Zip III sequences. No visible physiological effect of over-expression was observed on PtaHB7 transgenic trees, suggesting that PtaHB1 and PtaHB7 likely have distinct roles in tree development, which is in agreement with the functions that

  15. Gene family structure, expression and functional analysis of HD-Zip III genes in angiosperm and gymnosperm forest trees

    Directory of Open Access Journals (Sweden)

    Cooke Janice EK

    2010-12-01

    Full Text Available Abstract Background Class III Homeodomain Leucine Zipper (HD-Zip III proteins have been implicated in the regulation of cambium identity, as well as primary and secondary vascular differentiation and patterning in herbaceous plants. They have been proposed to regulate wood formation but relatively little evidence is available to validate such a role. We characterised and compared HD-Zip III gene family in an angiosperm tree, Populus spp. (poplar, and the gymnosperm Picea glauca (white spruce, representing two highly evolutionarily divergent groups. Results Full-length cDNA sequences were isolated from poplar and white spruce. Phylogenetic reconstruction indicated that some of the gymnosperm sequences were derived from lineages that diverged earlier than angiosperm sequences, and seem to have been lost in angiosperm lineages. Transcript accumulation profiles were assessed by RT-qPCR on tissue panels from both species and in poplar trees in response to an inhibitor of polar auxin transport. The overall transcript profiles HD-Zip III complexes in white spruce and poplar exhibited substantial differences, reflecting their evolutionary history. Furthermore, two poplar sequences homologous to HD-Zip III genes involved in xylem development in Arabidopsis and Zinnia were over-expressed in poplar plants. PtaHB1 over-expression produced noticeable effects on petiole and primary shoot fibre development, suggesting that PtaHB1 is involved in primary xylem development. We also obtained evidence indicating that expression of PtaHB1 affected the transcriptome by altering the accumulation of 48 distinct transcripts, many of which are predicted to be involved in growth and cell wall synthesis. Most of them were down-regulated, as was the case for several of the poplar HD-Zip III sequences. No visible physiological effect of over-expression was observed on PtaHB7 transgenic trees, suggesting that PtaHB1 and PtaHB7 likely have distinct roles in tree development

  16. Genomic survey of bZIP transcription factor genes related to tanshinone biosynthesis in Salvia miltiorrhiza

    Directory of Open Access Journals (Sweden)

    Yu Zhang

    2018-03-01

    Full Text Available Tanshinones are a class of bioactive components in the traditional Chinese medicine Salvia miltiorrhiza, and their biosynthesis and regulation have been widely studied. Current studies show that basic leucine zipper (bZIP proteins regulate plant secondary metabolism, growth and developmental processes. However, the bZIP transcription factors involved in tanshinone biosynthesis are unknown. Here, we conducted the first genome-wide survey of the bZIP gene family and analyzed the phylogeny, gene structure, additional conserved motifs and alternative splicing events in S. miltiorrhiza. A total of 70 SmbZIP transcription factors were identified and categorized into 11 subgroups based on their phylogenetic relationships with those in Arabidopsis. Moreover, seventeen SmbZIP genes underwent alternative splicing events. According to the transcriptomic data, the SmbZIP genes that were highly expressed in the Danshen root and periderm were selected. Based on the prediction of bZIP binding sites in the promoters and the co-expression analysis and co-induction patterns in response to Ag+ treatment via quantitative real-time polymerase chain reaction (qRT-PCR, we concluded that SmbZIP7 and SmbZIP20 potentially participate in the regulation of tanshinone biosynthesis. These results provide a foundation for further functional characterization of the candidate SmbZIP genes, which have the potential to increase tanshinone production. KEY WORDS: bZIP genes, Salvia miltiorrhiza, Phylogenetic analysis, Expression pattern analysis, Tanshinone biosynthesis

  17. Zip4 mediated zinc influx stimulates insulin secretion in pancreatic beta cells.

    Directory of Open Access Journals (Sweden)

    Alexandre B Hardy

    Full Text Available Zinc has an important role in normal pancreatic beta cell physiology as it regulates gene transcription, insulin crystallization and secretion, and cell survival. Nevertheless, little is known about how zinc is transported through the plasma membrane of beta cells and which of the class of zinc influx transporters (Zip is involved. Zip4 was previously shown to be expressed in human and mouse beta cells; however, its function there is still unknown. Therefore, the aim of this study was to define the zinc transport role of Zip4 in beta cells. To investigate this, Zip4 was over-expressed in MIN6 beta cells using a pCMV6-Zip4GFP plasmid. Organelle staining combined with confocal microscopy showed that Zip4 exhibits a widespread localization in MIN6 cells. Time-lapse zinc imaging experiments showed that Zip4 increases cytoplasmic zinc levels. This resulted in increased granular zinc content and glucose-stimulated insulin secretion. Interestingly, it is unlikely that the increased glucose stimulated insulin secretion was triggered by a modulation of mitochondrial function, as mitochondrial membrane potential remained unchanged. To define the role of Zip4 in-vivo, we generated a beta cell-specific knockout mouse model (Zip4BKO. Deletion of the Zip4 gene was confirmed in Zip4BKO islets by PCR, RT-PCR, and immuno-histochemistry. Zip4BKO mice showed slightly improved glucose homeostasis but no change in insulin secretion during an oral glucose tolerance test. While Zip4 was not found to be essential for proper glucose homeostasis and insulin secretion in vivo in mice, this study also found that Zip4 mediates increases in cytoplasmic and granular zinc pools and stimulates glucose dependant insulin secretion in-vitro.

  18. The bZIP protein from Tamarix hispida, ThbZIP1, is ACGT elements binding factor that enhances abiotic stress signaling in transgenic Arabidopsis.

    Science.gov (United States)

    Ji, Xiaoyu; Liu, Guifeng; Liu, Yujia; Zheng, Lei; Nie, Xianguang; Wang, Yucheng

    2013-10-04

    Tamarix spp. are woody halophyte, which are very tolerant to abiotic stresses such as salinity and drought, but little is known about their specific stress response systems. Basic leucine zipper proteins (bZIPs) play important roles in the ability of plants to withstand adverse environmental conditions. However, their exact roles in abiotic stress tolerance are still not fully known. In the current study, we functionally characterized a bZIP gene (ThbZIP1) from Tamarix hispida in response to abiotic stresses. We addressed the regulatory network of ThbZIP1 in three levels, i.e. its upstream regulators, the cis-acting elements recognized by ThbZIP1, and its downstream target genes. Two MYCs were found to bind to E-box, in the promoter of ThbZIP1 to activate its expression. Expression of ThbZIP1 is induced by ABA, salt, drought, methyl viologen and cold. ThbZIP1 can specifically bind to ACGT elements, with the highest binding affinity to the C-box, followed by the G-box and lastly the A-box. Compared with wild-type (Col-0) Arabidopsis, transgenic plants expressing ThbZIP1 had an increased tolerance to drought and salt, but had an increased sensitivity to ABA during seed germination and root growth; meanwhile, ROS level, cell death and water loss rate in transgenic plants were significantly reduced. Microarray analyses showed that many ROS scavenging genes were up-regulated by ThbZIP1 under salt stress conditions. Based on these data, we suggest that ThbZIP1 confers abiotic stress tolerance through activating stress tolerance genes to modulate ROS scavenging ability and other physiological changes involved in stress tolerance, and plays an important role in the ABA-mediated stress response of T. hispida.

  19. Topoisomerase II minimizes DNA entanglements by proofreading DNA topology after DNA strand passage.

    Science.gov (United States)

    Martínez-García, Belén; Fernández, Xavier; Díaz-Ingelmo, Ofelia; Rodríguez-Campos, Antonio; Manichanh, Chaysavanh; Roca, Joaquim

    2014-02-01

    By transporting one DNA double helix (T-segment) through a double-strand break in another (G-segment), topoisomerase II reduces fractions of DNA catenanes, knots and supercoils to below equilibrium values. How DNA segments are selected to simplify the equilibrium DNA topology is enigmatic, and the biological relevance of this activity is unclear. Here we examined the transit of the T-segment across the three gates of topoisomerase II (entry N-gate, DNA-gate and exit C-gate). Our experimental results uncovered that DNA transport probability is determined not only during the capture of a T-segment at the N-gate. When a captured T-segment has crossed the DNA-gate, it can backtrack to the N-gate instead of exiting by the C-gate. When such backtracking is precluded by locking the N-gate or by removing the C-gate, topoisomerase II no longer simplifies equilibrium DNA topology. Therefore, we conclude that the C-gate enables a post-DNA passage proofreading mechanism, which challenges the release of passed T-segments to either complete or cancel DNA transport. This proofreading activity not only clarifies how type-IIA topoisomerases simplify the equilibrium topology of DNA in free solution, but it may explain also why these enzymes are able to solve the topological constraints of intracellular DNA without randomly entangling adjacent chromosomal regions.

  20. A model of competing species that exhibits zip bifurcation

    Directory of Open Access Journals (Sweden)

    Luis F. Echeverri

    2017-01-01

    Full Text Available El objetivo de este trabajo es presentar un modelo concreto d e poblaciones de especies en competición que exhibe la bifurc ación Zip. La bifurcación zip fue introducida por Farkas en 1984 para un si stema tridi- mensional de ecuaciones diferenciales ordinarias que desc ribe un quimiostato. Estudiaremos un sistema tridimensional de ecuaciones dife renciales ordinarias que modela la competición de dos poblaciones distintas de pr edadores por una única población presa. El sistema usa funciones trigonomét ricas concretas pa- ra representar la tasa de crecimiento de la presa y la respues ta funcional del predador. El modelo exhibe diferentes clases de comportami entos y muestra ejemplos de los llamados principio de exclusión competitiva y la competición de un r-estratega contra un k-estratega . Adicionalmente, para ilustrar la bi- furcacion zip, presentaremos algunas simulaciones numéri cas.

  1. Data correction on July 4th, 2012 - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available e. There is no correction in the CEL files. - Hematology open_tggates_hematology.zip (636 KB) Simple search ...List Contact us Open TG-GATEs Data correction on July 4th, 2012 The data have been corrected because of having errors on the hematolo...gy and biochemistry data obtained from the in vivo tests with rats administered the

  2. Determining Market Categorization of United States Zip Codes for Purposes of Army Recruiting

    Science.gov (United States)

    2016-06-01

    to the areas that are expected to have higher production . This circular logic presents the risk that there are ZIP codes in the United States that... production activities deduction A03240 Income Tax Average Domestic production activities deduction amount N04470 Income Tax Percentage of returns...Zone Improvement Plan (ZIP) codes to assign recruiters and to track recruit production . ZIP codes have different densities of potential recruits; the

  3. Phylogenetic analysis of F-bZIP transcription factors indicates conservation of the zinc deficiency response across land plants

    DEFF Research Database (Denmark)

    Castro, Pedro Humberto Araújo R F; Lilay, Grmay Hailu; Muñoz-Mérida, Antonio

    2017-01-01

    data, we performed an evolutionary and structural characterization of plant F-bZIPs. We observed divergence during seed plant evolution, into two groups and inferred different selective pressures for each. Group 1 contains AtbZIP19 and AtbZIP23 and appears more conserved, whereas Group 2, containing......Basic leucine zipper (bZIP) transcription factors control important developmental and physiological processes in plants. In Arabidopsis thaliana, the three gene F-bZIP subfamily has been associated with zinc deficiency and salt stress response. Benefiting from the present abundance of plant genomic...... of AtZIP4. A survey of AtZIP4 orthologs promoters across different plant taxa revealed an enrichment of the Zinc Deficiency Response Element (ZDRE) to which both AtbZIP19/23 bind. Overall, our results indicate that while the AtbZIP24 function in the regulation of the salt stress response may...

  4. Stress sensing in plants by the ER stress sensor/transducer, bZIP28

    Directory of Open Access Journals (Sweden)

    Renu eSrivastava

    2014-02-01

    Full Text Available Two classes of ER stress sensors are known in plants, membrane associated bZIP transcription factors and RNA splicing factors. ER stress occurs under adverse environmental conditions and results from the accumulation of misfolded or unfolded proteins in the ER lumen. One of the membrane-associated transcription factors activated by heat and ER stress agents is bZIP28. In its inactive form, bZIP28 is a type II protein with a single pass transmembrane domain, residing in the ER. bZIP28’s N-terminus, containing a transcriptional activation domain, is oriented towards the cytoplasm and its C-terminal tail is inserted into the ER lumen. In response to stress, bZIP28 exits the ER and moves to the Golgi where it is proteolytically processed, liberating its cytosolic component which relocates to the nucleus to upregulate stress-response genes. bZIP28 is thought to sense stress through its interaction with the major ER chaperone, BIP. BiP binds to bZIP28’s lumenal domain under unstressed conditions and retains it in the ER. BIP binds to the intrinsically disordered regions on bZIP28’s lumen-facing tail. A truncated form of bZIP28, without its C-terminal tail is not retained in the ER but migrates constitutively to the nucleus. Upon stress, BiP releases bZIP28 allowing it to exit the ER. One model to account for the release of bZIP28 by BiP is that BiP is competed away from bZIP28 by the accumulation of misfolded proteins in the ER. However, other forces such as changes in energy charge levels, redox conditions or interaction with DNAJ proteins may also promote release of bZIP28 from BiP. Movement of bZIP28 from the ER to the Golgi is assisted by the interaction of elements of the COPII machinery with the cytoplasmic domain of bZIP28. Thus, the mobilization of bZIP28 in response to stress involves the dissociation of factors that retain it in the ER and the association of factors that mediate its further organelle-to-organelle movement.

  5. Extreme Population Differences in the Human Zinc Transporter ZIP4 (SLC39A4) Are Explained by Positive Selection in Sub-Saharan Africa

    Science.gov (United States)

    Pybus, Marc; Andrews, Glen K.; Lalueza-Fox, Carles; Comas, David; Sekler, Israel; de la Rasilla, Marco; Rosas, Antonio; Stoneking, Mark; Valverde, Miguel A.; Vicente, Rubén; Bosch, Elena

    2014-01-01

    Extreme differences in allele frequency between West Africans and Eurasians were observed for a leucine-to-valine substitution (Leu372Val) in the human intestinal zinc uptake transporter, ZIP4, yet no further evidence was found for a selective sweep around the ZIP4 gene (SLC39A4). By interrogating allele frequencies in more than 100 diverse human populations and resequencing Neanderthal DNA, we confirmed the ancestral state of this locus and found a strong geographical gradient for the derived allele (Val372), with near fixation in West Africa. In extensive coalescent simulations, we show that the extreme differences in allele frequency, yet absence of a classical sweep signature, can be explained by the effect of a local recombination hotspot, together with directional selection favoring the Val372 allele in Sub-Saharan Africans. The possible functional effect of the Leu372Val substitution, together with two pathological mutations at the same codon (Leu372Pro and Leu372Arg) that cause acrodermatitis enteropathica (a disease phenotype characterized by extreme zinc deficiency), was investigated by transient overexpression of human ZIP4 protein in HeLa cells. Both acrodermatitis mutations cause absence of the ZIP4 transporter cell surface expression and nearly absent zinc uptake, while the Val372 variant displayed significantly reduced surface protein expression, reduced basal levels of intracellular zinc, and reduced zinc uptake in comparison with the Leu372 variant. We speculate that reduced zinc uptake by the ZIP4-derived Val372 isoform may act by starving certain pathogens of zinc, and hence may have been advantageous in Sub-Saharan Africa. Moreover, these functional results may indicate differences in zinc homeostasis among modern human populations with possible relevance for disease risk. PMID:24586184

  6. Extreme population differences in the human zinc transporter ZIP4 (SLC39A4 are explained by positive selection in Sub-Saharan Africa.

    Directory of Open Access Journals (Sweden)

    Johannes Engelken

    2014-02-01

    Full Text Available Extreme differences in allele frequency between West Africans and Eurasians were observed for a leucine-to-valine substitution (Leu372Val in the human intestinal zinc uptake transporter, ZIP4, yet no further evidence was found for a selective sweep around the ZIP4 gene (SLC39A4. By interrogating allele frequencies in more than 100 diverse human populations and resequencing Neanderthal DNA, we confirmed the ancestral state of this locus and found a strong geographical gradient for the derived allele (Val372, with near fixation in West Africa. In extensive coalescent simulations, we show that the extreme differences in allele frequency, yet absence of a classical sweep signature, can be explained by the effect of a local recombination hotspot, together with directional selection favoring the Val372 allele in Sub-Saharan Africans. The possible functional effect of the Leu372Val substitution, together with two pathological mutations at the same codon (Leu372Pro and Leu372Arg that cause acrodermatitis enteropathica (a disease phenotype characterized by extreme zinc deficiency, was investigated by transient overexpression of human ZIP4 protein in HeLa cells. Both acrodermatitis mutations cause absence of the ZIP4 transporter cell surface expression and nearly absent zinc uptake, while the Val372 variant displayed significantly reduced surface protein expression, reduced basal levels of intracellular zinc, and reduced zinc uptake in comparison with the Leu372 variant. We speculate that reduced zinc uptake by the ZIP4-derived Val372 isoform may act by starving certain pathogens of zinc, and hence may have been advantageous in Sub-Saharan Africa. Moreover, these functional results may indicate differences in zinc homeostasis among modern human populations with possible relevance for disease risk.

  7. Translocation, switching and gating: potential roles for ATP in long-range communication on DNA by Type III restriction endonucleases.

    Science.gov (United States)

    Szczelkun, Mark D

    2011-04-01

    To cleave DNA, the Type III RM (restriction-modification) enzymes must communicate the relative orientation of two recognition sequences, which may be separated by many thousands of base pairs. This long-range interaction requires ATP hydrolysis by a helicase domain, and both active (DNA translocation) and passive (DNA sliding) modes of motion along DNA have been proposed. Potential roles for ATP binding and hydrolysis by the helicase domains are discussed, with a focus on bipartite ATPases that act as molecular switches.

  8. Simultaneous Detection of Different MicroRNA Types Using the ZIP-Code Array System

    Directory of Open Access Journals (Sweden)

    Sonja U. Weishaupt

    2013-01-01

    Full Text Available MicroRNAs (miRNAs are important negative regulators of gene expression. Their implication in tumorigenesis is based on their dysregulation in many human cancer diseases. Interestingly, in tumor cells, an altered ratio of precursor and mature miRNA levels has been described. Consequently, differences in miRNA type levels have a high potential as biomarkers and comparative high-throughput-based detection might permit a more accurate characterization of subtypes, especially in the case of very heterogeneous tumor entities. Several molecular methods exist for the detection of mature and precursor miRNAs. DNA microarrays are predestinated as a high-throughput method for comprehensive miRNA detection in tumors. However, the simultaneous array-based detection of both these miRNA types is limited because the mature miRNA sequence is identically present in both forms. Here we present a ZIP-code DNA microarray-based system in combination with a novel labeling approach, which enables the simultaneous detection of precursor and mature miRNAs in one single experiment. Using synthetic miRNA templates, we demonstrate the specificity of the method for the different miRNA types, as well as the detection range up to four orders of magnitude. Moreover, mature and precursor miRNAs were detected and validated in human tumor cells.

  9. HvZIP7 mediates zinc accumulation in barley (Hordeum vulgare) at moderately high zinc supply

    DEFF Research Database (Denmark)

    Tiong, Jingwen; Mcdonald, Glenn K.; Genc, Yusuf

    2014-01-01

    in dicots. Overexpression of HvZIP7 in barley plants increased Zn uptake when moderately high concentrations of Zn were supplied. Significantly, there was a specific enhancement of shoot Zn accumulation, with no measurable increase in iron (Fe), manganese (Mn), copper (Cu) or cadmium (Cd). HvZIP7 displays...

  10. Reprogramming of metabolism by the Arabidopsis thaliana bZIP11 transcription factor

    NARCIS (Netherlands)

    Ma, J.

    2012-01-01

    The Arabidopsis bZIP11 transcription factor is known to regulate amino acid metabolism, and transcriptomic analysis suggests that bZIP11 has a broader regulatory effects in metabolism. Moreover, sucrose controls its translation via its uORF and all the available evidences point to the fact that

  11. Differential expression of four soybean bZIP genes during Phakopsora pachyrhizi infection.

    Science.gov (United States)

    Alves, Murilo S; Soares, Zamira G; Vidigal, Pedro M P; Barros, Everaldo G; Poddanosqui, Adriana M P; Aoyagi, Luciano N; Abdelnoor, Ricardo V; Marcelino-Guimarães, Francismar C; Fietto, Luciano G

    2015-11-01

    Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is one of most important diseases in the soybean (Glycine max (L.) Merr.) agribusiness. The identification and characterization of genes related to plant defense responses to fungal infection are essential to develop ASR-resistant plants. In this work, we describe four soybean genes, GmbZIP62, GmbZIP105, GmbZIPE1, and GmbZIPE2, which encode transcription factors containing a basic leucine zipper (bZIP) domain from two divergent classes, and that are responsive to P. pachyrhizi infection. Molecular phylogenetic analyses demonstrated that these genes encode proteins similar to bZIP factors responsive to pathogens. Yeast transactivation assays showed that only GmbZIP62 has strong transactivation activity in yeast. In addition, three of the bZIP transcription factors analyzed were also differentially expressed by plant defense hormones, and all were differentially expressed by fungal attack, indicating that these proteins might participate in response to ASR infection. The results suggested that these bZIP proteins are part of the plant defense response to P. pachyrhizi infection, by regulating the gene expression related to ASR infection responses. These bZIP genes are potential targets to obtain new soybean genotypes resistant to ASR.

  12. Efficient Proximity Computation Techniques Using ZIP Code Data for Smart Cities †

    Directory of Open Access Journals (Sweden)

    Muhammad Harist Murdani

    2018-03-01

    Full Text Available In this paper, we are interested in computing ZIP code proximity from two perspectives, proximity between two ZIP codes (Ad-Hoc and neighborhood proximity (Top-K. Such a computation can be used for ZIP code-based target marketing as one of the smart city applications. A naïve approach to this computation is the usage of the distance between ZIP codes. We redefine a distance metric combining the centroid distance with the intersecting road network between ZIP codes by using a weighted sum method. Furthermore, we prove that the results of our combined approach conform to the characteristics of distance measurement. We have proposed a general and heuristic approach for computing Ad-Hoc proximity, while for computing Top-K proximity, we have proposed a general approach only. Our experimental results indicate that our approaches are verifiable and effective in reducing the execution time and search space.

  13. The Tumor Suppressor, P53, Decreases the Metal Transporter, ZIP14

    Directory of Open Access Journals (Sweden)

    Ningning Zhao

    2017-12-01

    Full Text Available Loss of p53’s proper function accounts for over half of identified human cancers. We identified the metal transporter ZIP14 (Zinc-regulated transporter (ZRT and Iron-regulated transporter (IRT-like Protein 14 as a p53-regulated protein. ZIP14 protein levels were upregulated by lack of p53 and downregulated by increased p53 expression. This regulation did not fully depend on the changes in ZIP14’s mRNA expression. Co-precipitation studies indicated that p53 interacts with ZIP14 and increases its ubiquitination and degradation. Moreover, knockdown of p53 resulted in higher non-transferrin-bound iron uptake, which was mediated by increased ZIP14 levels. Our study highlights a role for p53 in regulating nutrient metabolism and provides insight into how iron and possibly other metals such as zinc and manganese could be regulated in p53-inactivated tumor cells.

  14. Efficient Proximity Computation Techniques Using ZIP Code Data for Smart Cities †.

    Science.gov (United States)

    Murdani, Muhammad Harist; Kwon, Joonho; Choi, Yoon-Ho; Hong, Bonghee

    2018-03-24

    In this paper, we are interested in computing ZIP code proximity from two perspectives, proximity between two ZIP codes ( Ad-Hoc ) and neighborhood proximity ( Top-K ). Such a computation can be used for ZIP code-based target marketing as one of the smart city applications. A naïve approach to this computation is the usage of the distance between ZIP codes. We redefine a distance metric combining the centroid distance with the intersecting road network between ZIP codes by using a weighted sum method. Furthermore, we prove that the results of our combined approach conform to the characteristics of distance measurement. We have proposed a general and heuristic approach for computing Ad-Hoc proximity, while for computing Top-K proximity, we have proposed a general approach only. Our experimental results indicate that our approaches are verifiable and effective in reducing the execution time and search space.

  15. ZIP13: A Study of Drosophila Offers an Alternative Explanation for the Corresponding Human Disease

    Directory of Open Access Journals (Sweden)

    Guiran Xiao

    2018-01-01

    Full Text Available The fruit fly Drosophila melanogaster has become an important model organism to investigate metal homeostasis and human diseases. Previously we identified dZIP13 (CG7816, a member of the ZIP transporter family (SLC39A and presumably a zinc importer, is in fact physiologically primarily responsible to move iron from the cytosol into the secretory compartments in the fly. This review will discuss the implication of this finding for the etiology of Spondylocheirodysplasia-Ehlers-Danlos Syndrome (SCD–EDS, a human disease defective in ZIP13. We propose an entirely different model in that lack of iron in the secretory compartment may underlie SCD-EDS. Altogether three different working models are discussed, supported by relevant findings made in different studies, with uncertainties, and questions remained to be solved. We speculate that the distinct ZIP13 sequence features, different from those of all other ZIP family members, may confer it special transport properties.

  16. The regulatory network of ThbZIP1 in response to abscisic acid treatment

    Directory of Open Access Journals (Sweden)

    Xiaoyu eJi

    2015-02-01

    Full Text Available Previously, a bZIP transcription factor from Tamarix hispida, ThbZIP1, was characterized: plants overexpressing ThbZIP1 displayed improved salt stress tolerance but were sensitive to abscisic acid (ABA. In the current study, we further characterized the regulatory network of ThbZIP1 and the mechanism of ABA sensitivity mediated by ThbZIP1. An ABF transcription factor from T. hispida, ThABF1, directly regulates the expression of ThbZIP1. Microarray analysis identified 1,662 and 1,609 genes that were respectively significantly upregulated or downregulated by ThbZIP1 when exposed to ABA. GO analysis showed that the processes including response to stimulus, catalytic activity, binding function, and metabolic process were highly altered in ThbZIP1 expressing plants exposed to ABA. The gene expression in ThbZIP1 transformed plants were compared between exposed to ABA and salt on the genome scale. Genes differentially regulated by both salt and ABA treatment only accounted for 9.75% of total differentially regulated genes. GO analysis showed that structural molecule activity, organelle part, membrane-enclosed lumen, reproduction and reproductive process are enhanced by ABA but inhibited by salt stress. Conversely, immune system and multi-organism process were improved by salt but inhibited by ABA. Transcription regulator activity, enzyme regulator activity and developmental process were significantly altered by ABA but were not affected by salt stress. Our study provides insights into how ThbZIP1 mediates ABA and salt stress response at the molecular level.

  17. Identification of an Arabidopsis transmembrane bZIP transcription factor involved in the endoplasmic reticulum stress response

    International Nuclear Information System (INIS)

    Tajima, Hiromi; Iwata, Yuji; Iwano, Megumi; Takayama, Seiji; Koizumi, Nozomu

    2008-01-01

    Among 75 bZIP transcription factors identified in Arabidopsis, 3 (AtbZIP17, AtbZIP28, and AtbZIP49) possess a putative transmembrane domain (TMD) in addition to AtbZIP60, which was characterized previously. In the present study, cDNAs of AtbZIP17 and AtbZIP28 were isolated. Truncated forms of AtbZIP17 and AtbZIP28 lacking the C-terminal domain including TMD were examined as putative active forms. One of them, AtbZIP28ΔC, activated BiP1 and BiP3 promoters through the cis-elements P-UPRE and ERSE responsible for the ER stress response. Subsequently, a fusion protein of green fluorescent protein (GFP) and AtbZIP28 was expressed in Arabidopsis cultured cells. Under non-stress conditions, GFP fluorescence localization almost overlapped with an ER marker; however, tunicamycin and dithiothreitol treatment clearly increased GFP fluorescence in the nucleus suggesting that the N-terminal fragment of AtbZIP28 translocates to the nucleus in response to ER stress

  18. New gate opening hours

    CERN Multimedia

    GS Department

    2009-01-01

    Please note the new opening hours of the gates as well as the intersites tunnel from the 19 May 2009: GATE A 7h - 19h GATE B 24h/24 GATE C 7h - 9h\t17h - 19h GATE D 8h - 12h\t13h - 16h GATE E 7h - 9h\t17h - 19h Prévessin 24h/24 The intersites tunnel will be opened from 7h30 to 18h non stop. GS-SEM Group Infrastructure and General Services Department

  19. Structural insights of ZIP4 extracellular domain critical for optimal zinc transport

    Science.gov (United States)

    Zhang, Tuo; Sui, Dexin; Hu, Jian

    2016-06-01

    The ZIP zinc transporter family is responsible for zinc uptake from the extracellular milieu or intracellular vesicles. The LIV-1 subfamily, containing nine out of the 14 human ZIP proteins, is featured with a large extracellular domain (ECD). The critical role of the ECD is manifested by disease-causing mutations on ZIP4, a representative LIV-1 protein. Here we report the first crystal structure of a mammalian ZIP4-ECD, which reveals two structurally independent subdomains and an unprecedented dimer centred at the signature PAL motif. Structure-guided mutagenesis, cell-based zinc uptake assays and mapping of the disease-causing mutations indicate that the two subdomains play pivotal but distinct roles and that the bridging region connecting them is particularly important for ZIP4 function. These findings lead to working hypotheses on how ZIP4-ECD exerts critical functions in zinc transport. The conserved dimeric architecture in ZIP4-ECD is also demonstrated to be a common structural feature among the LIV-1 proteins.

  20. Molecular pathogenesis of Spondylocheirodysplastic Ehlers-Danlos syndrome caused by mutant ZIP13 proteins

    Science.gov (United States)

    Bin, Bum-Ho; Hojyo, Shintaro; Hosaka, Toshiaki; Bhin, Jinhyuk; Kano, Hiroki; Miyai, Tomohiro; Ikeda, Mariko; Kimura-Someya, Tomomi; Shirouzu, Mikako; Cho, Eun-Gyung; Fukue, Kazuhisa; Kambe, Taiho; Ohashi, Wakana; Kim, Kyu-Han; Seo, Juyeon; Choi, Dong-Hwa; Nam, Yeon-Ju; Hwang, Daehee; Fukunaka, Ayako; Fujitani, Yoshio; Yokoyama, Shigeyuki; Superti-Furga, Andrea; Ikegawa, Shiro; Lee, Tae Ryong; Fukada, Toshiyuki

    2014-01-01

    The zinc transporter protein ZIP13 plays critical roles in bone, tooth, and connective tissue development, and its dysfunction is responsible for the spondylocheirodysplastic form of Ehlers-Danlos syndrome (SCD-EDS, OMIM 612350). Here, we report the molecular pathogenic mechanism of SCD-EDS caused by two different mutant ZIP13 proteins found in human patients: ZIP13G64D, in which Gly at amino acid position 64 is replaced by Asp, and ZIP13ΔFLA, which contains a deletion of Phe-Leu-Ala. We demonstrated that both the ZIP13G64D and ZIP13ΔFLA protein levels are decreased by degradation via the valosin-containing protein (VCP)-linked ubiquitin proteasome pathway. The inhibition of degradation pathways rescued the protein expression levels, resulting in improved intracellular Zn homeostasis. Our findings uncover the pathogenic mechanisms elicited by mutant ZIP13 proteins. Further elucidation of these degradation processes may lead to novel therapeutic targets for SCD-EDS. PMID:25007800

  1. R2 & NE: NAVTEQ 2011 Q3 ZIP Code 5-Digit Area Points for the United States, including Puerto Rico and the US Virgin Islands in SDC Format

    Data.gov (United States)

    U.S. Environmental Protection Agency — The USA_ZIP5_PNTS layer contains 5 digit ZIP code points. Each feature in the USA_ZIP5_POLYS layer encloses an associated USA_ZIP5_PNTS feature. This NAVTEQ dataset...

  2. Compound list: pemoline [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available pemoline PML 00051 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/pemoline....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/pemoline....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/pemoline.Rat.in_vivo.Liver.Single.zip ftp://ftp.bi...-tggates/LATEST/Rat/in_vivo/Liver/Repeat/pemoline.Rat.in_vivo.Liver.Repeat.zip ...

  3. Compound list: ajmaline [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available ajmaline AJM 00118 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/ajmaline....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/ajmaline....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/ajmaline.Rat.in_vivo.Liver.Single.zip ftp://ftp.bi...-tggates/LATEST/Rat/in_vivo/Liver/Repeat/ajmaline.Rat.in_vivo.Liver.Repeat.zip ...

  4. Understanding evolutionary paradigm of knockdown resistance in mosquitoes by analyzing DNA sequence polymorphisms in voltage-gated sodium channel in Culex quinquefasciatus

    Directory of Open Access Journals (Sweden)

    Manas Sarkar

    2011-09-01

    Full Text Available The Voltage Gated Sodium Channel (VGSC is critical for binding of different insecticides and plays a key role in insecticide resistance. The insect sodium channel consists of four homologous domains (I to IV, each containing six transmembrane segments (S1 to S6. An important mechanism of resistance to DDT and pyrethroids is termed knockdown resistance (kdr, caused by a single nucleotide polymorphism in IIS6 domain of sodium channels. We analyzed the polymorphisms, nucleotide diversity, and phylogenies in VGSC-IIS6 gene in Culex quinquefasciatus from India. We analyzed the neutral model / hypothesis to infer if natural selection is acting upon the analyzed vgsc gene. Tajima’s D, Fu and Li’s D* and F* and Fu’s Fs test were performed to determine whether the distribution of nucleotide variation within the samples was consistent with neutral model. We theorized that the evolutionary pattern of intra-population distribution of variability in vgsc gene is consistent with the neutral expectation.

  5. Recipients of Excess Food by Zip Code, US and Territories, 2015, EPA Region 9

    Data.gov (United States)

    U.S. Environmental Protection Agency — This GIS dataset contains polygon features that represent generalized USPS 5-digit zip code boundaries for the US and its territories. Data is licensed to US EPA by...

  6. Interplay of auxin, KANADI and Class III HD-ZIP transcription factors in vascular tissue formation.

    Science.gov (United States)

    Ilegems, Michael; Douet, Véronique; Meylan-Bettex, Marlyse; Uyttewaal, Magalie; Brand, Lukas; Bowman, John L; Stieger, Pia A

    2010-03-01

    Class III HD-ZIP and KANADI gene family members have complementary expression patterns in the vasculature and their gain-of-function and loss-of-function mutants have complementary vascular phenotypes. This suggests that members of the two gene families are involved in the establishment of the spatial arrangement of phloem, cambium and xylem. In this study, we have investigated the role of these two gene families in vascular tissue differentiation, in particular their interactions with the plant hormone auxin. We have analyzed the vasculature of plants that have altered expression levels of Class III HD-ZIP and KANADI transcription factors in provascular cells. Removal of either KANADI or Class III HD-ZIP expression in procambium cells led to a wider distribution of auxin in internal tissues, to an excess of procambium cell recruitment and to increased cambium activity. Ectopic expression of KANADI1 in provascular cells inhibited procambium cell recruitment due to negative effects of KANADI1 on expression and polar localization of the auxin efflux-associated protein PIN-FORMED1. Ectopic expression of Class III HD-ZIP genes promoted xylem differentiation. We propose that Class III HD-ZIP and KANADI transcription factors control cambium activity: KANADI proteins by acting on auxin transport, and Class III HD-ZIP proteins by promoting axial cell elongation and xylem differentiation.

  7. Using Wireless Pedometers to Measure Children’s Physical Activity: How Reliable is the Fitbit Zip?

    Directory of Open Access Journals (Sweden)

    Tingting Xu

    2017-07-01

    Full Text Available The purpose of this study is to examine the reliability of wireless pedometers in measuring elementary school children’s physical activity. Activity measurement using a wireless pedometer Fitbit ZipTM was compared to activity measurement using Yamax Digi-WalkerTM SW701 for a group of randomly selected 25 children in Grades 3, 4, and 5. Fitbit ZipTM wireless pedometers were found to have an appropriate degree (Nunnally & Bernstein, 1994 of accuracy and reliability compared to the Yamax Digi-WalkerTM SW701 pedometer. The Fitbit ZipTM wireless pedometer collected more step counts than the Yamax Digi-WalkerTM SW701 pedometer; however, the difference was not statistically significant. Participants reported that they preferred wearing the Fitbit ZipTM to the Yamax Digi-WalkerTM SW701 because the Fitbit ZipTM was more comfortable to wear and less likely to fall off. Participants also reported being more motivated to move while wearing the Fitbit ZipTM.

  8. Mini review roles of the bZIP gene family in rice.

    Science.gov (United States)

    E, Z G; Zhang, Y P; Zhou, J H; Wang, L

    2014-04-16

    The basic leucine zipper (bZIP) genes encode transcription factors involved in the regulation of various biological processes. Similar to WRKY, basic helix-loop-helix, and several other groups of proteins, the bZIP proteins form a superfamily of transcription factors that mediate plant stress responses. In this review, we present the roles of bZIP proteins in multiple biological processes that include pathogen defense; responses to abiotic stresses; seed development and germination; senescence; and responses to salicylic, jasmonic, and abscisic acids in rice. We also examined the characteristics of the bZIP proteins and their genetic composition. To ascertain the evolutionary changes in and functions of this supergene family, we performed an exhaustive comparison among the 89 rice bZIP genes that were previously described and those more recently listed in the MSU Rice Genome Annotation Project Database using a Hidden Markov Model. We excluded 3 genes from the list, resulting in a total of 86 bZIP genes in japonica rice.

  9. Elucidation of the Specific Formation of Homo- and Heterodimeric Forms of ThbZIP1 and Its Role in Stress

    Directory of Open Access Journals (Sweden)

    Xianguang Nie

    2014-06-01

    Full Text Available Protein–protein interactions are important for the molecular understanding of the biological processes of proteins. The dimerization of bZIPs (basic leucine zipper proteins is involved in modifying binding site specificities, altering dimer stability, and permitting a new set of specific protein-to-protein interactions to occur at the promoter. In the present study, we studied the whether ThbZIP1 form homo- and heterodimers using the yeast two-hybrid method. Five bZIP genes were cloned from Tamarix hispida to investigate their interaction with ThbZIP1. Our results showed that ThbZIP1 can form homodimers with itself, and three out of five bZIPs could interact with the ThbZIP1 protein to form heterodimers. Real-time RT-PCR results suggested that these ThbZIPs can all respond to abiotic stresses and abscisic acid (ABA, and shared very similar expression patterns in response to NaCl, ABA or PEG6000. Subcellular localization studies showed that all ThbZIPs are targeted to the nucleus. Our results showed that ThbZIP1 are dimeric proteins, which can form homo- or heterodimers.

  10. A novel bZIP gene from Tamarix hispida mediates physiological responses to salt stress in tobacco plants.

    Science.gov (United States)

    Wang, Yucheng; Gao, Caiqiu; Liang, Yenan; Wang, Chao; Yang, Chuanping; Liu, Guifeng

    2010-02-15

    Basic leucine zipper proteins (bZIPs) are transcription factors that bind abscisic acid (ABA)-responsive elements (ABREs) and enable plants to withstand adverse environmental conditions. In the present study, a novel bZIP gene, ThbZIP1 was cloned from Tamarix hispida. Expression studies in T. hispida showed differential regulation of ThbZIP1 in response to treatment with NaCl, polyethylene glycol (PEG) 6000, NaHCO(3), and CdCl(2), suggesting that ThbZIP1 is involved in abiotic stress responses. To identify the physiological responses mediated by ThbZIP1, transgenic tobacco plants overexpressing exogenous ThbZIP1 were generated. Various physiological parameters related to salt stress were measured and compared between transgenic and wild type (WT) plants. Our results indicate that overexpression of ThbZIP1 can enhance the activity of both peroxidase (POD) and superoxide dismutase (SOD), and increase the content of soluble sugars and soluble proteins under salt stress conditions. These results suggest that ThbZIP1 contributes to salt tolerance by mediating signaling through multiple physiological pathways. Furthermore, ThbZIP1 confers stress tolerance to plants by enhancing reactive oxygen species (ROS) scavenging, facilitating the accumulation of compatible osmolytes, and inducing and/or enhancing the biosynthesis of soluble proteins. Copyright 2009 Elsevier GmbH. All rights reserved.

  11. ZipA binds to FtsZ with high affinity and enhances the stability of FtsZ protofilaments.

    Directory of Open Access Journals (Sweden)

    Anuradha Kuchibhatla

    Full Text Available A bacterial membrane protein ZipA that tethers FtsZ to the membrane is known to promote FtsZ assembly. In this study, the binding of ZipA to FtsZ was monitored using fluorescence spectroscopy. ZipA was found to bind to FtsZ with high affinities at three different (6.0, 6.8 and 8.0 pHs, albeit the binding affinity decreased with increasing pH. Further, thick bundles of FtsZ protofilaments were observed in the presence of ZipA under the pH conditions used in this study indicating that ZipA can promote FtsZ assembly and stabilize FtsZ polymers under unfavorable conditions. Bis-ANS, a hydrophobic probe, decreased the interaction of FtsZ and ZipA indicating that the interaction between FtsZ and ZipA is hydrophobic in nature. ZipA prevented the dilution induced disassembly of FtsZ polymers suggesting that it stabilizes FtsZ protofilaments. Fluorescein isothiocyanate-labeled ZipA was found to be uniformly distributed along the length of the FtsZ protofilaments indicating that ZipA stabilizes FtsZ protofilaments by cross-linking them.

  12. Slc39a7/zip7 plays a critical role in development and zinc homeostasis in zebrafish.

    Directory of Open Access Journals (Sweden)

    Guang Yan

    Full Text Available BACKGROUND: Slc39a7/Zip7, also known as Ke4, is a member of solute carrier family 39 (Slc39a and plays a critical role in regulating cell growth and death. Because the function of Zip7 in vivo was unclear, the present study investigated the function of zip7 in vertebrate development and zinc metabolism using zebrafish as a model organism. PRINCIPAL FINDING: Using real-time PCR to determine the gene expression pattern of zip7 during zebrafish development, we found that zip7 mRNA is expressed throughout embryonic development and into maturity. Interestingly, whole mount in situ hybridization revealed that while zip7 mRNA is ubiquitously expressed until 12 hours post-fertilization (hpf; at 24 hpf and beyond, zip7 mRNA was specifically detected only in eyes. Morpholino-antisense (MO gene knockdown assay revealed that downregulation of zip7 expression resulted in several morphological defects in zebrafish including decreased head size, smaller eyes, shorter palates, and shorter and curved spinal cords. Analysis by synchrotron radiation X-ray fluorescence (SR-XRF showed reduced concentrations of zinc in brain, eyes, and gills of zip7-MO-injected embryos. Furthermore, incubation of the zip7 knockdown embryos in a zinc-supplemented solution was able to rescue the MO-induced morphological defects. SIGNIFICANCE: Our data suggest that zip7 is required for eye, brain, and skeleton formation during early embryonic development in zebrafish. Moreover, zinc supplementation can partially rescue defects resulting from zip7 gene knockdown. Taken together, our data provide critical insight into a novel function of zip7 in development and zinc homeostasis in vivo in zebrafish.

  13. Characterization of pollen-expressed bZIP protein interactions and the role of ATbZIP18 in the male gametophyte

    Czech Academy of Sciences Publication Activity Database

    Gibalová, A.; Steinbachová, L.; Hafidh, S.; Bláhová, Veronika; Gadiou, Z.; Michailidis, Ch.; Müller, K.; Pleskot, Roman; Dupľáková, N.; Honys, D.

    2017-01-01

    Roč. 30, č. 1 (2017), s. 1-17 ISSN 2194-7953 Institutional support: RVO:67985823 ; RVO:61388963 Keywords : bZIP * transcription factors * regulatory network * male gametophyte * Y2H * pollen development Subject RIV: ED - Physiology; CE - Biochemistry (UOCHB-X) OBOR OECD: Physiology (including cytology); Biochemistry and molecular biology (UOCHB-X) Impact factor: 2.629, year: 2016

  14. A Petunia Homeodomain-Leucine Zipper Protein, PhHD-Zip, Plays an Important Role in Flower Senescence

    Science.gov (United States)

    Chang, Xiaoxiao; Donnelly, Linda; Sun, Daoyang; Rao, Jingping; Reid, Michael S.; Jiang, Cai-Zhong

    2014-01-01

    Flower senescence is initiated by developmental and environmental signals, and regulated by gene transcription. A homeodomain-leucine zipper transcription factor, PhHD-Zip, is up-regulated during petunia flower senescence. Virus-induced gene silencing of PhHD-Zip extended flower life by 20% both in unpollinated and pollinated flowers. Silencing PhHD-Zip also dramatically reduced ethylene production and the abundance of transcripts of genes involved in ethylene (ACS, ACO), and ABA (NCED) biosynthesis. Abundance of transcripts of senescence-related genes (SAG12, SAG29) was also dramatically reduced in the silenced flowers. Over-expression of PhHD-Zip accelerated petunia flower senescence. Furthermore, PhHD-Zip transcript abundance in petunia flowers was increased by application of hormones (ethylene, ABA) and abiotic stresses (dehydration, NaCl and cold). Our results suggest that PhHD-Zip plays an important role in regulating petunia flower senescence. PMID:24551088

  15. A Petunia homeodomain-leucine zipper protein, PhHD-Zip, plays an important role in flower senescence.

    Science.gov (United States)

    Chang, Xiaoxiao; Donnelly, Linda; Sun, Daoyang; Rao, Jingping; Reid, Michael S; Jiang, Cai-Zhong

    2014-01-01

    Flower senescence is initiated by developmental and environmental signals, and regulated by gene transcription. A homeodomain-leucine zipper transcription factor, PhHD-Zip, is up-regulated during petunia flower senescence. Virus-induced gene silencing of PhHD-Zip extended flower life by 20% both in unpollinated and pollinated flowers. Silencing PhHD-Zip also dramatically reduced ethylene production and the abundance of transcripts of genes involved in ethylene (ACS, ACO), and ABA (NCED) biosynthesis. Abundance of transcripts of senescence-related genes (SAG12, SAG29) was also dramatically reduced in the silenced flowers. Over-expression of PhHD-Zip accelerated petunia flower senescence. Furthermore, PhHD-Zip transcript abundance in petunia flowers was increased by application of hormones (ethylene, ABA) and abiotic stresses (dehydration, NaCl and cold). Our results suggest that PhHD-Zip plays an important role in regulating petunia flower senescence.

  16. A Petunia homeodomain-leucine zipper protein, PhHD-Zip, plays an important role in flower senescence.

    Directory of Open Access Journals (Sweden)

    Xiaoxiao Chang

    Full Text Available Flower senescence is initiated by developmental and environmental signals, and regulated by gene transcription. A homeodomain-leucine zipper transcription factor, PhHD-Zip, is up-regulated during petunia flower senescence. Virus-induced gene silencing of PhHD-Zip extended flower life by 20% both in unpollinated and pollinated flowers. Silencing PhHD-Zip also dramatically reduced ethylene production and the abundance of transcripts of genes involved in ethylene (ACS, ACO, and ABA (NCED biosynthesis. Abundance of transcripts of senescence-related genes (SAG12, SAG29 was also dramatically reduced in the silenced flowers. Over-expression of PhHD-Zip accelerated petunia flower senescence. Furthermore, PhHD-Zip transcript abundance in petunia flowers was increased by application of hormones (ethylene, ABA and abiotic stresses (dehydration, NaCl and cold. Our results suggest that PhHD-Zip plays an important role in regulating petunia flower senescence.

  17. Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors; a potential source of functional diversity

    Directory of Open Access Journals (Sweden)

    Cabello Julieta V

    2011-03-01

    Full Text Available Abstract Background Plant HD-Zip transcription factors are modular proteins in which a homeodomain is associated to a leucine zipper. Of the four subfamilies in which they are divided, the tested members from subfamily I bind in vitro the same pseudopalindromic sequence CAAT(A/TATTG and among them, several exhibit similar expression patterns. However, most experiments in which HD-Zip I proteins were over or ectopically expressed under the control of the constitutive promoter 35S CaMV resulted in transgenic plants with clearly different phenotypes. Aiming to elucidate the structural mechanisms underlying such observation and taking advantage of the increasing information in databases of sequences from diverse plant species, an in silico analysis was performed. In addition, some of the results were also experimentally supported. Results A phylogenetic tree of 178 HD-Zip I proteins together with the sequence conservation presented outside the HD-Zip domains allowed the distinction of six groups of proteins. A motif-discovery approach enabled the recognition of an activation domain in the carboxy-terminal regions (CTRs and some putative regulatory mechanisms acting in the amino-terminal regions (NTRs and CTRs involving sumoylation and phosphorylation. A yeast one-hybrid experiment demonstrated that the activation activity of ATHB1, a member of one of the groups, is located in its CTR. Chimerical constructs were performed combining the HD-Zip domain of one member with the CTR of another and transgenic plants were obtained with these constructs. The phenotype of the chimerical transgenic plants was similar to the observed in transgenic plants bearing the CTR of the donor protein, revealing the importance of this module inside the whole protein. Conclusions The bioinformatical results and the experiments conducted in yeast and transgenic plants strongly suggest that the previously poorly analyzed NTRs and CTRs of HD-Zip I proteins play an important

  18. Salt and drought stress and ABA responses related to bZIP genes from V. radiata and V. angularis.

    Science.gov (United States)

    Wang, Lanfen; Zhu, Jifeng; Li, Xiaoming; Wang, Shumin; Wu, Jing

    2018-04-20

    Mung bean and adzuki bean are warm-season legumes widely cultivated in China. However, bean production in major producing regions is limited by biotic and abiotic stress, such as drought and salt stress. Basic leucine zipper (bZIP) genes play key roles in responses to various biotic and abiotic stresses. However, only several bZIP genes involved in drought and salt stress in legumes, especially Vigna radiata and Vigna angularis, have been identified. In this study, we identified 54 and 50 bZIP proteins from whole-genome sequences of V. radiata and V. angularis, respectively. First, we comprehensively surveyed the characteristics of all bZIP genes, including their gene structure, chromosome distribution and motif composition. Phylogenetic trees showed that VrbZIP and VabZIP proteins were divided into ten clades comprising nine known and one unknown subgroup. The results of the nucleotide substitution rate of the orthologous gene pairs showed that bZIP proteins have undergone strong purifying selection: V. radiata and V. angularis diverged 1.25 million years ago (mya) to 9.20 mya (average of 4.95 mya). We also found that many cis-acting regulatory elements (CAREs) involved in abiotic stress and plant hormone responses were detected in the putative promoter regions of the bZIP genes. Finally, using the quantitative real-time PCR (qRT-PCR) method, we performed expression profiling of the bZIP genes in response to drought, salt and abscisic acid (ABA). We identified several bZIP genes that may be involved in drought and salt responses. Generally, our results provided useful and rich resources of VrbZIP and VabZIP genes for the functional characterization and understanding of bZIP transcription factors (TFs) in warm-season legumes. In addition, our results revealed important and interesting data - a subset of VrbZIP and VabZIP gene expression profiles in response to drought, salt and ABA stress. These results provide gene expression evidence for the selection of

  19. A modified detector concept for SuperCDMS: The HiZIP and its charge performance

    Energy Technology Data Exchange (ETDEWEB)

    Page, Kedar Mohan [Queen' s U.

    2013-01-01

    SuperCDMS (Super Cryogenic Dark Matter Search) is a leading direct dark mat-ter search experiment which uses solid state detectors (Ge crystals) at milliKelvintemperatures to look for nuclear recoils caused by dark matter interactions in the de-tector. `Weakly Interacting Massive Particles' (WIMPs) are the most favoured darkmatter candidate particles. SuperCDMS, like many other direct dark matter searchexperiments, primarily looks for WIMPs. The measurement of both the ionizationand the lattice vibration (phonon) signals from an interaction in the detector allow itto discriminate against electron recoils which are the main source of background forWIMP detection.SuperCDMS currently operates about 9 kg of Ge detectors at the Soudan under-ground lab in northern Minnesota. In its next phase, SuperCDMS SNOLAB plansto use 100-200 kg of target mass (Ge) which would allow it to probe more of theinteresting and and as of yet unexplored parameter space for WIMPs predicted bytheoretical models. The SuperCDMS Queen's Test Facility is a detector test facilitywhich is intended to serve as detector testing and detector research and developmentpurposes for the SuperCDMS experiment.A modifed detector called the HiZIP (Half-iZIP), which is reduced in complex-ity in comparison to the currently used iZIP (interleaved Z-sensitive Ionization and Phonon mediated) detectors, is studied in this thesis. The HiZIP detector designalso serves to discriminate against background from multiple scatter events occurringclose to the surfaces in a single detector. Studies carried out to compare the surfaceevent leakage in the HiZIP detector using limited information from iZIP data takenat SuperCDMS test facility at UC Berkley produce a highly conservative upper limitof 5 out of 10,000 events at 90% condence level. This upper limit is the best amongmany different HiZIP congurations that were investigated and is comparable to theupper limit calculated for an HiZIP detector in the same way

  20. The Populus Class III HD ZIP transcription factor POPCORONA affects cell differentiation during secondary growth of woody stems

    Science.gov (United States)

    Juan Du; Eriko Miura; Marcel Robischon; Ciera Martinez; Andrew Groover

    2011-01-01

    The developmental mechanisms regulating cell differentiation and patterning during the secondary growth of woody tissues are poorly understood. Class III HD ZIP transcription factors are evolutionarily ancient and play fundamental roles in various aspects of plant development. Here we investigate the role of a Class III HD ZIP transcription factor, ...

  1. Genome-Wide Identification and Structural Analysis of bZIP Transcription Factor Genes in Brassica napus

    Directory of Open Access Journals (Sweden)

    Yan Zhou

    2017-10-01

    Full Text Available The basic region/leucine zipper motif (bZIP transcription factor family is one of the largest families of transcriptional regulators in plants. bZIP genes have been systematically characterized in some plants, but not in rapeseed (Brassica napus. In this study, we identified 247 BnbZIP genes in the rapeseed genome, which we classified into 10 subfamilies based on phylogenetic analysis of their deduced protein sequences. The BnbZIP genes were grouped into functional clades with Arabidopsis genes with similar putative functions, indicating functional conservation. Genome mapping analysis revealed that the BnbZIPs are distributed unevenly across all 19 chromosomes, and that some of these genes arose through whole-genome duplication and dispersed duplication events. All expression profiles of 247 bZIP genes were extracted from RNA-sequencing data obtained from 17 different B. napus ZS11 tissues with 42 various developmental stages. These genes exhibited different expression patterns in various tissues, revealing that these genes are differentially regulated. Our results provide a valuable foundation for functional dissection of the different BnbZIP homologs in B. napus and its parental lines and for molecular breeding studies of bZIP genes in B. napus.

  2. Genome-Wide Identification and Structural Analysis of bZIP Transcription Factor Genes in Brassica napus.

    Science.gov (United States)

    Zhou, Yan; Xu, Daixiang; Jia, Ledong; Huang, Xiaohu; Ma, Guoqiang; Wang, Shuxian; Zhu, Meichen; Zhang, Aoxiang; Guan, Mingwei; Lu, Kun; Xu, Xinfu; Wang, Rui; Li, Jiana; Qu, Cunmin

    2017-10-24

    The basic region/leucine zipper motif (bZIP) transcription factor family is one of the largest families of transcriptional regulators in plants. bZIP genes have been systematically characterized in some plants, but not in rapeseed ( Brassica napus ). In this study, we identified 247 BnbZIP genes in the rapeseed genome, which we classified into 10 subfamilies based on phylogenetic analysis of their deduced protein sequences. The BnbZIP genes were grouped into functional clades with Arabidopsis genes with similar putative functions, indicating functional conservation. Genome mapping analysis revealed that the BnbZIPs are distributed unevenly across all 19 chromosomes, and that some of these genes arose through whole-genome duplication and dispersed duplication events. All expression profiles of 247 bZIP genes were extracted from RNA-sequencing data obtained from 17 different B . napus ZS11 tissues with 42 various developmental stages. These genes exhibited different expression patterns in various tissues, revealing that these genes are differentially regulated. Our results provide a valuable foundation for functional dissection of the different BnbZIP homologs in B . napus and its parental lines and for molecular breeding studies of bZIP genes in B . napus .

  3. Genomic identification of bZIP family genes involved in drought and heat stresses in strawberry (Fragaria vesca)

    Science.gov (United States)

    Basic leucine zipper (bZIP) genes are known to play dominant roles in plant response to development signals, as well as abiotic or biotic stress stimuli. Fifty bZIP genes across the woodland strawberry (Fragaria vesca) genome were identified and analyzed. They can be divided into 10 clades according...

  4. Expression analysis of OsbZIP transcription factors in resistance ...

    African Journals Online (AJOL)

    zino

    2013-08-21

    Aug 21, 2013 ... eukaryotes, which shared two common structures: a. DNA-bonding basic region and the Leu ... days and then transferred to plant growth chamber to grow for 14 days before treatments. For the hormone ... Total RNA was extracted from a sample of leaf tissue at each time point using the TRIzol reagent ...

  5. Compound list: diazepam [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available diazepam DZP 00023 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/diazepam....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/diazepam....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/diazepam...-tggates/LATEST/Rat/in_vivo/Liver/Repeat/diazepam.Rat.in_vivo.Liver.Repeat.zip ...

  6. Compound list: phenobarbital [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available phenobarbital PB 00004 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/phenobar...bital.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/phenobar...bital.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_...dbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/phenobarbital.Rat.in_vivo.Liver.Repeat.zip ...

  7. Compound list: sulindac [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available sulindac SUL 00100 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/sulinda...c.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/sulinda...c.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/sulinda...-tggates/LATEST/Rat/in_vivo/Liver/Repeat/sulindac.Rat.in_vivo.Liver.Repeat.zip ...

  8. Compound list: diclofenac [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available diclofenac DFNa 00019 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/diclofenac....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/diclofenac....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/diclofenac...hive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/diclofenac.Rat.in_vivo.Liver.Repeat.zip ...

  9. Compound list: papaverine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available papaverine PAP 00098 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/papa...verine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/papa...verine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/papa...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/papaverine.Rat.in_vivo.Liver.Repeat.zip ...

  10. Compound list: LPS [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available LPS LPS 00A07 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/LPS....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/LPS.Rat.in..._vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/LPS.Rat.in_vivo.Liver.Single.zip ...

  11. Compound list: ethambutol [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available ethambutol EBU 00083 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/etham...butol.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/etham...butol.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/etham...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/ethambutol.Rat.in_vivo.Liver.Repeat.zip ...

  12. Compound list: glibenclamide [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available glibenclamide GBC 00042 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/glib...enclamide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/glib...enclamide.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/glib...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/glibenclamide.Rat.in_vivo.Liver.Repeat.zip ...

  13. Compound list: phalloidin [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available phalloidin PHA 00A11 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/phallo...idin.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/phallo...idin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/phallo...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/phalloidin.Rat.in_vivo.Liver.Repeat.zip ...

  14. Compound list: labetalol [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available labetalol LBT 00040 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/labeta...lol.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/labeta...lol.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/labeta...open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/labetalol.Rat.in_vivo.Liver.Repeat.zip ...

  15. Compound list: chlorpropamide [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available chlorpropamide CPP 00080 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/chlorpropa...mide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/chlorpropa.../in_vivo/Liver/Single/chlorpropamide.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosc...iencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/chlorpropamide.Rat.in_vivo.Liver.Repeat.zip ...

  16. Compound list: methyldopa [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available methyldopa MDP 00056 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/methyldopa....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/methyldopa....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/methyldopa...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/methyldopa.Rat.in_vivo.Liver.Repeat.zip ...

  17. Compound list: furosemide [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available furosemide FUR 00078 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/furosem...ide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/furosem...ide.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/furosem...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/furosemide.Rat.in_vivo.Liver.Repeat.zip ...

  18. Compound list: griseofulvin [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available griseofulvin GF 00043 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/griseo...fulvin.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/griseo...fulvin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/griseo...jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/griseofulvin.Rat.in_vivo.Liver.Repeat.zip ...

  19. Compound list: haloperidol [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available haloperidol HPL 00036 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/haloperidol....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/haloperidol....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/haloperidol...archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/haloperidol.Rat.in_vivo.Liver.Repeat.zip ...

  20. Compound list: flutamide [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available flutamide FT 00044 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/flut...amide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/flut...amide.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/flut...pen-tggates/LATEST/Rat/in_vivo/Liver/Repeat/flutamide.Rat.in_vivo.Liver.Repeat.zip ...

  1. Compound list: TNFα [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available TNFα TNF 00A08 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/TNF...a.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/TNFa.Rat....in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/TNFa.Rat.in_vivo.Liver.Single.zip ...

  2. Compound list: propranolol [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available propranolol PPL 00170 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/propra...nolol.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/propra...nolol.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/propranolol.Rat.in_vivo.Liver.Repeat.zip ...

  3. Compound list: terbinafine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available terbinafine TBF 00123 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/terbinafine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/terbinafine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/terbinafine...archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/terbinafine.Rat.in_vivo.Liver.Repeat.zip ...

  4. Compound list: carbamazepine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available carbamazepine CBZ 00018 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/carbamazepine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/carbamazepine..._vivo/Liver/Single/carbamazepine.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscienc...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/carbamazepine.Rat.in_vivo.Liver.Repeat.zip ...

  5. Compound list: amitriptyline [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available amitriptyline AMT 00070 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/amitriptyline....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/amitriptyline..._vivo/Liver/Single/amitriptyline.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscienc...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/amitriptyline.Rat.in_vivo.Liver.Repeat.zip ...

  6. Compound list: chlorpromazine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available chlorpromazine CPZ 00016 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Hum...an/in_vitro/chlorpromazine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/R.../in_vivo/Liver/Single/chlorpromazine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosc...iencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/chlorpromazine.Rat.in_vivo.Liver.Repeat.zip ...

  7. Compound list: sulfasalazine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available sulfasalazine SS 00034 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/sulfasalazine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/sulfasalazine...vivo/Liver/Single/sulfasalazine.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscience...dbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/sulfasalazine.Rat.in_vivo.Liver.Repeat.zip ...

  8. Compound list: mexiletine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available mexiletine MEX 00103 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/mexiletine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/mexiletine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/mexiletine...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/mexiletine.Rat.in_vivo.Liver.Repeat.zip ...

  9. Compound list: quinidine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available quinidine QND 00074 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/quinidine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/quinidine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/quinidine...open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/quinidine.Rat.in_vivo.Liver.Repeat.zip ...

  10. Compound list: clomipramine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available clomipramine CPM 00121 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/clomipramine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/clomipramine...vo/Liver/Single/clomipramine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc....jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/clomipramine.Rat.in_vivo.Liver.Repeat.zip ...

  11. Compound list: ticlopidine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available ticlopidine TCP 00146 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/ticlopidine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/ticlopidine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/ticlopidine...archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/ticlopidine.Rat.in_vivo.Liver.Repeat.zip ...

  12. Compound list: perhexiline [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available perhexiline PH 00045 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/perhexiline....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/perhexiline....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/perhexiline...rchive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/perhexiline.Rat.in_vivo.Liver.Repeat.zip ...

  13. Compound list: ranitidine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available ranitidine RAN 00086 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/ranitidine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/ranitidine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/ranitidine...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/ranitidine.Rat.in_vivo.Liver.Repeat.zip ...

  14. Compound list: famotidine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available famotidine FAM 00085 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/famotidine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/famotidine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/famotidine...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/famotidine.Rat.in_vivo.Liver.Repeat.zip ...

  15. Compound list: theophylline [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available theophylline TEO 00096 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/theophylline....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/theophylline...vo/Liver/Single/theophylline.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc....jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/theophylline.Rat.in_vivo.Liver.Repeat.zip ...

  16. Compound list: thioridazine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available thioridazine TRZ 00038 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/thioridazine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/thioridazine...vo/Liver/Single/thioridazine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc....jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/thioridazine.Rat.in_vivo.Liver.Repeat.zip ...

  17. Compound list: galactosamine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available galactosamine GaN 00A06 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/galactosamine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/galactosamine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/galactosamine.Rat.in_vivo.Liver.Single.zip ...

  18. Compound list: azathioprine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available azathioprine AZP 00046 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/azathioprine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/azathioprine...vo/Liver/Single/azathioprine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc....jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/azathioprine.Rat.in_vivo.Liver.Repeat.zip ...

  19. Compound list: hydroxyzine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available hydroxyzine HYZ 00071 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/hydroxyzine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/hydroxyzine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/hydroxyzine...archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/hydroxyzine.Rat.in_vivo.Liver.Repeat.zip ...

  20. Compound list: cimetidine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available cimetidine CIM 00035 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/cimetidine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/cimetidine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/cimetidine...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/cimetidine.Rat.in_vivo.Liver.Repeat.zip ...

  1. Compound list: promethazine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available promethazine PMZ 00110 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/promethazine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/promethazine...vo/Liver/Single/promethazine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc....jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/promethazine.Rat.in_vivo.Liver.Repeat.zip ...

  2. Compound list: penicillamine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available penicillamine PEN 00099 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/penicillamine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/penicillamine..._vivo/Liver/Single/penicillamine.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscienc...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/penicillamine.Rat.in_vivo.Liver.Repeat.zip ...

  3. Compound list: colchicine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available colchicine COL 00113 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/colchicine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/colchicine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/colchicine...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/colchicine.Rat.in_vivo.Liver.Repeat.zip ...

  4. Compound list: nifedipine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available nifedipine NIF 00091 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/nifedipine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/nifedipine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/nifedipine...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/nifedipine.Rat.in_vivo.Liver.Repeat.zip ...

  5. Compound list: chloramphenicol [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available chloramphenicol CMP 00064 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/chlora...mphenicol.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/chlora...Rat/in_vivo/Liver/Single/chloramphenicol.Rat.in_vivo.Liver.Single.zip ftp://ftp.b...iosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/chloramphenicol.Rat.in_vivo.Liver.Repeat.zip ...

  6. Gated community Na Krutci

    Czech Academy of Sciences Publication Activity Database

    Hnídková, Vendula

    2012-01-01

    Roč. 91, č. 12 (2012), s. 750-752 ISSN 0042-4544 Institutional support: RVO:68378033 Keywords : Gated community * Czech contemporary architecture * Kuba Pilař Subject RIV: AL - Art, Architecture , Cultural Heritage

  7. Compound list: ethanol [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available ethanol ETN 00137 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/ethanol....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/ethanol....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/ethanol....Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/ethanol.Rat.in_vivo.Liver.Repeat.zip ...

  8. Compound list: caffeine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available caffeine CAF 00097 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/caffeine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/caffeine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/caffeine...-tggates/LATEST/Rat/in_vivo/Liver/Repeat/caffeine.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.biosciencedbc.jp/ar...chive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/caffeine.Rat.in_vivo.Kidney.Single.zip ftp://ftp.bioscie

  9. Compound list: captopril [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available captopril CAP 00094 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/captopril....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/captopril....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/captopril...open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/captopril.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.biosciencedbc....jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/captopril.Rat.in_vivo.Kidney.Single.zip ftp://ftp.b

  10. Compound list: adapin [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available adapin ADP 00039 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/adapi...n.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/adapi...n.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/adapi...n.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/adapin.Rat.in_vivo.Liver.Repeat.zip ...

  11. Compound list: aspirin [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available aspirin ASA 00014 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/aspirin....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/aspirin....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/aspirin....Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/aspirin.Rat.in_vivo.Liver.Repeat.zip ...

  12. Compound list: nitrosodiethylamine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available nitrosodiethylamine DEN 00145 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATES...s/LATEST/Rat/in_vitro/nitrosodiethylamine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tgg...ates/LATEST/Rat/in_vivo/Liver/Single/nitrosodiethylamine.Rat.in_vivo.Liver.Single....zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/nitrosodiethylamine.Rat.in_vivo.Liver.Repeat.zip ... ...T/Human/in_vitro/nitrosodiethylamine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggate

  13. Compound list: allopurinol [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available allopurinol APL 00028 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/allopurin...ol.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/allopurin...ol.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/allopurin...archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/allopurinol.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.bios...ciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/allopurinol.Rat.in_vivo.Kidney.Single.zip

  14. Compound list: omeprazole [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available omeprazole OPZ 00012 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/omeprazole....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/omeprazole....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/omeprazole...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/omeprazole.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.bioscienc...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/omeprazole.Rat.in_vivo.Kidney.Single.zip ftp:/

  15. Compound list: fluphenazine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available fluphenazine FP 00037 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/fluphenazine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/fluphenazine...jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/fluphenazine.Rat.in_vivo.Liver.Repeat.zip ... ....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_viv...o/Liver/Single/fluphenazine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.

  16. Compound list: tetracycline [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available tetracycline TC 00048 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/tetracycline....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/tetracycline...jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/tetracycline.Rat.in_vivo.Liver.Repeat.zip ... ....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_viv...o/Liver/Single/tetracycline.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.

  17. Compound list: tacrine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available tacrine TAC 00060 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/tacrine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/tacrine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/tacrine....Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/tacrine.Rat.in_vivo.Liver.Repeat.zip ...

  18. Compound list: imipramine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available imipramine IMI 00069 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/imipramine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/imipramine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/imipramine...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/imipramine.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.bioscienc...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/imipramine.Rat.in_vivo.Kidney.Single.zip ftp:/

  19. Compound list: lomustine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available lomustine LS 00049 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/lomustine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/lomustine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/lomustine...pen-tggates/LATEST/Rat/in_vivo/Liver/Repeat/lomustine.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.biosciencedbc.j...p/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/lomustine.Rat.in_vivo.Kidney.Single.zip ftp://ftp.bi

  20. Compound list: ethionine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available ethionine ET 00013 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/ethionine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/ethionine....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/ethionine...pen-tggates/LATEST/Rat/in_vivo/Liver/Repeat/ethionine.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.biosciencedbc.j...p/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/ethionine.Rat.in_vivo.Kidney.Single.zip ftp://ftp.bi

  1. Compound list: chlorpheniramine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available chlorpheniramine CHL 00090 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/H...uman/in_vitro/chlorpheniramine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATE...ST/Rat/in_vitro/chlorpheniramine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATE...ST/Rat/in_vivo/Liver/Single/chlorpheniramine.Rat.in_vivo.Liver.Single.zip ftp://f...tp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/chlorpheniramine.Rat.in_vivo.Liver.Repeat.zip ...

  2. Compound list: bromobenzene [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available bromobenzene BBZ 00032 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/bromobenzene....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/bromobenzene....jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/bromobenzene.Rat.in_vivo.Liver.Repeat.zip ftp://ftp....biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/bromobenzene.Rat.in_vivo.Kidney.Sing...le.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Repeat/bromobenzene.Rat.in_vivo.Kidney.Repeat.zip ...

  3. Compound list: acetamidofluorene [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available acetamidofluorene AAF 00144 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/...TEST/Rat/in_vitro/acetamidofluorene.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/L...ATEST/Rat/in_vivo/Liver/Single/acetamidofluorene.Rat.in_vivo.Liver.Single.zip ftp...://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/acetamidofluorene.Rat.in_vivo.Liver.Repeat.zip ... ...Human/in_vitro/acetamidofluorene.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LA

  4. Reversible gates and circuits descriptions

    Science.gov (United States)

    Gracki, Krzystof

    2017-08-01

    This paper presents basic methods of reversible circuit description. To design reversible circuit a set of gates has to be chosen. Most popular libraries are composed of three types of gates so called CNT gates (Control, NOT and Toffoli). The gate indexing method presented in this paper is based on the CNT gates set. It introduces a uniform indexing of the gates used during synthesis process of reversible circuits. The paper is organized as follows. Section 1 recalls basic concepts of reversible logic. In Section 2 and 3 a graphical representation of the reversible gates and circuits is described. Section 4 describes proposed uniform NCT gates indexing. The presented gate indexing method provides gate numbering scheme independent of lines number of the designed circuit. The solution for a circuit consisting of smaller number of lines is a subset of solution for a larger circuit.

  5. Advanced insulated gate bipolar transistor gate drive

    Science.gov (United States)

    Short, James Evans [Monongahela, PA; West, Shawn Michael [West Mifflin, PA; Fabean, Robert J [Donora, PA

    2009-08-04

    A gate drive for an insulated gate bipolar transistor (IGBT) includes a control and protection module coupled to a collector terminal of the IGBT, an optical communications module coupled to the control and protection module, a power supply module coupled to the control and protection module and an output power stage module with inputs coupled to the power supply module and the control and protection module, and outputs coupled to a gate terminal and an emitter terminal of the IGBT. The optical communications module is configured to send control signals to the control and protection module. The power supply module is configured to distribute inputted power to the control and protection module. The control and protection module outputs on/off, soft turn-off and/or soft turn-on signals to the output power stage module, which, in turn, supplies a current based on the signal(s) from the control and protection module for charging or discharging an input capacitance of the IGBT.

  6. The human respiratory gate

    Science.gov (United States)

    Eckberg, Dwain L.

    2003-01-01

    Respiratory activity phasically alters membrane potentials of preganglionic vagal and sympathetic motoneurones and continuously modulates their responsiveness to stimulatory inputs. The most obvious manifestation of this 'respiratory gating' is respiratory sinus arrhythmia, the rhythmic fluctuations of electrocardiographic R-R intervals observed in healthy resting humans. Phasic autonomic motoneurone firing, reflecting the throughput of the system, depends importantly on the intensity of stimulatory inputs, such that when levels of stimulation are low (as with high arterial pressure and sympathetic activity, or low arterial pressure and vagal activity), respiratory fluctuations of sympathetic or vagal firing are also low. The respiratory gate has a finite capacity, and high levels of stimulation override the ability of respiration to gate autonomic responsiveness. Autonomic throughput also depends importantly on other factors, including especially, the frequency of breathing, the rate at which the gate opens and closes. Respiratory sinus arrhythmia is small at rapid, and large at slow breathing rates. The strong correlation between systolic pressure and R-R intervals at respiratory frequencies reflects the influence of respiration on these two measures, rather than arterial baroreflex physiology. A wide range of evidence suggests that respiratory activity gates the timing of autonomic motoneurone firing, but does not influence its tonic level. I propose that the most enduring significance of respiratory gating is its use as a precisely controlled experimental tool to tease out and better understand otherwise inaccessible human autonomic neurophysiological mechanisms.

  7. Potential novel bZIP-like gene for resistance to Erysiphe necator ...

    African Journals Online (AJOL)

    Results reveal that it was in lower lever in flower than in leaf, stem, tendril and fruit. The CDS of VpbZIP-like was inserted into the prokaryotic expression construct pGEX-4T-1, and then transformed into Escherichia coli BL21-code induced by isopropyl-b-D-thiogalactopyranoside (IPTG) which resulted in the production of a ...

  8. ZmbZIP60 mRNA is spliced in maize in response to ER stress

    Directory of Open Access Journals (Sweden)

    Li Yanjie

    2012-03-01

    Full Text Available Abstract Background Adverse environmental conditions produce ER stress and elicit the unfolded protein response (UPR in plants. Plants are reported to have two "arms" of the ER stress signaling pathway-one arm involving membrane-bound transcription factors and the other involving a membrane-associated RNA splicing factor, IRE1. IRE1 in yeast to mammals recognizes a conserved twin loop structure in the target RNA. Results A segment of the mRNA encoding ZmbZIP60 in maize can be folded into a twin loop structure, and in response to ER stress this mRNA is spliced, excising a 20b intron. Splicing converts the predicted protein from a membrane-associated transcription factor to one that is targeted to the nucleus. Splicing of ZmbZIP60 can be elicited in maize seedlings by ER stress agents such as dithiothreitol (DTT or tunicamycin (TM or by heat treatment. Younger, rather than older seedlings display a more robust splicing response as do younger parts of leaf, along a developmental gradient in a leaf. The molecular signature of an ER stress response in plants includes the upregulation of Binding Protein (BIP genes. Maize has numerous BIP-like genes, and ER stress was found to upregulate one of these, ZmBIPb. Conclusions The splicing of ZmbZIP60 mRNA is an indicator of ER stress in maize seedlings resulting from adverse environmental conditions such as heat stress. ZmbZIP60 mRNA splicing in maize leads predictively to the formation of active bZIP transcription factor targeted to the nucleus to upregulate stress response genes. Among the genes upregulated by ER stress in maize is one of 22 BIP-like genes, ZmBIPb.

  9. Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions

    Science.gov (United States)

    Potapov, Vladimir; Kaplan, Jenifer B.; Keating, Amy E.

    2015-01-01

    Selective dimerization of the basic-region leucine-zipper (bZIP) transcription factors presents a vivid example of how a high degree of interaction specificity can be achieved within a family of structurally similar proteins. The coiled-coil motif that mediates homo- or hetero-dimerization of the bZIP proteins has been intensively studied, and a variety of methods have been proposed to predict these interactions from sequence data. In this work, we used a large quantitative set of 4,549 bZIP coiled-coil interactions to develop a predictive model that exploits knowledge of structurally conserved residue-residue interactions in the coiled-coil motif. Our model, which expresses interaction energies as a sum of interpretable residue-pair and triplet terms, achieves a correlation with experimental binding free energies of R = 0.68 and significantly out-performs other scoring functions. To use our model in protein design applications, we devised a strategy in which synthetic peptides are built by assembling 7-residue native-protein heptad modules into new combinations. An integer linear program was used to find the optimal combination of heptads to bind selectively to a target human bZIP coiled coil, but not to target paralogs. Using this approach, we designed peptides to interact with the bZIP domains from human JUN, XBP1, ATF4 and ATF5. Testing more than 132 candidate protein complexes using a fluorescence resonance energy transfer assay confirmed the formation of tight and selective heterodimers between the designed peptides and their targets. This approach can be used to make inhibitors of native proteins, or to develop novel peptides for applications in synthetic biology or nanotechnology. PMID:25695764

  10. The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes.

    Directory of Open Access Journals (Sweden)

    Luiz Gustavo Guedes Corrêa

    Full Text Available BACKGROUND: Transcription factors of the basic leucine zipper (bZIP family control important processes in all eukaryotes. In plants, bZIPs are regulators of many central developmental and physiological processes including photomorphogenesis, leaf and seed formation, energy homeostasis, and abiotic and biotic stress responses. Here we performed a comprehensive phylogenetic analysis of bZIP genes from algae, mosses, ferns, gymnosperms and angiosperms. METHODOLOGY/PRINCIPAL FINDINGS: We identified 13 groups of bZIP homologues in angiosperms, three more than known before, that represent 34 Possible Groups of Orthologues (PoGOs. The 34 PoGOs may correspond to the complete set of ancestral angiosperm bZIP genes that participated in the diversification of flowering plants. Homologous genes dedicated to seed-related processes and ABA-mediated stress responses originated in the common ancestor of seed plants, and three groups of homologues emerged in the angiosperm lineage, of which one group plays a role in optimizing the use of energy. CONCLUSIONS/SIGNIFICANCE: Our data suggest that the ancestor of green plants possessed four bZIP genes functionally involved in oxidative stress and unfolded protein responses that are bZIP-mediated processes in all eukaryotes, but also in light-dependent regulations. The four founder genes amplified and diverged significantly, generating traits that benefited the colonization of new environments.

  11. A specific role for the ZipA protein in cell division: stabilization of the FtsZ protein.

    Science.gov (United States)

    Pazos, Manuel; Natale, Paolo; Vicente, Miguel

    2013-02-01

    In Escherichia coli, the cell division protein FtsZ is anchored to the cytoplasmic membrane by the action of the bitopic membrane protein ZipA and the cytoplasmic protein FtsA. Although the presence of both ZipA and FtsA is strictly indispensable for cell division, an FtsA gain-of-function mutant FtsA* (R286W) can bypass the ZipA requirement for cell division. This observation casts doubts on the role of ZipA and its need for cell division. Maxicells are nucleoid-free bacterial cells used as a whole cell in vitro system to probe protein-protein interactions without the need of protein purification. We show that ZipA protects FtsZ from the ClpXP-directed degradation observed in E. coli maxicells and that ZipA-stabilized FtsZ forms membrane-attached spiral-like structures in the bacterial cytoplasm. The overproduction of the FtsZ-binding ZipA domain is sufficient to protect FtsZ from degradation, whereas other C-terminal ZipA partial deletions lacking it are not. Individual overproduction of the proto-ring component FtsA or its gain-of-function mutant FtsA* does not result in FtsZ protection. Overproduction of FtsA or FtsA* together with ZipA does not interfere with the FtsZ protection. Moreover, neither FtsA nor FtsA* protects FtsZ when overproduced together with ZipA mutants lacking the FZB domain. We propose that ZipA protects FtsZ from degradation by ClpP by making the FtsZ site of interaction unavailable to the ClpX moiety of the ClpXP protease. This role cannot be replaced by either FtsA or FtsA*, suggesting a unique function for ZipA in proto-ring stability.

  12. Does it really matter that people zip through ads? Testing the effectiveness of simultaneous presentation advertising in an IDTV environment.

    Science.gov (United States)

    Nam, Yoonjae; Kwon, Kyonghee H; Lee, Sungjoon

    2010-04-01

    In an IDTV environment, which facilitates self-scheduling, skipping advertisements by zipping is an emerging ad-avoidance behavior. This study explores whether an alternative ad format, called simultaneous presentation advertising (SPA), may overcome the limitations of classical sequential advertising (CSA) in controlling zipping behavior and increasing the effectiveness of ads. The experiment revealed that SPA is more effective than CSA in reducing zipping and increasing recall, but SPA was more intrusive and produced a negative product image. There was no difference regarding cognitive avoidance. This work discusses the implications of these findings in the interactive media environment.

  13. Characterization of pollen-expressed bZIP protein interactions and the role of ATbZIP18 in the male gametophyte

    Czech Academy of Sciences Publication Activity Database

    Gibalová, Antónia; Steinbachová, Lenka; Hafidh, Said; Bláhová, Veronika; Gadiou, Zuzana; Michailidis, Christos; Müller, Karel; Pleskot, Roman; Dupľáková, Nikoleta; Honys, David

    2017-01-01

    Roč. 30, č. 1 (2017), s. 1-17 ISSN 2194-7953 R&D Projects: GA ČR GA15-22720S; GA ČR(CZ) GA14-32292S; GA ČR GP13-41444P; GA MŠk(CZ) LD14109 Institutional support: RVO:61389030 Keywords : reticulum stress -response * transcription factor * arabidopsis-thaliana * molecular-interactions * plant transformation * gene-expression * heterodimerization * dimerization * evolution * specificity * bZIP * Transcription factors * Regulatory network * Male gametophyte * y2h * Pollen development Subject RIV: ED - Physiology OBOR OECD: Plant sciences, botany Impact factor: 2.629, year: 2016

  14. Spin gating electrical current

    Science.gov (United States)

    Ciccarelli, C.; Zârbo, L. P.; Irvine, A. C.; Campion, R. P.; Gallagher, B. L.; Wunderlich, J.; Jungwirth, T.; Ferguson, A. J.

    2012-09-01

    The level of the chemical potential is a fundamental parameter of the electronic structure of a physical system, which consequently plays an important role in defining the properties of active electrical devices. We directly measure the chemical potential shift in the relativistic band structure of the ferromagnetic semiconductor (Ga,Mn)As, controlled by changes in its magnetic order parameter. Our device comprises a non-magnetic aluminum single electron channel capacitively coupled to the (Ga,Mn)As gate electrode. The chemical potential shifts of the gate are directly read out from the shifts in the Coulomb blockade oscillations of the single electron transistor. The experiments introduce a concept of spin gating electrical current. In our spin transistor spin manipulation is completely removed from the electrical current carrying channel.

  15. Cardiac gated ventilation

    Science.gov (United States)

    Hanson, C. William, III; Hoffman, Eric A.

    1995-05-01

    There are several theoretic advantages to synchronizing positive pressure breaths with the cardiac cycle, including the potential for improving distribution of pulmonary and myocardial blood flow and enhancing cardiac output. We evaluated the effects of synchronizing respiration to the cardiac cycle using a programmable ventilator and electron beam CT (EBCT) scanning. The hearts of anesthetized dogs were imaged during cardiac gated respiration with a 50msec scan aperture. Multislice, short axis, dynamic image data sets spanning the apex to base of the left ventricle were evaluated to determine the volume of the left ventricular chamber at end-diastole and end-systole during apnea, systolic and diastolic cardiac gating. We observed an increase in cardiac output of up to 30% with inspiration gated to the systolic phase of the cardiac cycle in a nonfailing model of the heart.

  16. Compound list: alpidem [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available alpidem ADM 00171 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/alpid...em.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/alpidem.Rat.in_vitro.Liver.zip ...

  17. Compound list: venlafaxine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available venlafaxine VLF 00172 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/venlafaxine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/venlafaxine.Rat.in_vitro.Liver.zip ...

  18. Compound list: clozapine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available clozapine CZP 00174 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/clozapine....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/clozapine.Rat.in_vitro.Liver.zip ...

  19. Compound list: acetamide [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available acetamide AAA 00169 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/acetam...ide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/acetamide.Rat.in_vivo.Liver.Repeat.zip ...

  20. Up-regulation of Slc39A2(Zip2) mRNA in peripheral blood mononuclear cells from patients with pulmonary tuberculosis.

    Science.gov (United States)

    Tao, Yan-ting; Huang, Qing; Jiang, Ya-li; Wang, Xiao-lei; Sun, Ping; Tian, Yuanyuan; Wu, Hai-liang; Zhang, Min; Meng, Si-bo; Wang, Yu-shu; Sun, Qing; Zhang, Lian-ying

    2013-08-01

    Zinc is the most common trace mineral after iron in the human body. In organisms, zinc transporters help zinc influx and efflux from cells. A previous study has reported that Zip2 was up-regulated over 27-fold in human monocytic THP-1 cells, when intracellular zinc was depleted by TPEN. Our study found Zip2 was over-expressed in leukocytes of asthmatic infants, especially those in which the serum zinc level was lower than those in healthy infants. Pulmonary tuberculosis (PTB) patients have significantly low serum zinc levels. Here we investigated whether Zip2 level was changed in the patients with PTB. Zip2 mRNA and protein levels in peripheral blood mononuclear cells (PBMC) from PTB (n1=23) and healthy controls (n2=42) were detected by quantitative real-time PCR and western blot, respectively. mRNA expression levels of another four zinc transporters, Zip1, Zip6, Zip8 and ZnT1, were detected by quantitative real-time PCR. Zip2 mRNA level was significantly up-regulated in PTB patients (P=0.001), and Zip8 mRNA level was significantly down-regulated compared with control individuals (Plevels of Zip1, Zip6 and ZnT1 in either group (P>0.05). Zip2 protein expression levels increased in PTB patients compared with control individuals. Our study found that knockdown of ZIP2 with siRNA caused a decrease in Zip2 levels in PBMC of PTB patients, while reducing the expression of INF-γ (Pinitial infection control of the human body, by promoting and maintaining the immune response of adaptive T cells.

  1. Functional mapping of brain synapses by the enriching activity-marker SynaptoZip.

    Science.gov (United States)

    Ferro, Mattia; Lamanna, Jacopo; Ripamonti, Maddalena; Racchetti, Gabriella; Arena, Alessandro; Spadini, Sara; Montesano, Giovanni; Cortese, Riccardo; Zimarino, Vincenzo; Malgaroli, Antonio

    2017-10-31

    Ideally, elucidating the role of specific brain circuits in animal behavior would require the ability to measure activity at all involved synapses, possibly with unrestricted field of view, thus even at those boutons deeply located into the brain. Here, we introduce and validate an efficient scheme reporting synaptic vesicle cycling in vivo. This is based on SynaptoZip, a genetically encoded molecule deploying in the vesicular lumen a bait moiety designed to capture upon exocytosis a labeled alien peptide, Synbond. The resulting signal is cumulative and stores the number of cycling events occurring at individual synapses. Since this functional signal is enduring and measurable both online and ex post, SynaptoZip provides a unique method for the analysis of the history of synaptic activity in regions several millimeters below the brain surface. We show its broad applicability by reporting stimulus-evoked and spontaneous circuit activity in wide cortical fields, in anesthetized and freely moving animals.

  2. The use of ZIP and CART to model cryptosporidiosis in relation to climatic variables.

    Science.gov (United States)

    Hu, Wenbiao; Mengersen, Kerrie; Fu, Shiu-Yun; Tong, Shilu

    2010-07-01

    This research assesses the potential impact of weekly weather variability on the incidence of cryptosporidiosis disease using time series zero-inflated Poisson (ZIP) and classification and regression tree (CART) models. Data on weather variables, notified cryptosporidiosis cases and population size in Brisbane were supplied by the Australian Bureau of Meteorology, Queensland Department of Health, and Australian Bureau of Statistics, respectively. Both time series ZIP and CART models show a clear association between weather variables (maximum temperature, relative humidity, rainfall and wind speed) and cryptosporidiosis disease. The time series CART models indicated that, when weekly maximum temperature exceeded 31 degrees C and relative humidity was less than 63%, the relative risk of cryptosporidiosis rose by 13.64 (expected morbidity: 39.4; 95% confidence interval: 30.9-47.9). These findings may have applications as a decision support tool in planning disease control and risk-management programs for cryptosporidiosis disease.

  3. Gate valve performance prediction

    International Nuclear Information System (INIS)

    Harrison, D.H.; Damerell, P.S.; Wang, J.K.; Kalsi, M.S.; Wolfe, K.J.

    1994-01-01

    The Electric Power Research Institute is carrying out a program to improve the performance prediction methods for motor-operated valves. As part of this program, an analytical method to predict the stem thrust required to stroke a gate valve has been developed and has been assessed against data from gate valve tests. The method accounts for the loads applied to the disc by fluid flow and for the detailed mechanical interaction of the stem, disc, guides, and seats. To support development of the method, two separate-effects test programs were carried out. One test program determined friction coefficients for contacts between gate valve parts by using material specimens in controlled environments. The other test program investigated the interaction of the stem, disc, guides, and seat using a special fixture with full-sized gate valve parts. The method has been assessed against flow-loop and in-plant test data. These tests include valve sizes from 3 to 18 in. and cover a considerable range of flow, temperature, and differential pressure. Stem thrust predictions for the method bound measured results. In some cases, the bounding predictions are substantially higher than the stem loads required for valve operation, as a result of the bounding nature of the friction coefficients in the method

  4. Life Expectancy at Birth in Milwaukee County: A Zip Code-Level Analysis

    Directory of Open Access Journals (Sweden)

    Erica S. LeCounte

    2017-11-01

    Full Text Available Purpose: Life expectancy at birth is used as a barometer of the health and well-being of a population. Life expectancies vary widely across Wisconsin counties. While much of the analysis of life expectancy in Wisconsin has focused on counties, there may be important differences in life expectancy within counties by zip code. Methods: To calculate life expectancy, death count data and population estimates were entered into an abridged life table using the Chiang methodology. Data were linked with measures from the American Community Survey to examine the relationship between life expectancy and zip code characteristics. Results: Life expectancy varies greatly across zip codes in Milwaukee County. Overall, there was a 12-year difference in the life expectancy of children born into zip codes with the lowest and highest life expectancy: 53206 (71.3 years and 53217 (83.2 years. There was a strong positive correlation between life expectancy and median household income (r = 0.784, P < 0.0001, educational attainment of a bachelor’s degree or higher (r = 0.741, P < 0.0001 and the socioeconomic index combining education and income (r = 0.819, P < 0.0001. Conclusions: Disparities in life expectancy within Milwaukee County are stark and correlate with differences in social and economic factors. To improve health outcomes such as life expectancy, health care practitioners and health care systems must become more involved in activities at the social and policy levels to improve social and economic conditions that would allow their patients to live healthier and longer lives.

  5. The four-gate transistor

    Science.gov (United States)

    Mojarradi, M. M.; Cristoveanu, S.; Allibert, F.; France, G.; Blalock, B.; Durfrene, B.

    2002-01-01

    The four-gate transistor or G4-FET combines MOSFET and JFET principles in a single SOI device. Experimental results reveal that each gate can modulate the drain current. Numerical simulations are presented to clarify the mechanisms of operation. The new device shows enhanced functionality, due to the combinatorial action of the four gates, and opens rather revolutionary applications.

  6. Stanford, Duke, Rice,... and Gates?

    Science.gov (United States)

    Carey, Kevin

    2009-01-01

    This article presents an open letter to Bill Gates. In his letter, the author suggests that Bill Gates should build a brand-new university, a great 21st-century institution of higher learning. This university will be unlike anything the world has ever seen. He asks Bill Gates not to stop helping existing colleges create the higher-education system…

  7. Master equation approach to DNA breathing in heteropolymer DNA

    DEFF Research Database (Denmark)

    Ambjörnsson, Tobias; Banik, Suman K; Lomholt, Michael A

    2007-01-01

    After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies up to a few k(B)T. Thermal motion within the DNA double strand therefore causes the opening of intermittent single-stranded denaturation zones......, the DNA bubbles. The unzipping and zipping dynamics of bps at the two zipper forks of a bubble, where the single strand of the denatured zone joins the still intact double strand, can be monitored by single molecule fluorescence or NMR methods. We here establish a dynamic description of this DNA breathing...... in a heteropolymer DNA with given sequence in terms of a master equation that governs the time evolution of the joint probability distribution for the bubble size and position along the sequence. The transfer coefficients are based on the Poland-Scheraga free energy model. We derive the autocorrelation function...

  8. Gene family structure, expression and functional analysis of HD-Zip III genes in angiosperm and gymnosperm forest trees

    OpenAIRE

    C?t?, Caroline L; Boileau, Francis; Roy, Vicky; Ouellet, Mario; Levasseur, Caroline; Morency, Marie-Jos?e; Cooke, Janice EK; S?guin, Armand; MacKay, John J

    2010-01-01

    Abstract Background Class III Homeodomain Leucine Zipper (HD-Zip III) proteins have been implicated in the regulation of cambium identity, as well as primary and secondary vascular differentiation and patterning in herbaceous plants. They have been proposed to regulate wood formation but relatively little evidence is available to validate such a role. We characterised and compared HD-Zip III gene family in an angiosperm tree, Populus spp. (poplar), and the gymnosperm Picea glauca (white spruc...

  9. Overexpression of ZmIRT1 and ZmZIP3 Enhances Iron and Zinc Accumulation in Transgenic Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Suzhen Li

    Full Text Available Iron and zinc are important micronutrients for both the growth and nutrient availability of crop plants, and their absorption is tightly controlled by a metal uptake system. Zinc-regulated transporters, iron-regulated transporter-like proteins (ZIP, is considered an essential metal transporter for the acquisition of Fe and Zn in graminaceous plants. Several ZIPs have been identified in maize, although their physiological function remains unclear. In this report, ZmIRT1 was shown to be specifically expressed in silk and embryo, whereas ZmZIP3 was a leaf-specific gene. Both ZmIRT1 and ZmZIP3 were shown to be localized to the plasma membrane and endoplasmic reticulum. In addition, transgenic Arabidopsis plants overexpressing ZmIRT1 or ZmZIP3 were generated, and the metal contents in various tissues of transgenic and wild-type plants were examined based on ICP-OES and Zinpyr-1 staining. The Fe and Zn concentration increased in roots and seeds of ZmIRT1-overexpressing plants, while the Fe content in shoots decreased. Overexpressing ZmZIP3 enhanced Zn accumulation in the roots of transgenic plants, while that in shoots was repressed. In addition, the transgenic plants showed altered tolerance to various Fe and Zn conditions compared with wild-type plants. Furthermore, the genes associated with metal uptake were stimulated in ZmIRT1 transgenic plants, while those involved in intra- and inter- cellular translocation were suppressed. In conclusion, ZmIRT1 and ZmZIP3 are functional metal transporters with different ion selectivities. Ectopic overexpression of ZmIRT1 may stimulate endogenous Fe uptake mechanisms, which may facilitate metal uptake and homeostasis. Our results increase our understanding of the functions of ZIP family transporters in maize.

  10. Changes in skin structure of the Zip13-KO mouse by Makomo (Zizania latifolia) feeding.

    Science.gov (United States)

    Yamauchi, Takeshi; Hirose, Takuya; Sato, Kaho; Iwai, Kenji; Takahashi, Naoki; Minaguchi, Jun; Ueno, Takeshi; Tangkawattana, Prasarn; Takehana, Kazushige

    2017-09-29

    Ehlers-Danlos syndrome (EDS) is a group of disorders caused by abnormalities in the extracellular matrix (ECM). Transforming growth factor-β (TGF-β) plays a crucial role in formation of the ECM by the SMAD (Sma-and Mad-related protein, mothers against decapentaplegic homolog) pathway. It has been reported that loss of function of zinc transporter ZRT/IRT-like protein 13 (ZIP13) is the cause of the spondylocheiro dysplastic form of EDS (SCD-EDS: OMIM 612350). Our previous study suggested that TGF-β1 has a relationship with the skin pathological condition in the Zip13-Knockout (KO) mouse, which is a model of SCD-EDS. Thus far, effective treatment based on modern medicine for this syndrome has not yet been established. According to an approach of traditional Chinese medicine, the present study investigates the medicinal effects of Makomo (Zizania latifolia) on certain aspects of SCD-EDS, such as skin morphology and plasma TGF-β1, in Zip13-KO mice. Increases in densities of collagen fibers and fibrils without a significant change in thickness of the dermal layer were observed in the group of mice fed a Makomo-containing diet. No change in the amount of collagen suggests that Makomo feed does not elevate collagen synthesis, but changes the length of glycosaminoglycan chains and decreases the distance between collagen fibrils. In conclusion, the changes of the skin structure suggest that Makomo can increase the mechanical strength of skin.

  11. Tissue Plasminogen Activator Alters Intracellular Sequestration of Zinc through Interaction with the Transporter ZIP4

    Energy Technology Data Exchange (ETDEWEB)

    Emmetsberger, Jaime; Mirrione, Martine M.; Zhou, Chun; Fernandez-Monreal, Monica; Siddiq, Mustafa M.; Ji, Kyungmin; Tsirka, Stella E. (SBU)

    2010-09-17

    Glutamatergic neurons contain free zinc packaged into neurotransmitter-loaded synaptic vesicles. Upon neuronal activation, the vesicular contents are released into the synaptic space, whereby the zinc modulates activity of postsynaptic neurons though interactions with receptors, transporters and exchangers. However, high extracellular concentrations of zinc trigger seizures and are neurotoxic if substantial amounts of zinc reenter the cells via ion channels and accumulate in the cytoplasm. Tissue plasminogen activator (tPA), a secreted serine protease, is also proepileptic and excitotoxic. However, tPA counters zinc toxicity by promoting zinc import back into the neurons in a sequestered form that is nontoxic. Here, we identify the zinc influx transporter, ZIP4, as the pathway through which tPA mediates the zinc uptake. We show that ZIP4 is upregulated after excitotoxin stimulation of the mouse, male and female, hippocampus. ZIP4 physically interacts with tPA, correlating with an increased intracellular zinc influx and lysosomal sequestration. Changes in prosurvival signals support the idea that this sequestration results in neuroprotection. These experiments identify a mechanism via which neurons use tPA to efficiently neutralize the toxic effects of excessive concentrations of free zinc.

  12. Enhancement of biomass and lipid productivity by overexpression of a bZIP transcription factor in Nannochloropsis salina.

    Science.gov (United States)

    Kwon, Sohee; Kang, Nam Kyu; Koh, Hyun Gi; Shin, Sung-Eun; Lee, Bongsoo; Jeong, Byeong-Ryool; Chang, Yong Keun

    2018-02-01

    Microalgae are considered as excellent platforms for biomaterial production that can replace conventional fossil fuel-based fuels and chemicals. Genetic engineering of microalgae is prerequisite to maximize production of materials and to reduce costs for the production. Transcription factors (TFs) are emerging as key regulators of metabolic pathways to enhance production of molecules for biofuels and other materials. TFs with the basic leucine zipper (bZIP) domain have been known as stress regulators and are associated with lipid metabolism in plants. We overexpressed a bZIP TF, NsbZIP1, in Nannochloropsis salina, and found that transformants showed enhanced growth with concomitant increase in lipid contents. The improved phenotypes were also notable under stress conditions including N limitation and high salt. To understand the mechanism underlying improved phenotypes, we analyzed expression patterns of predicted target genes involved in lipid metabolism via quantitative RT-PCR, confirming increases transcript levels. NsbZIP1 appeared to be one of type C bZIPs in plants that has been known to regulate lipid metabolism under stress. Taken together, we demonstrated that NsbZIP1 could improve both growth and lipid production, and TF engineering can serve as an excellent genetic engineering tool for production of biofuels and biomaterials in microalgae. © 2017 Wiley Periodicals, Inc.

  13. Functional characterization of a transition metal ion transporter, OsZIP6 from rice (Oryza sativa L.).

    Science.gov (United States)

    P G, Kavitha; Kuruvilla, Sam; Mathew, M K

    2015-12-01

    Micronutrients are important for the growth and development of plants, which deploy families of transporters for their uptake and distribution. We have functionally characterized a novel transition metal ion transporter from rice, OsZIP6 (Oryza sativa zinc regulated transporter, iron regulated transporter-like protein 6). The transporter was found to be transcriptionally activated in shoot and root tissues in response to deficiency in Fe(2+), Zn(2+) and Mn(2+). OsZIP6 was expressed in Xenopus laevis oocytes, where currents were observed on addition of Co(2+), Fe(2+) and Cd(2+) but not Zn(2+), Mn(2+) and Ni(2+). This substrate range for OsZIP6, identified using two-electrode voltage clamp electrophysiology was confirmed by atomic absorption spectroscopy. Ion transport by OsZIP6 was found to be pH dependent and enhanced transport was observed at acidic pH. Radioisotope uptake suggested that Co(2+) competitively inhibits Fe(2+) uptake by OsZIP6. Identification and characterization of ZIP family members from crop plants will contribute to an understanding of nutrient mineral homeostasis in these plants. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  14. ZIP8 zinc transporter: indispensable role for both multiple-organ organogenesis and hematopoiesis in utero.

    Directory of Open Access Journals (Sweden)

    Marina Gálvez-Peralta

    Full Text Available Previously this laboratory characterized Slc39a8-encoded ZIP8 as a Zn(2+/(HCO(3(-(2 symporter; yet, the overall physiological importance of ZIP8 at the whole-organism level remains unclear. Herein we describe the phenotype of the hypomorphic Slc39a8(neo/neo mouse which has retained the neomycin-resistance gene in intron 3, hence causing significantly decreased ZIP8 mRNA and protein levels in embryo, fetus, placenta, yolk sac, and several tissues of neonates. The Slc39a8(neo allele is associated with diminished zinc and iron uptake in mouse fetal fibroblast and liver-derived cultures; consequently, Slc39a8(neo/neo newborns exhibit diminished zinc and iron levels in several tissues. Slc39a8(neo/neo homozygotes from gestational day(GD-11.5 onward are pale, growth-stunted, and die between GD18.5 and 48 h postnatally. Defects include: severely hypoplastic spleen; hypoplasia of liver, kidney, lung, and lower limbs. Histologically, Slc39a8(neo/neo neonates show decreased numbers of hematopoietic islands in yolk sac and liver. Low hemoglobin, hematocrit, red cell count, serum iron, and total iron-binding capacity confirmed severe anemia. Flow cytometry of fetal liver cells revealed the erythroid series strikingly affected in the hypomorph. Zinc-dependent 5-aminolevulinic acid dehydratase, required for heme synthesis, was not different between Slc39a8(+/+ and Slc39a8(neo/neo offspring. To demonstrate further that the mouse phenotype is due to ZIP8 deficiency, we bred Slc39a8(+/neo with BAC-transgenic BTZIP8-3 line (carrying three extra copies of the Slc39a8 allele; this cross generated viable Slc39a8(neo/neo_BTZIP8-3(+/+ pups showing none of the above-mentioned congenital defects-proving Slc39a8(neo/neo causes the described phenotype. Our study demonstrates that ZIP8-mediated zinc transport plays an unappreciated critical role during in utero and neonatal growth, organ morphogenesis, and hematopoiesis.

  15. High permittivity gate dielectric materials

    CERN Document Server

    2013-01-01

    "The book comprehensively covers all the current and the emerging areas of the physics and the technology of high permittivity gate dielectric materials, including, topics such as MOSFET basics and characteristics, hafnium-based gate dielectric materials, Hf-based gate dielectric processing, metal gate electrodes, flat-band and threshold voltage tuning, channel mobility, high-k gate stack degradation and reliability, lanthanide-based high-k gate stack materials, ternary hafnia and lanthania based high-k gate stack films, crystalline high-k oxides, high mobility substrates, and parameter extraction. Each chapter begins with the basics necessary for understanding the topic, followed by a comprehensive review of the literature, and ultimately graduating to the current status of the technology and our scientific understanding and the future prospects."

  16. Noise Gating Solar Images

    Science.gov (United States)

    DeForest, Craig; Seaton, Daniel B.; Darnell, John A.

    2017-08-01

    I present and demonstrate a new, general purpose post-processing technique, "3D noise gating", that can reduce image noise by an order of magnitude or more without effective loss of spatial or temporal resolution in typical solar applications.Nearly all scientific images are, ultimately, limited by noise. Noise can be direct Poisson "shot noise" from photon counting effects, or introduced by other means such as detector read noise. Noise is typically represented as a random variable (perhaps with location- or image-dependent characteristics) that is sampled once per pixel or once per resolution element of an image sequence. Noise limits many aspects of image analysis, including photometry, spatiotemporal resolution, feature identification, morphology extraction, and background modeling and separation.Identifying and separating noise from image signal is difficult. The common practice of blurring in space and/or time works because most image "signal" is concentrated in the low Fourier components of an image, while noise is evenly distributed. Blurring in space and/or time attenuates the high spatial and temporal frequencies, reducing noise at the expense of also attenuating image detail. Noise-gating exploits the same property -- "coherence" -- that we use to identify features in images, to separate image features from noise.Processing image sequences through 3-D noise gating results in spectacular (more than 10x) improvements in signal-to-noise ratio, while not blurring bright, resolved features in either space or time. This improves most types of image analysis, including feature identification, time sequence extraction, absolute and relative photometry (including differential emission measure analysis), feature tracking, computer vision, correlation tracking, background modeling, cross-scale analysis, visual display/presentation, and image compression.I will introduce noise gating, describe the method, and show examples from several instruments (including SDO

  17. Compound list: ethinylestradiol [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available ethinylestradiol EE 00055 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/ethinylestr...adiol.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/ethinylest...T/Rat/in_vivo/Liver/Single/ethinylestradiol.Rat.in_vivo.Liver.Single.zip ftp://ft...p.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/ethinylestradiol.Rat.in_vivo.Liver.R...epeat.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/ethinylestradiol.

  18. Compound list: cyclophosphamide [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available cyclophosphamide CPA 00024 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/H...ST/Rat/in_vitro/cyclophosphamide.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATE...ST/Rat/in_vivo/Liver/Single/cyclophosphamide.Rat.in_vivo.Liver.Single.zip ftp://f...tp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/cyclophosphamide.Rat.in_vivo.Liver....Repeat.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/cyclophosphamide

  19. Compound list: methyltestosterone [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available methyltestosterone MTS 00041 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/methyltes...LATEST/Rat/in_vitro/methyltestosterone.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggate...s/LATEST/Rat/in_vivo/Liver/Single/methyltestosterone.Rat.in_vivo.Liver.Single.zip... ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/methyltestosterone.Rat.in_v...ivo.Liver.Repeat.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/methyltest

  20. Compound list: ketoconazole [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available ketoconazole KC 00047 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/ketoc...onazole.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/ketoc...onazole.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/ketoc...jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/ketoconazole.Rat.in_vivo.Liver.Repeat.zip ftp://ftp....biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/ketoconazole.Rat.in_vivo.Kidney.Singl

  1. Compound list: monocrotaline [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available monocrotaline MCT 00058 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/monocrotaline....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/monocrotaline..._vivo/Liver/Single/monocrotaline.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscienc...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/monocrotaline.Rat.in_vivo.Liver.Repeat.zip ftp:...//ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/monocrotaline.Rat.in_vivo.Kidne

  2. Compound list: bromoethylamine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available bromoethylamine BEA 00134 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Hu...man/in_vitro/bromoethylamine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST.../Rat/in_vitro/bromoethylamine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/...Rat/in_vivo/Liver/Single/bromoethylamine.Rat.in_vivo.Liver.Single.zip ftp://ftp.b...iosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/bromoethylamine.Rat.in_vivo.Liver.Repea

  3. Compound list: thioacetamide [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available thioacetamide TAA 00017 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/thioacetam...ide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/thioacetam..._vivo/Liver/Single/thioacetamide.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscienc...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/thioacetamide.Rat.in_vivo.Liver.Repeat.zip ftp:...//ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/thioacetamide.Rat.in_vivo.Kidne

  4. Compound list: acetaminophen [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available acetaminophen APAP 00001 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/acetam...inophen.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/acetam...inophen.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/aceta...cedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/acetaminophen.Rat.in_vivo.Liver.Repeat.zip ftp...://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/acetaminophen.Rat.in_vivo.Kidn

  5. Compound list: hexachlorobenzene [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available hexachlorobenzene HCB 00022 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/...Human/in_vitro/hexachlorobenzene.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LA...TEST/Rat/in_vitro/hexachlorobenzene.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/L...ATEST/Rat/in_vivo/Liver/Single/hexachlorobenzene.Rat.in_vivo.Liver.Single.zip ftp...://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/hexachlorobenzene.Rat.in_vivo.L

  6. A quantum Fredkin gate.

    Science.gov (United States)

    Patel, Raj B; Ho, Joseph; Ferreyrol, Franck; Ralph, Timothy C; Pryde, Geoff J

    2016-03-01

    Minimizing the resources required to build logic gates into useful processing circuits is key to realizing quantum computers. Although the salient features of a quantum computer have been shown in proof-of-principle experiments, difficulties in scaling quantum systems have made more complex operations intractable. This is exemplified in the classical Fredkin (controlled-SWAP) gate for which, despite theoretical proposals, no quantum analog has been realized. By adding control to the SWAP unitary, we use photonic qubit logic to demonstrate the first quantum Fredkin gate, which promises many applications in quantum information and measurement. We implement example algorithms and generate the highest-fidelity three-photon Greenberger-Horne-Zeilinger states to date. The technique we use allows one to add a control operation to a black-box unitary, something that is impossible in the standard circuit model. Our experiment represents the first use of this technique to control a two-qubit operation and paves the way for larger controlled circuits to be realized efficiently.

  7. 100-nm gate lithography for double-gate transistors

    Science.gov (United States)

    Krasnoperova, Azalia A.; Zhang, Ying; Babich, Inna V.; Treichler, John; Yoon, Jung H.; Guarini, Kathryn; Solomon, Paul M.

    2001-09-01

    The double gate field effect transistor (FET) is an exploratory device that promises certain performance advantages compared to traditional CMOS FETs. It can be scaled down further than the traditional devices because of the greater electrostatic control by the gates on the channel (about twice as short a channel length for the same gate oxide thickness), has steeper sub-threshold slope and about double the current for the same width. This paper presents lithographic results for double gate FET's developed at IBM's T. J. Watson Research Center. The device is built on bonded wafers with top and bottom gates self-aligned to each other. The channel is sandwiched between the top and bottom polysilicon gates and the gate length is defined using DUV lithography. An alternating phase shift mask was used to pattern gates with critical dimensions of 75 nm, 100 nm and 125 nm in photoresist. 50 nm gates in photoresist have also been patterned by 20% over-exposure of nominal 100 nm lines. No trim mask was needed because of a specific way the device was laid out. UV110 photoresist from Shipley on AR-3 antireflective layer were used. Process windows, developed and etched patterns are presented.

  8. LiZIP3 is a cellular zinc transporter that mediates the tightly regulated import of zinc in Leishmania infantum parasites

    Science.gov (United States)

    Carvalho, Sandra; da Silva, Rosa Barreira; Shawki, Ali; Castro, Helena; Lamy, Márcia; Eide, David; Costa, Vítor; Mackenzie, Bryan; Tomás, Ana M.

    2016-01-01

    Summary Cellular zinc homeostasis ensures that the intracellular concentration of this element is kept within limits that enable its participation in critical physiological processes without exerting toxic effects. We report here the identification and characterization of the first mediator of zinc homeostasis in Leishmania infantum, LiZIP3, a member of the ZIP family of divalent metal-ion transporters. The zinc transporter activity of LiZIP3 was first disclosed by its capacity to rescue the growth of Saccharomyces cerevisiae strains deficient in zinc acquisition. Subsequent expression of LiZIP3 in Xenopus laevis oocytes was shown to stimulate the uptake of a broad range of metal ions, among which Zn2+ was the preferred LiZIP3 substrate (K0.5 ≈ 0.1 μM). Evidence that LiZIP3 functions as a zinc importer in L. infantum came from the observations that the protein locates to the cell membrane and that its overexpression leads to augmented zinc internalization. Importantly, expression and cell-surface location of LiZIP3 are lost when parasites face high zinc bioavailability. LiZIP3 decline in response to zinc is regulated at the mRNA level in a process involving (a) short-lived protein(s). Collectively, our data reveal that LiZIP3 enables L. infantum to acquire zinc in a highly regulated manner, hence contributing to zinc homeostasis. PMID:25644708

  9. Transcriptome-Wide Survey and Expression Profile Analysis of Putative Chrysanthemum HD-Zip I and II Genes

    Directory of Open Access Journals (Sweden)

    Aiping Song

    2016-05-01

    Full Text Available The homeodomain-leucine zipper (HD-Zip transcription factor family is a key transcription factor family and unique to the plant kingdom. It consists of a homeodomain and a leucine zipper that serve in combination as a dimerization motif. The family can be classified into four subfamilies, and these subfamilies participate in the development of hormones and mediation of hormone action and are involved in plant responses to environmental conditions. However, limited information on this gene family is available for the important chrysanthemum ornamental species (Chrysanthemum morifolium. Here, we characterized 17 chrysanthemum HD-Zip genes based on transcriptome sequences. Phylogenetic analyses revealed that 17 CmHB genes were distributed in the HD-Zip subfamilies I and II and identified two pairs of putative orthologous proteins in Arabidopsis and chrysanthemum and four pairs of paralogous proteins in chrysanthemum. The software MEME was used to identify 7 putative motifs with E values less than 1e-3 in the chrysanthemum HD-Zip factors, and they can be clearly classified into two groups based on the composition of the motifs. A bioinformatics analysis predicted that 8 CmHB genes could be targeted by 10 miRNA families, and the expression of these 17 genes in response to phytohormone treatments and abiotic stresses was characterized. The results presented here will promote research on the various functions of the HD-Zip gene family members in plant hormones and stress responses.

  10. System-wide characterization of bZIP transcription factor proteins involved in infection-related morphogenesis of Magnaporthe oryzae.

    Science.gov (United States)

    Tang, Wei; Ru, Yanyan; Hong, Li; Zhu, Qian; Zuo, Rongfang; Guo, Xianxian; Wang, Jingzhen; Zhang, Haifeng; Zheng, Xiaobo; Wang, Ping; Zhang, Zhengguang

    2015-04-01

    The basic leucine zipper (bZIP) domain-containing transcription factors (TFs) function as key regulators of cellular growth and differentiation in eukaryotic organisms including fungi. We have previously identified MoAp1 and MoAtf1 as bZIP TFs in Magnaporthe oryzae and demonstrated that they regulate the oxidative stress response and are critical in conidiogenesis and pathogenicity. Studies of bZIP proteins could provide a novel strategy for controlling rice blast, but a systematic examination of the bZIP proteins has not been carried out. Here, we identified 19 additional bZIP TFs and characterized their functions. We found that the majority of these TFs exhibit active functions, most notably, in conidiogenesis. We showed that MoHac1 regulates the endoplasmic reticulum stress response through a conserved unfolded protein response pathway, MoMetR controls amino acid metabolism to govern growth and differentiation, and MoBzip10 governs appressorium function and invasive hyphal growth. Moreover, MoBzip5 participates in appressorium formation through a pathway distinct from that MoBzip10, and MoMeaB appears to exert a regulatory role through nutrient uptake and nitrogen utilization. Collectively, our results provide insights into shared and specific functions associated with each of these TFs and link the regulatory roles to the fungal growth, conidiation, appressorium formation, host penetration and pathogenicity. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  11. Expert Oracle GoldenGate

    CERN Document Server

    Prusinski, Ben; Chung, Richard

    2011-01-01

    Expert Oracle GoldenGate is a hands-on guide to creating and managing complex data replication environments using the latest in database replication technology from Oracle. GoldenGate is the future in replication technology from Oracle, and aims to be best-of-breed. GoldenGate supports homogeneous replication between Oracle databases. It supports heterogeneous replication involving other brands such as Microsoft SQL Server and IBM DB2 Universal Server. GoldenGate is high-speed, bidirectional, highly-parallelized, and makes only a light impact on the performance of databases involved in replica

  12. Molecular logic gate arrays.

    Science.gov (United States)

    de Silva, A Prasanna

    2011-03-01

    Chemists are now able to emulate the ideas and instruments of mathematics and computer science with molecules. The integration of molecular logic gates into small arrays has been a growth area during the last few years. The design principles underlying a collection of these cases are examined. Some of these computing molecules are applicable in medical- and biotechnologies. Cases of blood diagnostics, 'lab-on-a-molecule' systems, and molecular computational identification of small objects are included. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Systematic analysis of sequences and expression patterns of drought-responsive members of the HD-Zip gene family in maize.

    Directory of Open Access Journals (Sweden)

    Yang Zhao

    Full Text Available BACKGROUND: Members of the homeodomain-leucine zipper (HD-Zip gene family encode transcription factors that are unique to plants and have diverse functions in plant growth and development such as various stress responses, organ formation and vascular development. Although systematic characterization of this family has been carried out in Arabidopsis and rice, little is known about HD-Zip genes in maize (Zea mays L.. METHODS AND FINDINGS: In this study, we described the identification and structural characterization of HD-Zip genes in the maize genome. A complete set of 55 HD-Zip genes (Zmhdz1-55 were identified in the maize genome using Blast search tools and categorized into four classes (HD-Zip I-IV based on phylogeny. Chromosomal location of these genes revealed that they are distributed unevenly across all 10 chromosomes. Segmental duplication contributed largely to the expansion of the maize HD-ZIP gene family, while tandem duplication was only responsible for the amplification of the HD-Zip II genes. Furthermore, most of the maize HD-Zip I genes were found to contain an overabundance of stress-related cis-elements in their promoter sequences. The expression levels of the 17 HD-Zip I genes under drought stress were also investigated by quantitative real-time PCR (qRT-PCR. All of the 17 maize HD-ZIP I genes were found to be regulated by drought stress, and the duplicated genes within a sister pair exhibited the similar expression patterns, suggesting their conserved functions during the process of evolution. CONCLUSIONS: Our results reveal a comprehensive overview of the maize HD-Zip gene family and provide the first step towards the selection of Zmhdz genes for cloning and functional research to uncover their roles in maize growth and development.

  14. bZIP transcription factor interactions regulate DIF responses in Dictyostelium.

    Science.gov (United States)

    Huang, Eryong; Blagg, Simone L; Keller, Thomas; Katoh, Mariko; Shaulsky, Gad; Thompson, Christopher R L

    2006-02-01

    The signalling molecule DIF-1 is required for normal cell fate choice and patterning in Dictyostelium. To understand how these developmental processes are regulated will require knowledge of how cells receive and respond to the DIF-1 signal. Previously, we have described a bZIP transcription factor, DimA, which is required for cells to respond to DIF-1. However, it was unknown whether DimA activity is required to activate the DIF response pathway in certain cells or is a component of the response pathway itself. In this study, we describe the identification of a DimA-related bZIP transcription factor, DimB. Rapid changes in the subcellular localisation of both DimA and DimB in response to DIF-1 suggest that they are directly downstream of the DIF-1 signal. Genetic and biochemical interactions between DimA and DimB provides evidence that their ability to regulate diverse targets in response to DIF-1 is partly due to their ability to form homo- and heterodimeric complexes. DimA and DimB are therefore direct regulators of cellular responses to DIF-1.

  15. Works close to gate B

    CERN Document Server

    GS Department

    2011-01-01

    In connection to the TRAM project, drainage works will be carried out close to gate B until the end of next week. In order to avoid access problems, if arriving by car, please use gates A and E. Department of General Infrastructure Services (GS) GS-SE Group

  16. Penn State DOE GATE Program

    Energy Technology Data Exchange (ETDEWEB)

    Anstrom, Joel

    2012-08-31

    The Graduate Automotive Technology Education (GATE) Program at The Pennsylvania State University (Penn State) was established in October 1998 pursuant to an award from the U.S. Department of Energy (U.S. DOE). The focus area of the Penn State GATE Program is advanced energy storage systems for electric and hybrid vehicles.

  17. Assessment of uncertainties in core melt phenomenology and their impact on risk at the Z/IP facilities

    International Nuclear Information System (INIS)

    Pratt, W.T.; Ludewig, H.; Bari, R.A.; Meyer, J.F.

    1983-01-01

    An evaluation of core meltdown accidents in the Z/IP facilities has been performed. Containment event trees have been developed to relate the progression of a given accident to various potential containment building failure modes. An extensive uncertainty analysis related to core melt phenomenology has been performed. A major conclusion of the study is that large variations in parameters associated with major phenomenological uncertainties have a relatively minor impact on risk when external initiators are considered. This is due to the inherent capability fo the Z/IP containment buildings to contain a wide range of core meltdown accidents. 12 references, 2 tables

  18. GATE: Improving the computational efficiency

    Energy Technology Data Exchange (ETDEWEB)

    Staelens, S. [UGent-ELIS, St-Pietersnieuwstraat, 41, B-9000 Gent (Belgium)]. E-mail: steven.staelens@ugent.be; De Beenhouwer, J. [UGent-ELIS, St-Pietersnieuwstraat, 41, B-9000 Gent (Belgium); Kruecker, D. [Institute of Medicine-Forschungszemtrum Juelich, D-52425 Juelich (Germany); Maigne, L. [Departement de Curietherapie-Radiotherapie, Centre Jean Perrin, F-63000 Clermont-Ferrand (France); Rannou, F. [Departamento de Ingenieria Informatica, Universidad de Santiago de Chile, Santiago (Chile); Ferrer, L. [INSERM U601, CHU Nantes, F-44093 Nantes (France); D' Asseler, Y. [UGent-ELIS, St-Pietersnieuwstraat, 41, B-9000 Gent (Belgium); Buvat, I. [INSERM U678 UPMC, CHU Pitie-Salpetriere, F-75634 Paris (France); Lemahieu, I. [UGent-ELIS, St-Pietersnieuwstraat, 41, B-9000 Gent (Belgium)

    2006-12-20

    GATE is a software dedicated to Monte Carlo simulations in Single Photon Emission Computed Tomography (SPECT) and Positron Emission Tomography (PET). An important disadvantage of those simulations is the fundamental burden of computation time. This manuscript describes three different techniques in order to improve the efficiency of those simulations. Firstly, the implementation of variance reduction techniques (VRTs), more specifically the incorporation of geometrical importance sampling, is discussed. After this, the newly designed cluster version of the GATE software is described. The experiments have shown that GATE simulations scale very well on a cluster of homogeneous computers. Finally, an elaboration on the deployment of GATE on the Enabling Grids for E-Science in Europe (EGEE) grid will conclude the description of efficiency enhancement efforts. The three aforementioned methods improve the efficiency of GATE to a large extent and make realistic patient-specific overnight Monte Carlo simulations achievable.

  19. GATE: Improving the computational efficiency

    International Nuclear Information System (INIS)

    Staelens, S.; De Beenhouwer, J.; Kruecker, D.; Maigne, L.; Rannou, F.; Ferrer, L.; D'Asseler, Y.; Buvat, I.; Lemahieu, I.

    2006-01-01

    GATE is a software dedicated to Monte Carlo simulations in Single Photon Emission Computed Tomography (SPECT) and Positron Emission Tomography (PET). An important disadvantage of those simulations is the fundamental burden of computation time. This manuscript describes three different techniques in order to improve the efficiency of those simulations. Firstly, the implementation of variance reduction techniques (VRTs), more specifically the incorporation of geometrical importance sampling, is discussed. After this, the newly designed cluster version of the GATE software is described. The experiments have shown that GATE simulations scale very well on a cluster of homogeneous computers. Finally, an elaboration on the deployment of GATE on the Enabling Grids for E-Science in Europe (EGEE) grid will conclude the description of efficiency enhancement efforts. The three aforementioned methods improve the efficiency of GATE to a large extent and make realistic patient-specific overnight Monte Carlo simulations achievable

  20. The phylogeny of C/S1 bZIP transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of S1 transcripts

    NARCIS (Netherlands)

    Peviani, Alessia; Lastdrager, Jeroen; Hanson, Johannes; Snel, Berend

    2016-01-01

    Basic leucine zippers (bZIPs) form a large plant transcription factor family. C and S1 bZIP groups can heterodimerize, fulfilling crucial roles in seed development and stress response. S1 sequences also harbor a unique regulatory mechanism, termed Sucrose-Induced Repression of Translation (SIRT).

  1. Genome-wide analysis of the HD-ZIP IV transcription factor family in Gossypium arboreum and GaHDG11 involved in osmotic tolerance in transgenic Arabidopsis.

    Science.gov (United States)

    Chen, Eryong; Zhang, Xueyan; Yang, Zhaoen; Wang, Xiaoqian; Yang, Zuoren; Zhang, Chaojun; Wu, Zhixia; Kong, Depei; Liu, Zhao; Zhao, Ge; Butt, Hamama Islam; Zhang, Xianlong; Li, Fuguang

    2017-06-01

    HD-ZIP IV proteins belong to the homeodomain-leucine zipper (HD-ZIP) transcription factor family and are involved in trichome development and drought stress in plants. Although some functions of the HD-ZIP IV group are well understood in Arabidopsis, little is known about their function in cotton. In this study, HD-ZIP genes were identified from three Gossypium species (G. arboreum, G. raimondii and G. hirsutum) and clustered into four families (HD-ZIP I, II, III and IV) to separate HD-ZIP IV from the other three families. Systematic analyses of phylogeny, gene structure, conserved domains, and expression profiles in different plant tissues and the expression patterns under osmotic stress in leaves were further conducted in G. arboreum. More importantly, ectopic overexpression of GaHDG11, a representative of the HD-ZIP IV family, confers enhanced osmotic tolerance in transgenic Arabidopsis plants, possibly due to elongated primary root length, lower water loss rates, high osmoprotectant proline levels, significant levels of antioxidants CAT, and/or SOD enzyme activity with reduced levels of MDA. Taken together, these observations may lay the foundation for future functional analysis of cotton HD-ZIP IV genes to unravel their biological roles in cotton.

  2. Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress

    Science.gov (United States)

    The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are well characterized in Arabidopsis (Arabidopsis thaliana), ...

  3. Zinc Deficiency via a Splice Switch in Zinc Importer ZIP2/SLC39A2 Causes Cystic Fibrosis-Associated MUC5AC Hypersecretion in Airway Epithelial Cells

    Directory of Open Access Journals (Sweden)

    Shunsuke Kamei

    2018-01-01

    Full Text Available Airway mucus hyperproduction and fluid imbalance are important hallmarks of cystic fibrosis (CF, the most common life-shortening genetic disorder in Caucasians. Dysregulated expression and/or function of airway ion transporters, including cystic fibrosis transmembrane conductance regulator (CFTR and epithelial sodium channel (ENaC, have been implicated as causes of CF-associated mucus hypersecretory phenotype. However, the contributory roles of other substances and transporters in the regulation of CF airway pathogenesis remain unelucidated. Here, we identified a novel connection between CFTR/ENaC expression and the intracellular Zn2+ concentration in the regulation of MUC5AC, a major secreted mucin that is highly expressed in CF airway. CFTR-defective and ENaC-hyperactive airway epithelial cells specifically and highly expressed a unique, alternative splice isoform of the zinc importer ZIP2/SLC39A2 (ΔC-ZIP2, which lacks the C-terminal domain. Importantly, ΔC-ZIP2 levels correlated inversely with wild-type ZIP2 and intracellular Zn2+ levels. Moreover, the splice switch to ΔC-ZIP2 as well as decreased expression of other ZIPs caused zinc deficiency, which is sufficient for induction of MUC5AC; while ΔC-ZIP2 expression per se induced ENaC expression and function. Thus, our findings demonstrate that the novel splicing switch contributes to CF lung pathology via the novel interplay of CFTR, ENaC, and ZIP2 transporters.

  4. Monitoring structural changes in intrinsically disordered proteins using QCM-D: application to the bacterial cell division protein ZipA.

    Science.gov (United States)

    Mateos-Gil, Pablo; Tsortos, Achilleas; Vélez, Marisela; Gizeli, Electra

    2016-05-05

    The sensitivity of QCM-D to molecular hydrodynamic properties is applied in this work to study conformational changes of the intrinsically disordered protein ZipA. Acoustic measurements can clearly follow ZipA's unstructured domain expansion and contraction with salt content and be correlated with changes in the hydrodynamic radius of 1.8 nm or less.

  5. Gated equilibrium bloodpool scintigraphy

    International Nuclear Information System (INIS)

    Reinders Folmer, S.C.C.

    1981-01-01

    This thesis deals with the clinical applications of gated equilibrium bloodpool scintigraphy, performed with either a gamma camera or a portable detector system, the nuclear stethoscope. The main goal has been to define the value and limitations of noninvasive measurements of left ventricular ejection fraction as a parameter of cardiac performance in various disease states, both for diagnostic purposes as well as during follow-up after medical or surgical intervention. Secondly, it was attempted to extend the use of the equilibrium bloodpool techniques beyond the calculation of ejection fraction alone by considering the feasibility to determine ventricular volumes and by including the possibility of quantifying valvular regurgitation. In both cases, it has been tried to broaden the perspective of the observations by comparing them with results of other, invasive and non-invasive, procedures, in particular cardiac catheterization, M-mode echocardiography and myocardial perfusion scintigraphy. (Auth.)

  6. DINÁMICA DE LA BIFURCACIÓN DE HOPF EN UNA CLASE DE MODELOS DE COMPETENCIA QUE EXHIBEN LA BIFURCACIÓN ZIP Hopf Bifurcation Dynamic in a Class of Competence Model Exhibiting Zip Bifurcation

    Directory of Open Access Journals (Sweden)

    Carlos Mario Escobar Callejas

    2011-12-01

    Full Text Available En el presente artículo de investigación se caracteriza el tipo de bifurcación de Hopf que se presenta en el fenómeno de la bifurcación de zip para un sistema tridimensional no lineal de ecuaciones diferenciales que satisface las condiciones planteadas por Butler y Farkas, las cuales modelan la competición de dos especies predadoras por una presa singular que se regenera. Se demuestra que en todas las variedades bidimensionales invariantes del sistema considerado se desarrolla una bifurcación de Hopf supercrítica lo cual es una extensión de algunos resultados sobre el tipo de bifurcación de Hopf que se forma en el fenómeno de la bifurcación de zip en sistema con respuesta funcional del predador del tipo Holling II, [1].This research article characterizes the type of Hopf bifurcation occurring in the Zip bifurcation phenomenon for a non-linear 3D system of differential equations which meets the conditions stated by Butler and Farkas to model competition of two predators struggling for a prey. It is shown that a supercritical Hopf bifurcation is developed in all invariant two-dimensional varieties of the system considered, which is an extension of some results about the kind of Hopf bifurcation which is formed in the Zip bifurcation phenomenon in a system with functional response of the Holling-type predator.

  7. Induction of a bZIP Type Transcription Factor and Amino Acid Catabolism-Related Genes in Soybean Seedling in Response to Starvation Stress

    Directory of Open Access Journals (Sweden)

    Takashi Yuasa

    2013-01-01

    Full Text Available To address roles of bZIP transcription factors on regulation of amino acid catabolism under autophagy-induced plant cells, we examined the effect of nutrient starvation on the expression of low energy stress-related transcription factor homologs, GmbZIP53A and GmbZIP53B, and amino acid catabolism-related genes in soybean (Glycine max (L. Merr.. Sucrose starvation treatment significantly enhanced the expressions of GmbZIP53A, but not GmbZIP53B asparagine synthase (GmASN1, proline dehydrogenase1 (GmProDH, and branched chain amino acid transaminase 3 (GmBCAT3. GmbZIP53-related immunoreactive signals were upregulated under severe starvation with sucrose starvation and protease inhibitors, while 3% sucrose and sucrose starvation had no or marginal effects on the signal. Profiles of induction of GmASN1, GmProDH and GmBCAT3 under various nutrient conditions were consistent with the profiles of GmbZIP53 protein levels but not with those of GmbZIP mRNA levels. These results indicate that GmbZIP53 proteins levels are regulated by posttranslational mechanism in response to severe starvation stress and that the increased protein of GmbZIP53 under severe starvation accelerates transcriptional induction of GmASN1, GmProDH, and GmBCAT3. Furthermore, it is conceivable that decrease of branched chain amino acid level by the BCAT-mediated degradation eventually enhances autophagy under severe starvation.

  8. Characterization of a putative grapevine Zn transporter, VvZIP3, suggests its involvement in early reproductive development in Vitis vinifera L

    Directory of Open Access Journals (Sweden)

    Gainza-Cortés Felipe

    2012-07-01

    Full Text Available Abstract Background Zinc (Zn deficiency is one of the most widespread mineral nutritional problems that affect normal development in plants. Because Zn cannot passively diffuse across cell membranes, it must be transported into intracellular compartments for all biological processes where Zn is required. Several members of the Zinc-regulated transporters, Iron-regulated transporter-like Protein (ZIP gene family have been characterized in plants, and have shown to be involved in metal uptake and transport. This study describes the first putative Zn transporter in grapevine. Unravelling its function may explain an important symptom of Zn deficiency in grapevines, which is the production of clusters with fewer and usually smaller berries than normal. Results We identified and characterized a putative Zn transporter from berries of Vitis vinifera L., named VvZIP3. Compared to other members of the ZIP family identified in the Vitis vinifera L. genome, VvZIP3 is mainly expressed in reproductive tissue - specifically in developing flowers - which correlates with the high Zn accumulation in these organs. Contrary to this, the low expression of VvZIP3 in parthenocarpic berries shows a relationship with the lower Zn accumulation in this tissue than in normal seeded berries where its expression is induced by Zn. The predicted protein sequence indicates strong similarity with several members of the ZIP family from Arabidopsis thaliana and other species. Moreover, VvZIP3 complemented the growth defect of a yeast Zn-uptake mutant, ZHY3, and is localized in the plasma membrane of plant cells, suggesting that VvZIP3 has the function of a Zn uptake transporter. Conclusions Our results suggest that VvZIP3 encodes a putative plasma membrane Zn transporter protein member of the ZIP gene family that might play a role in Zn uptake and distribution during the early reproductive development in Vitis vinifera L., indicating that the availability of this micronutrient

  9. Ultrafast, high precision gated integrator

    Energy Technology Data Exchange (ETDEWEB)

    Wang, X.

    1995-01-01

    An ultrafast, high precision gated integrator has been developed by introducing new design approaches that overcome the problems associated with earlier gated integrator circuits. The very high speed is evidenced by the output settling time of less than 50 ns and 20 MHz input pulse rate. The very high precision is demonstrated by the total output offset error of less than 0.2mV and the output droop rate of less than 10{mu}V/{mu}s. This paper describes the theory of this new gated integrator circuit operation. The completed circuit test results are presented.

  10. cDNA table - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ile URL: ftp://ftp.biosciencedbc.jp/archive/rpd/LATEST/rpd_cdna.zip File size: 15 KB Simple search URL http:...age About This Database Database Description Download License Update History of This Database Site Policy | Contact Us cDNA table - RPD | LSDB Archive ...

  11. Peptide-DNA conjugates as tailored bivalent binders of the oncoprotein c-Jun.

    Science.gov (United States)

    Pazos, Elena; Portela, Cecilia; Penas, Cristina; Vázquez, M Eugenio; Mascareñas, José L

    2015-05-21

    We describe a ds-oligonucleotide-peptide conjugate that is able to efficiently dismount preformed DNA complexes of the bZIP regions of oncoproteins c-Fos and c-Jun (AP-1), and therefore might be useful as disrupters of AP-1-mediated gene expression pathways.

  12. The Populus class III HD ZIP, popREVOLUTA, influences cambium initiation and patterning of woody stems.

    Science.gov (United States)

    Robischon, Marcel; Du, Juan; Miura, Eriko; Groover, Andrew

    2011-03-01

    The secondary growth of a woody stem requires the formation of a vascular cambium at an appropriate position and proper patterning of the vascular tissues derived from the cambium. Class III homeodomain-leucine zipper (HD ZIP) transcription factors have been implicated in polarity determination and patterning in lateral organs and primary vascular tissues and in the initiation and function of shoot apical meristems. We report here the functional characterization of a Populus class III HD ZIP gene, popREVOLUTA (PRE), that demonstrates another role for class III HD ZIPs in regulating the development of cambia and secondary vascular tissues. PRE is orthologous to Arabidopsis (Arabidopsis thaliana) REVOLUTA and is expressed in both the shoot apical meristem and in the cambial zone and secondary vascular tissues. Transgenic Populus expressing a microRNA-resistant form of PRE presents unstable phenotypic abnormalities affecting both primary and secondary growth. Surprisingly, phenotypic changes include abnormal formation of cambia within cortical parenchyma that can produce secondary vascular tissues in reverse polarity. Genes misexpressed in PRE mutants include transcription factors and auxin-related genes previously implicated in class III HD ZIP functions during primary growth. Together, these results suggest that PRE plays a fundamental role in the initiation of the cambium and in regulating the patterning of secondary vascular tissues.

  13. The Populus Class III HD ZIP, popREVOLUTA, influences cambium initiation and patterning of woody stems

    Science.gov (United States)

    Marcel Robischon; Juan Du; Eriko Miura; Andrew Groover

    2011-01-01

    The secondary growth of a woody stem requires the formation of a vascular cambium at an appropriate position and proper patterning of the vascular tissues derived from the cambium. Class III homeodomain-leucine zipper (HD ZIP) transcription factors have been implicated in polarity determination and patterning in lateral organs and primary vascular tissues and in the...

  14. Arabidopsis IRE1 catalyses unconventional splicing of bZIP60 mRNA to produce the active transcription factor

    KAUST Repository

    Nagashima, Yukihiro

    2011-07-01

    IRE1 plays an essential role in the endoplasmic reticulum (ER) stress response in yeast and mammals. We found that a double mutant of Arabidopsis IRE1A and IRE1B (ire1a/ire1b) is more sensitive to the ER stress inducer tunicamycin than the wild-type. Transcriptome analysis revealed that genes whose induction was reduced in ire1a/ire1b largely overlapped those in the bzip60 mutant. We observed that the active form of bZIP60 protein detected in the wild-type was missing in ire1a/ire1b. We further demonstrated that bZIP60 mRNA is spliced by ER stress, removing 23 ribonucleotides and therefore causing a frameshift that replaces the C-terminal region of bZIP60 including the transmembrane domain (TMD) with a shorter region without a TMD. This splicing was detected in ire1a and ire1b single mutants, but not in the ire1a/ire1b double mutant. We conclude that IRE1A and IRE1B catalyse unconventional splicing of bZIP60 mRNA to produce the active transcription factor.

  15. Gene expression of the zinc transporter ZIP14 (SLC39a14) is affected by weight loss and metabolic status and associates with PPARγ in human adipose tissue and 3T3-L1 pre-adipocytes

    DEFF Research Database (Denmark)

    Juul, Trine Maxel; Smidt, Kamille; Larsen, Agnete

    2015-01-01

    of clinical importance, including body mass index, triglyceride, and insulin resistance, were inversely correlated with ZIP14. During early adipogensis an up-regulation of ZIP14 gene expression was found. PPARγ gene expression was positively correlated with the ZIP14 gene expression in both adipose tissue...... as a potential biomarker for metabolic stress....

  16. Compound list: butylated hydroxyanisole [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available butylated hydroxyanisole BHA 00156 ftp://ftp.biosciencedbc.jp/archive/open-tggates/...LATEST/Human/in_vitro/butylated_hydroxyanisole.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/o...pen-tggates/LATEST/Rat/in_vivo/Liver/Single/butylated_hydroxyanisole.Rat.in_vivo.Liver.Single.zip ftp://ftp....biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/butylated_hydroxyanisole.Rat.in_vivo.Liver.Repeat.zip ...

  17. Compound list: diethyl maleate [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available diethyl maleate DEM 00A05 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/diet...hyl_maleate.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/diet...hyl_maleate.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/diethyl_maleate.Rat.in_vivo.Liver.Single.zip ...

  18. Compound list: mefenamic acid [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available mefenamic acid MEF 00084 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/mefenamic_aci...d.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/mefenamic_aci.../in_vivo/Liver/Single/mefenamic_acid.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosc...iencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/mefenamic_acid.Rat.in_vivo.Liver.Repeat.zip ...

  19. Compound list: tannic acid [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available tannic acid TAN 00093 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/tannic_acid....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/tannic_acid....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/tannic_acid...archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/tannic_acid.Rat.in_vivo.Liver.Repeat.zip ...

  20. Compound list: nicotinic acid [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available nicotinic acid NIC 00081 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/nicotinic_aci...d.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/nicotinic_aci.../in_vivo/Liver/Single/nicotinic_acid.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosc...iencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/nicotinic_acid.Rat.in_vivo.Liver.Repeat.zip ...

  1. Compound list: buthionine sulfoximine [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available buthionine sulfoximine BSO 00A04 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LA...TEST/Human/in_vitro/buthionine_sulfoximine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-...tggates/LATEST/Rat/in_vitro/buthionine_sulfoximine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive.../open-tggates/LATEST/Rat/in_vivo/Liver/Single/buthionine_sulfoximine.Rat.in_vivo.Liver.Single.zip ...

  2. 49 CFR 234.223 - Gate arm.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Gate arm. 234.223 Section 234.223 Transportation... Maintenance Standards § 234.223 Gate arm. Each gate arm, when in the downward position, shall extend across... clearly viewed by approaching highway users. Each gate arm shall start its downward motion not less than...

  3. Demonstration of a Quantum Nondemolition Sum Gate

    DEFF Research Database (Denmark)

    Yoshikawa, J.; Miwa, Y.; Huck, Alexander

    2008-01-01

    The sum gate is the canonical two-mode gate for universal quantum computation based on continuous quantum variables. It represents the natural analogue to a qubit C-NOT gate. In addition, the continuous-variable gate describes a quantum nondemolition (QND) interaction between the quadrature...

  4. Reversible logic gates on Physarum Polycephalum

    International Nuclear Information System (INIS)

    Schumann, Andrew

    2015-01-01

    In this paper, we consider possibilities how to implement asynchronous sequential logic gates and quantum-style reversible logic gates on Physarum polycephalum motions. We show that in asynchronous sequential logic gates we can erase information because of uncertainty in the direction of plasmodium propagation. Therefore quantum-style reversible logic gates are more preferable for designing logic circuits on Physarum polycephalum

  5. Compound list: allyl alcohol [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available allyl alcohol AA 00010 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/allyl_alcohol....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/allyl_alcohol...dbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/allyl_alcohol.Rat.in_vivo.Liver.Repeat.zip ftp:/.../ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/allyl_alcohol.Rat.in_vivo.Kidney....Single.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Repeat/allyl_alcohol.Rat.in_vivo.Kidney.Repeat.zip ...

  6. Bill Gates vil redde Folkeskolen

    DEFF Research Database (Denmark)

    Fejerskov, Adam Moe

    2014-01-01

    Det amerikanske uddannelsessystem bliver for tiden udsat for hård kritik, ledt an af Microsoft stifteren Bill Gates. Gates har indtil videre brugt 3 mia. kroner på at skabe opbakning til tiltag som præstationslønning af lærere og strømlining af pensum på tværs af alle skoler i landet...

  7. Latest design of gate valves

    Energy Technology Data Exchange (ETDEWEB)

    Kurzhofer, U.; Stolte, J.; Weyand, M.

    1996-12-01

    Babcock Sempell, one of the most important valve manufacturers in Europe, has delivered valves for the nuclear power industry since the beginning of the peaceful application of nuclear power in the 1960s. The latest innovation by Babcock Sempell is a gate valve that meets all recent technical requirements of the nuclear power technology. At the moment in the United States, Germany, Sweden, and many other countries, motor-operated gate and globe valves are judged very critically. Besides the absolute control of the so-called {open_quotes}trip failure,{close_quotes} the integrity of all valve parts submitted to operational forces must be maintained. In case of failure of the limit and torque switches, all valve designs have been tested with respect to the quality of guidance of the gate. The guidances (i.e., guides) shall avoid a tilting of the gate during the closing procedure. The gate valve newly designed by Babcock Sempell fulfills all these characteristic criteria. In addition, the valve has cobalt-free seat hardfacing, the suitability of which has been proven by friction tests as well as full-scale blowdown tests at the GAP of Siemens in Karlstein, West Germany. Babcock Sempell was to deliver more than 30 gate valves of this type for 5 Swedish nuclear power stations by autumn 1995. In the presentation, the author will report on the testing performed, qualifications, and sizing criteria which led to the new technical design.

  8. Magnetic resonance diagnosis of posterior horn tears of the lateral meniscus using a thin axial plane: the zip sign - a preliminary study

    International Nuclear Information System (INIS)

    Savoye, P.Y.; Ravey, J.N.; Dubois, C.; Barbier, L.P.; Ferretti, G.; Courvoisier, A.; Saragaglia, D.

    2011-01-01

    The ''zip'' sign is a newly described form of meniscal tear progressing from the distal insertion of menisco-femoral ligaments (MFLs) through the lateral meniscal wall; the tear occurs during anterior cruciate ligament (ACL) rupture. The purpose of this study was to evaluate the zip sign on knee MRI within the context of ACL injuries. From a series of 261 MR examinations for acute knee injury, we selected 97 patients with both MR and arthroscopic data for a retrospective blinded review. The zip sign was defined on axial thin MR sections as a straight line from the distal insertion of MFLs in association with five sagittal images lateral to the posterior cruciate ligament (PCL) where the MFLs were identified. Sensitivity and specificity in detecting lateral meniscal tears before and after having defined the zip sign were calculated. Sensitivity in detecting the tears of the posterior horn of the lateral meniscus (PHLM) reached 87.5% (CI 0.68-0.97) after zip sign criteria were defined. The zip sign has excellent inter-observer agreement, K > 0.90. The zip sign indicates a lesion at the insertion site of MFLs into the PHLM on thin axial images associated with sagittal MR sections that may improve MR sensitivity in detecting PHLM tears. (orig.)

  9. Magnetic resonance diagnosis of posterior horn tears of the lateral meniscus using a thin axial plane: the zip sign - a preliminary study

    Energy Technology Data Exchange (ETDEWEB)

    Savoye, P.Y.; Ravey, J.N.; Dubois, C.; Barbier, L.P.; Ferretti, G. [CHU Grenoble, Clinique Universitaire de Radiologie et d' Imagerie Medicale, B.P 217, Grenoble Cedex 09 (France); Courvoisier, A.; Saragaglia, D. [CHU Grenoble, Clinique Universitaire de Chirurgie Orthopedique et Traumatologique, Grenoble (France)

    2011-01-15

    The ''zip'' sign is a newly described form of meniscal tear progressing from the distal insertion of menisco-femoral ligaments (MFLs) through the lateral meniscal wall; the tear occurs during anterior cruciate ligament (ACL) rupture. The purpose of this study was to evaluate the zip sign on knee MRI within the context of ACL injuries. From a series of 261 MR examinations for acute knee injury, we selected 97 patients with both MR and arthroscopic data for a retrospective blinded review. The zip sign was defined on axial thin MR sections as a straight line from the distal insertion of MFLs in association with five sagittal images lateral to the posterior cruciate ligament (PCL) where the MFLs were identified. Sensitivity and specificity in detecting lateral meniscal tears before and after having defined the zip sign were calculated. Sensitivity in detecting the tears of the posterior horn of the lateral meniscus (PHLM) reached 87.5% (CI 0.68-0.97) after zip sign criteria were defined. The zip sign has excellent inter-observer agreement, K > 0.90. The zip sign indicates a lesion at the insertion site of MFLs into the PHLM on thin axial images associated with sagittal MR sections that may improve MR sensitivity in detecting PHLM tears. (orig.)

  10. Membrane androgen receptor characteristics of human ZIP9 (SLC39A) zinc transporter in prostate cancer cells: Androgen-specific activation and involvement of an inhibitory G protein in zinc and MAP kinase signaling.

    Science.gov (United States)

    Thomas, Peter; Pang, Yefei; Dong, Jing

    2017-05-15

    Characteristics of novel human membrane androgen receptor (mAR), ZIP9 (SLC39A9), were investigated in ZIP9-transfected PC-3 cells (PC3-ZIP9). Ligand blot analysis showed plasma membrane [ 3 H]-T binding corresponds to the position of ZIP9 on Western blots which suggests ZIP9 can bind [ 3 H]-T alone, without a protein partner. Progesterone antagonized testosterone actions, blocking increases in zinc, Erk phosphorylation and apoptosis, further evidence that ZIP9 is specifically activated by androgens. Pre-treatment with GTPγS and pertussis toxin decreased plasma membrane [ 3 H]-T binding and blocked testosterone-induced increases in Erk phosphorylation and intracellular zinc, indicating ZIP9 is coupled to an inhibitory G protein (Gi) that mediates both MAP kinase and zinc signaling. Testosterone treatment of nuclei and mitochondria which express ZIP9 decreased their zinc contents, suggesting ZIP9 also regulates free zinc through releasing it from these intracellular organelles. The results show ZIP9 is a specific Gi coupled-mAR mediating testosterone-induced MAP kinase and zinc signaling in PC3-ZIP9 cells. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. IRE1/bZIP60-mediated unfolded protein response plays distinct roles in plant immunity and abiotic stress responses.

    Directory of Open Access Journals (Sweden)

    Adrian A Moreno

    Full Text Available Endoplasmic reticulum (ER-mediated protein secretion and quality control have been shown to play an important role in immune responses in both animals and plants. In mammals, the ER membrane-located IRE1 kinase/endoribonuclease, a key regulator of unfolded protein response (UPR, is required for plasma cell development to accommodate massive secretion of immunoglobulins. Plant cells can secrete the so-called pathogenesis-related (PR proteins with antimicrobial activities upon pathogen challenge. However, whether IRE1 plays any role in plant immunity is not known. Arabidopsis thaliana has two copies of IRE1, IRE1a and IRE1b. Here, we show that both IRE1a and IRE1b are transcriptionally induced during chemically-induced ER stress, bacterial pathogen infection and treatment with the immune signal salicylic acid (SA. However, we found that IRE1a plays a predominant role in the secretion of PR proteins upon SA treatment. Consequently, the ire1a mutant plants show enhanced susceptibility to a bacterial pathogen and are deficient in establishing systemic acquired resistance (SAR, whereas ire1b is unaffected in these responses. We further demonstrate that the immune deficiency in ire1a is due to a defect in SA- and pathogen-triggered, IRE1-mediated cytoplasmic splicing of the bZIP60 mRNA, which encodes a transcription factor involved in the expression of UPR-responsive genes. Consistently, IRE1a is preferentially required for bZIP60 splicing upon pathogen infection, while IRE1b plays a major role in bZIP60 processing upon Tunicamycin (Tm-induced stress. We also show that SA-dependent induction of UPR-responsive genes is altered in the bzip60 mutant resulting in a moderate susceptibility to a bacterial pathogen. These results indicate that the IRE1/bZIP60 branch of UPR is a part of the plant response to pathogens for which the two Arabidopsis IRE1 isoforms play only partially overlapping roles and that IRE1 has both bZIP60-dependent and bZIP60-independent

  12. SynBioLGDB: a resource for experimentally validated logic gates in synthetic biology

    Science.gov (United States)

    Wang, Liqiang; Qian, Kun; Huang, Yan; Jin, Nana; Lai, Hongyan; Zhang, Ting; Li, Chunhua; Zhang, Chunrui; Bi, Xiaoman; Wu, Deng; Wang, Changliang; Wu, Hao; Tan, Puwen; Lu, Jianping; Chen, Liqun; Li, Kongning; Li, Xia; Wang, Dong

    2015-01-01

    Synthetic biologists have developed DNA/molecular modules that perform genetic logic operations in living cells to track key moments in a cell's life or change the fate of a cell. Increasing evidence has also revealed that diverse genetic logic gates capable of generating a Boolean function play critically important roles in synthetic biology. Basic genetic logic gates have been designed to combine biological science with digital logic. SynBioLGDB (http://bioinformatics.ac.cn/synbiolgdb/) aims to provide the synthetic biology community with a useful resource for efficient browsing and visualization of genetic logic gates. The current version of SynBioLGDB documents more than 189 genetic logic gates with experimental evidence involving 80 AND gates and 16 NOR gates, etc. in three species (Human, Escherichia coli and Bacillus clausii). SynBioLGDB provides a user-friendly interface through which conveniently to query and browse detailed information about these genetic logic gates. SynBioLGDB will enable more comprehensive understanding of the connection of genetic logic gates to execute complex cellular functions in living cells.

  13. Sensory gating in primary insomnia.

    Science.gov (United States)

    Hairston, Ilana S; Talbot, Lisa S; Eidelman, Polina; Gruber, June; Harvey, Allison G

    2010-06-01

    Although previous research indicates that sleep architecture is largely intact in primary insomnia (PI), the spectral content of the sleeping electroencephalographic trace and measures of brain metabolism suggest that individuals with PI are physiologically more aroused than good sleepers. Such observations imply that individuals with PI may not experience the full deactivation of sensory and cognitive processing, resulting in reduced filtering of external sensory information during sleep. To test this hypothesis, gating of sensory information during sleep was tested in participants with primary insomnia (n = 18) and good sleepers (n = 20). Sensory gating was operationally defined as (i) the difference in magnitude of evoked response potentials elicited by pairs of clicks presented during Wake and Stage II sleep, and (ii) the number of K complexes evoked by the same auditory stimulus. During wake the groups did not differ in magnitude of sensory gating. During sleep, sensory gating of the N350 component was attenuated and completely diminished in participants with insomnia. P450, which occurred only during sleep, was strongly gated in good sleepers, and less so in participants with insomnia. Additionally, participants with insomnia showed no stimulus-related increase in K complexes. Thus, PI is potentially associated with impaired capacity to filter out external sensory information, especially during sleep. The potential of using stimulus-evoked K complexes as a biomarker for primary insomnia is discussed.

  14. New opening hours of the gates

    CERN Multimedia

    GS Department

    2009-01-01

    Please note the new opening hours of the gates as well as the intersites tunnel from the 19 May 2009: GATE A 7h - 19h GATE B 24h/24 GATE C 7h - 9h\t17h - 19h GATE D 8h - 12h\t13h - 16h GATE E 7h - 9h\t17h - 19h Prévessin 24h/24 The intersites tunnel will be opened from 7h30 to 18h non stop. GS-SEM Group Infrastructure and General Services Department

  15. Compound list: aflatoxin B1 [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available aflatoxin B1 AFB1 00165 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/aflatoxin..._B1.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/aflatoxin_B1.Rat.in_vivo.Liver.Single.zip ...

  16. Compound list: 2-nitrofluorene [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available 2-nitrofluorene 2NF 00160 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/2-nitrofluor...ene.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/2-nitrofluorene.Rat.in_vivo.Liver.Single.zip ...

  17. Major zircon megacryst suites of the Indo-Pacific lithospheric margin (ZIP) and their petrogenetic and regional implications

    Science.gov (United States)

    Sutherland, Lin; Graham, Ian; Yaxley, Gregory; Armstrong, Richard; Giuliani, Gaston; Hoskin, Paul; Nechaev, Victor; Woodhead, Jon

    2016-04-01

    Zircon megacrysts (± gem corundum) appear in basalt fields of Indo-Pacific origin over a 12,000 km zone (ZIP) along West Pacific continental margins. Age-dating, trace element, oxygen and hafnium isotope studies on representative zircons (East Australia-Asia) indicate diverse magmatic sources. The U-Pb (249 to 1 Ma) and zircon fission track (ZFT) ages (65 to 1 Ma) suggest thermal annealing during later basalt transport, with slab subduction.

  18. Respiratory gating in cardiac PET

    DEFF Research Database (Denmark)

    Lassen, Martin Lyngby; Rasmussen, Thomas; Christensen, Thomas E

    2017-01-01

    BACKGROUND: Respiratory motion due to breathing during cardiac positron emission tomography (PET) results in spatial blurring and erroneous tracer quantification. Respiratory gating might represent a solution by dividing the PET coincidence dataset into smaller respiratory phase subsets. The aim...... stress (82)RB-PET. Respiratory rates and depths were measured by a respiratory gating system in addition to registering actual respiratory rates. Patients undergoing adenosine stress showed a decrease in measured respiratory rate from initial to later scan phase measurements [12.4 (±5.7) vs 5.6 (±4.......7) min(-1), P PET...

  19. Activation of the Arabidopsis membrane-bound transcription factor bZIP28 is mediated by site-2 protease, but not site-1 protease.

    Science.gov (United States)

    Iwata, Yuji; Ashida, Makoto; Hasegawa, Chisa; Tabara, Kazuki; Mishiba, Kei-Ichiro; Koizumi, Nozomu

    2017-08-01

    The unfolded protein response (UPR) is a homeostatic cellular response conserved in eukaryotic cells to alleviate the accumulation of unfolded proteins in the endoplasmic reticulum (ER). Arabidopsis bZIP28 is a membrane-bound transcription factor activated by proteolytic cleavage in response to ER stress, thereby releasing its cytosolic portion containing the bZIP domain from the membrane to translocate into the nucleus where it induces the transcription of genes encoding ER-resident molecular chaperones and folding enzymes. It has been widely recognized that the proteolytic activation of bZIP28 is mediated by the sequential cleavage of site-1 protease (S1P) and site-2 protease (S2P). In the present study we provide evidence that bZIP28 protein is cleaved by S2P, but not by S1P. We demonstrated that wild-type and s1p mutant plants produce the active, nuclear form of bZIP28 in response to the ER stress inducer tunicamycin. In contrast, tunicamycin-treated s2p mutants do not accumulate the active, nuclear form of bZIP28. Consistent with these observations, s2p mutants, but not s1p mutants, exhibited a defective transcriptional response of ER stress-responsive genes and significantly higher sensitivity to tunicamycin. Interestingly, s2p mutants accumulate two membrane-bound bZIP28 fragments with a shorter ER lumen-facing C-terminal domain. Importantly, the predicted cleavage sites are located far from the canonical S1P recognition motif previously described. We propose that ER stress-induced proteolytic activation of bZIP28 is mediated by the sequential actions of as-yet-unidentified protease(s) and S2P, and does not require S1P. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  20. AtbZIP34 is required for Arabidopsis pollen wall patterning and the control of several metabolic pathways in developing pollen

    Czech Academy of Sciences Publication Activity Database

    Gibalová, Antónia; Reňák, David; Matczuk, Katarzyna; Dupľáková, Nikoleta; Cháb, David; Twell, D.; Honys, David

    2009-01-01

    Roč. 70, č. 5 (2009), s. 581-601 ISSN 0167-4412 R&D Projects: GA ČR GA522/06/0896; GA ČR GA522/09/0858; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : bZIP transcription factor * AtbZIP34 * Male gametophyte development Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.978, year: 2009

  1. The bZIP transcription factor PERIANTHIA: A multifunctional hub for meristem control

    Directory of Open Access Journals (Sweden)

    Jan eLohmann

    2011-11-01

    Full Text Available As sessile organisms, plants are exposed to extreme variations in environmental conditions over the course of their lives. Since plants grow and initiate new organs continuously, they have to modulate the underlying developmental program accordingly to cope with this challenge. At the heart of this extraordinary developmental plasticity are pluripotent stem cells, which are maintained during the entire life-cycle of the plant and that are embedded within dynamic stem cell niches. While the complex regulatory principles of plant stem cell control under artificial constant growth conditions begin to emerge, virtually nothing is known about how this circuit adapts to variations in the environment. In addition to the local feedback system constituted by the homeodomain transcription factor WUSCHEL (WUS and the CLAVATA signaling cascade in the center of the shoot apical meristem (SAM, the bZIP transcription factor PERIANTHIA (PAN not only has a broader expression domain in SAM and flowers, but also carries out more diverse functions in meristem maintenance: pan mutants show alterations in environmental response, shoot meristem size, floral organ number and exhibit severe defects in termination of floral stem cells in an environment dependent fashion. Genetic and genomic analyses indicate that PAN interacts with a plethora of developmental pathways including light, plant hormone and meristem control systems, suggesting that PAN is as an important regulatory node in the network of plant stem cell control.

  2. A bZIP/bRLZ transcription factor required for DIF signaling in Dictyostelium.

    Science.gov (United States)

    Thompson, Christopher R L; Fu, Qing; Buhay, Caroline; Kay, Robert R; Shaulsky, Gad

    2004-02-01

    The intermingled differentiation and sorting out of Dictyostelium prestalk-O and prespore cells requires the diffusible signaling molecule DIF-1, and provides an example of a spatial information-independent patterning mechanism. To further understand this patterning process, we used genetic selection to isolate mutants in the DIF-1 response pathway. The disrupted gene in one such mutant, dimA(-), encodes a bZIP/bRLZ transcription factor, which is required for every DIF-1 response investigated. Furthermore, the dimA(-) mutant shows strikingly similar developmental defects to the dmtA(-) mutant, which is specifically defective in DIF-1 synthesis. However, key differences exist: (1) the dmtA(-) mutant responds to DIF-1 but does not produce DIF-1; (2) the dimA(-) mutant produces DIF-1 but does not respond to DIF-1; and (3) the dimA(-) mutant exhibits cell autonomous defects in cell type differentiation. These results suggest that dimA encodes the key transcriptional regulator required to integrate DIF-1 signaling and subsequent patterning in Dictyostelium.

  3. HTLV-1 bZIP factor induces T-cell lymphoma and systemic inflammation in vivo.

    Directory of Open Access Journals (Sweden)

    Yorifumi Satou

    2011-02-01

    Full Text Available Human T-cell leukemia virus type 1 (HTLV-1 is the causal agent of a neoplastic disease of CD4+ T cells, adult T-cell leukemia (ATL, and inflammatory diseases including HTLV-1 associated myelopathy/tropical spastic paraparesis, dermatitis, and inflammatory lung diseases. ATL cells, which constitutively express CD25, resemble CD25+CD4+ regulatory T cells (T(reg. Approximately 60% of ATL cases indeed harbor leukemic cells that express FoxP3, a key transcription factor for T(reg cells. HTLV-1 encodes an antisense transcript, HTLV-1 bZIP factor (HBZ, which is expressed in all ATL cases. In this study, we show that transgenic expression of HBZ in CD4+ T cells induced T-cell lymphomas and systemic inflammation in mice, resembling diseases observed in HTLV-1 infected individuals. In HBZ-transgenic mice, CD4+Foxp3+ T(reg cells and effector/memory CD4+ T cells increased in vivo. As a mechanism of increased T(reg cells, HBZ expression directly induced Foxp3 gene transcription in T cells. The increased CD4+Foxp3+ T(reg cells in HBZ transgenic mice were functionally impaired while their proliferation was enhanced. HBZ could physically interact with Foxp3 and NFAT, thereby impairing the suppressive function of T(reg cells. Thus, the expression of HBZ in CD4+ T cells is a key mechanism of HTLV-1-induced neoplastic and inflammatory diseases.

  4. Development of solution-gated graphene transistor model for biosensors

    Science.gov (United States)

    Karimi, Hediyeh; Yusof, Rubiyah; Rahmani, Rasoul; Hosseinpour, Hoda; Ahmadi, Mohammad T.

    2014-02-01

    The distinctive properties of graphene, characterized by its high carrier mobility and biocompatibility, have stimulated extreme scientific interest as a promising nanomaterial for future nanoelectronic applications. In particular, graphene-based transistors have been developed rapidly and are considered as an option for DNA sensing applications. Recent findings in the field of DNA biosensors have led to a renewed interest in the identification of genetic risk factors associated with complex human diseases for diagnosis of cancers or hereditary diseases. In this paper, an analytical model of graphene-based solution gated field effect transistors (SGFET) is proposed to constitute an important step towards development of DNA biosensors with high sensitivity and selectivity. Inspired by this fact, a novel strategy for a DNA sensor model with capability of single-nucleotide polymorphism detection is proposed and extensively explained. First of all, graphene-based DNA sensor model is optimized using particle swarm optimization algorithm. Based on the sensing mechanism of DNA sensors, detective parameters ( I ds and V gmin) are suggested to facilitate the decision making process. Finally, the behaviour of graphene-based SGFET is predicted in the presence of single-nucleotide polymorphism with an accuracy of more than 98% which guarantees the reliability of the optimized model for any application of the graphene-based DNA sensor. It is expected to achieve the rapid, quick and economical detection of DNA hybridization which could speed up the realization of the next generation of the homecare sensor system.

  5. The Populus Class III HD ZIP transcription factor POPCORONA affects cell differentiation during secondary growth of woody stems.

    Directory of Open Access Journals (Sweden)

    Juan Du

    Full Text Available The developmental mechanisms regulating cell differentiation and patterning during the secondary growth of woody tissues are poorly understood. Class III HD ZIP transcription factors are evolutionarily ancient and play fundamental roles in various aspects of plant development. Here we investigate the role of a Class III HD ZIP transcription factor, POPCORONA, during secondary growth of woody stems. Transgenic Populus (poplar trees expressing either a miRNA-resistant POPCORONA or a synthetic miRNA targeting POPCORONA were used to infer function of POPCORONA during secondary growth. Whole plant, histological, and gene expression changes were compared for transgenic and wild-type control plants. Synthetic miRNA knock down of POPCORONA results in abnormal lignification in cells of the pith, while overexpression of a miRNA-resistant POPCORONA results in delayed lignification of xylem and phloem fibers during secondary growth. POPCORONA misexpression also results in coordinated changes in expression of genes within a previously described transcriptional network regulating cell differentiation and cell wall biosynthesis, and hormone-related genes associated with fiber differentiation. POPCORONA illustrates another function of Class III HD ZIPs: regulating cell differentiation during secondary growth.

  6. The Populus Class III HD ZIP transcription factor POPCORONA affects cell differentiation during secondary growth of woody stems.

    Science.gov (United States)

    Du, Juan; Miura, Eriko; Robischon, Marcel; Martinez, Ciera; Groover, Andrew

    2011-02-28

    The developmental mechanisms regulating cell differentiation and patterning during the secondary growth of woody tissues are poorly understood. Class III HD ZIP transcription factors are evolutionarily ancient and play fundamental roles in various aspects of plant development. Here we investigate the role of a Class III HD ZIP transcription factor, POPCORONA, during secondary growth of woody stems. Transgenic Populus (poplar) trees expressing either a miRNA-resistant POPCORONA or a synthetic miRNA targeting POPCORONA were used to infer function of POPCORONA during secondary growth. Whole plant, histological, and gene expression changes were compared for transgenic and wild-type control plants. Synthetic miRNA knock down of POPCORONA results in abnormal lignification in cells of the pith, while overexpression of a miRNA-resistant POPCORONA results in delayed lignification of xylem and phloem fibers during secondary growth. POPCORONA misexpression also results in coordinated changes in expression of genes within a previously described transcriptional network regulating cell differentiation and cell wall biosynthesis, and hormone-related genes associated with fiber differentiation. POPCORONA illustrates another function of Class III HD ZIPs: regulating cell differentiation during secondary growth.

  7. Variation Analysis of Physiological Traits in Betula platyphylla Overexpressing TaLEA-ThbZIP Gene under Salt Stress.

    Directory of Open Access Journals (Sweden)

    Xiyang Zhao

    Full Text Available The aim of this study was to determine whether transgenic birch (Betula platyphylla ectopic overexpressing a late embryogenesis abundant (LEA gene and a basic leucine zipper (bZIP gene from the salt-tolerant genus Tamarix (salt cedar show increased tolerance to salt (NaCl stress. Co-transfer of TaLEA and ThbZIP in birch under the control of two independent CaMV 35S promoters significantly enhanced salt stress. PCR and northern blot analyses indicated that the two genes were ectopically overexpressed in several dual-gene transgenic birch lines. We compared the effects of salt stress among three transgenic birch lines (L-4, L-5, and L-8 and wild type (WT. In all lines, the net photosynthesis values were higher before salt stress treatment than afterwards. After the salt stress treatment, the transgenic lines L-4 and L-8 showed higher values for photosynthetic traits, chlorophyll fluorescence, peroxidase and superoxide dismutase activities, and lower malondialdehyde and Na+ contents, compared with those in WT and L-5. These different responses to salt stress suggested that the transcriptional level of the TaLEA and ThbZIP genes differed among the transgenic lines, resulting in a variety of genetic and phenotypic effects. The results of this research can provide a theoretical basis for the genetic engineering of salt-tolerant trees.

  8. Bias with respect to socioeconomic status: A closer look at zip code matching in a pneumococcal vaccine effectiveness study

    Directory of Open Access Journals (Sweden)

    Ruth Link-Gelles

    2016-12-01

    Full Text Available In 2010, 13-valent pneumococcal conjugate vaccine (PCV13 was introduced in the US for prevention of invasive pneumococcal disease in children. Individual-level socioeconomic status (SES is a potential confounder of the estimated effectiveness of PCV13 and is often controlled for in observational studies using zip code as a proxy. We assessed the utility of zip code matching for control of SES in a post-licensure evaluation of the effectiveness of PCV13 (calculated as [1-matched odds ratio]*100. We used a directed acyclic graph to identify subsets of confounders and collected SES variables from birth certificates, geocoding, a parent interview, and follow-up with medical providers. Cases tended to be more affluent than eligible controls (for example, 48.3% of cases had private insurance vs. 44.6% of eligible controls, but less affluent than enrolled controls (52.9% of whom had private insurance. Control of confounding subsets, however, did not result in a meaningful change in estimated vaccine effectiveness (original estimate: 85.1%, 95% CI 74.8–91.9%; adjusted estimate: 82.5%, 95% CI 65.6–91.1%. In the context of a post-licensure vaccine effectiveness study, zip code appears to be an adequate, though not perfect, proxy for individual SES. Keywords: Socioeconomic status, PCV13, Pneumococcus, Pneumococcal vaccine, Vaccine effectiveness, Matched case-control

  9. SnRK1-triggered switch of bZIP63 dimerization mediates the low-energy response in plants.

    Science.gov (United States)

    Mair, Andrea; Pedrotti, Lorenzo; Wurzinger, Bernhard; Anrather, Dorothea; Simeunovic, Andrea; Weiste, Christoph; Valerio, Concetta; Dietrich, Katrin; Kirchler, Tobias; Nägele, Thomas; Vicente Carbajosa, Jesús; Hanson, Johannes; Baena-González, Elena; Chaban, Christina; Weckwerth, Wolfram; Dröge-Laser, Wolfgang; Teige, Markus

    2015-08-11

    Metabolic adjustment to changing environmental conditions, particularly balancing of growth and defense responses, is crucial for all organisms to survive. The evolutionary conserved AMPK/Snf1/SnRK1 kinases are well-known metabolic master regulators in the low-energy response in animals, yeast and plants. They act at two different levels: by modulating the activity of key metabolic enzymes, and by massive transcriptional reprogramming. While the first part is well established, the latter function is only partially understood in animals and not at all in plants. Here we identified the Arabidopsis transcription factor bZIP63 as key regulator of the starvation response and direct target of the SnRK1 kinase. Phosphorylation of bZIP63 by SnRK1 changed its dimerization preference, thereby affecting target gene expression and ultimately primary metabolism. A bzip63 knock-out mutant exhibited starvation-related phenotypes, which could be functionally complemented by wild type bZIP63, but not by a version harboring point mutations in the identified SnRK1 target sites.

  10. Human prostate cancer ZIP1/zinc/citrate genetic/metabolic relationship in the TRAMP prostate cancer animal model.

    Science.gov (United States)

    Costello, Leslie C; Franklin, Renty B; Zou, Jing; Feng, Pei; Bok, Robert; Swanson, Mark G; Kurhanewicz, John

    2011-12-15

    Prostate cancer is the second leading cause of cancer deaths among men. The availability of animal models that represent the events and factors that exist in the natural history and biology of human prostate cancer is essential in dealing with prostate cancer. In recent decades and presently, emphasis has been directed at the development and employment of prostate cancer induced in transgenic mice. However, the important consistent hallmark characteristic and event of decrease in zinc and citrate and downregulation of ZIP1 zinc transporter in prostate malignancy has not been studied or identified in any animal model. We investigated the status of these parameters in TRAMP tumors as compared with human prostate cancer. The results show that citrate levels are markedly decreased in the developing and advancing stages of malignancy in TRAMP. Zinc levels are also decreased and ZIP1 transporter is lost in TRAMP tumors. In vitro studies show that zinc treatment of TRAMP C2 cells exhibits cytotoxic effects. Collectively, these results mimic the ZIP1, zinc, and citrate status and relationship that exist in human prostate cancer. This is the first report that establishes the existence of the human prostate zinc/citrate hallmark characteristic and relationship in an animal model. It now appears that the TRAMP model will be suitable for studies relating to the implications and role of zinc- and citrate-related metabolism in the development and progression of human prostate cancer.

  11. Robust logic gates and realistic quantum computation

    International Nuclear Information System (INIS)

    Xiao Li; Jones, Jonathan A.

    2006-01-01

    The composite rotation approach has been used to develop a range of robust quantum logic gates, including single qubit gates and two qubit gates, which are resistant to systematic errors in their implementation. Single qubit gates based on the BB1 family of composite rotations have been experimentally demonstrated in a variety of systems, but little study has been made of their application in extended computations, and there has been no experimental study of the corresponding robust two qubit gates to date. Here we describe an application of robust gates to nuclear magnetic resonance studies of approximate quantum counting. We find that the BB1 family of robust gates is indeed useful, but that the related NB1, PB1, B4, and P4 families of tailored logic gates are less useful than initially expected

  12. Gating Technology for Vertically Parted Green Sand Moulds

    DEFF Research Database (Denmark)

    Larsen, Per

    Gating technology for vertically parted green sand moulds. Literature study of different ways of designing gating systems.......Gating technology for vertically parted green sand moulds. Literature study of different ways of designing gating systems....

  13. Dynamic gating window for compensation of baseline shift in respiratory-gated radiation therapy

    International Nuclear Information System (INIS)

    Pepin, Eric W.; Wu Huanmei; Shirato, Hiroki

    2011-01-01

    Purpose: To analyze and evaluate the necessity and use of dynamic gating techniques for compensation of baseline shift during respiratory-gated radiation therapy of lung tumors. Methods: Motion tracking data from 30 lung tumors over 592 treatment fractions were analyzed for baseline shift. The finite state model (FSM) was used to identify the end-of-exhale (EOE) breathing phase throughout each treatment fraction. Using duty cycle as an evaluation metric, several methods of end-of-exhale dynamic gating were compared: An a posteriori ideal gating window, a predictive trend-line-based gating window, and a predictive weighted point-based gating window. These methods were evaluated for each of several gating window types: Superior/inferior (SI) gating, anterior/posterior beam, lateral beam, and 3D gating. Results: In the absence of dynamic gating techniques, SI gating gave a 39.6% duty cycle. The ideal SI gating window yielded a 41.5% duty cycle. The weight-based method of dynamic SI gating yielded a duty cycle of 36.2%. The trend-line-based method yielded a duty cycle of 34.0%. Conclusions: Dynamic gating was not broadly beneficial due to a breakdown of the FSM's ability to identify the EOE phase. When the EOE phase was well defined, dynamic gating showed an improvement over static-window gating.

  14. Bill Gates eyes healthcare market.

    Science.gov (United States)

    Dunbar, C

    1995-02-01

    The entrepreneurial spirit is still top in Bill Gates' mind as he look toward healthcare and other growth industries. Microsoft's CEO has not intention of going the way of other large technology companies that became obsolete before they could compete today.

  15. Simultaneous G-Quadruplex DNA Logic.

    Science.gov (United States)

    Bader, Antoine; Cockroft, Scott L

    2018-04-03

    A fundamental principle of digital computer operation is Boolean logic, where inputs and outputs are described by binary integer voltages. Similarly, inputs and outputs may be processed on the molecular level as exemplified by synthetic circuits that exploit the programmability of DNA base-pairing. Unlike modern computers, which execute large numbers of logic gates in parallel, most implementations of molecular logic have been limited to single computing tasks, or sensing applications. This work reports three G-quadruplex-based logic gates that operate simultaneously in a single reaction vessel. The gates respond to unique Boolean DNA inputs by undergoing topological conversion from duplex to G-quadruplex states that were resolved using a thioflavin T dye and gel electrophoresis. The modular, addressable, and label-free approach could be incorporated into DNA-based sensors, or used for resolving and debugging parallel processes in DNA computing applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Gate induced drain leakage reduction with analysis of gate fringing field effect on high-κ/metal gate CMOS technology

    Science.gov (United States)

    Jang, Esan; Shin, Sunhae; Jung, Jae Won; Rok Kim, Kyung

    2015-06-01

    We suggest the optimum permittivity for a high-κ/metal gate (HKMG) CMOS structure based on the trade-off characteristics between the fringing field induced barrier lowering (FIBL) and gate induced drain leakage (GIDL). By adopting the high-κ gate dielectric, the GIDL from the band-to-band tunneling at the interface of gate and lightly doped drain (LDD) is suppressed with wide tunneling width owing to the enhanced fringing field, while the FIBL effects is degenerated as the previous reports. These two effects from the gate fringing field are studied extensively to manage the leakage current of HKMG for low power applications.

  17. ``Gate-to-gate`` BJT obtained from the double-gate input JFET to reset charge preamplifiers

    Energy Technology Data Exchange (ETDEWEB)

    Fazzi, A. [Politecnico di Milano (Italy). Dipartimento di Ingegneria Nucleare; Rehak, P. [Brookhaven National Laboratory, Upton, NY 11973 (United States)

    1996-08-01

    A novel charge restoration mechanism to reset charge sensitive preamplifiers is presented. The ``gate-to-gate`` Bipolar Junction Transistor transversal to the input JFET with independent top and bottom gates is exploited as a ``reset transistor`` embodied in the preamplifier input device. The p-n junction between the bottom gate and the channel is forward-biased by a proper feedback loop supplying the necessary restoration current to the input node capacitance through the top gate-channel reversed-biased junction. The continuous reset mode is here analysed with reference to the DC stability, the pulse response and the noise behaviour. Experimental results are reported. (orig.).

  18. A DNA nanocapsule with aptamer-controlled open-closure function for targeted delivery

    DEFF Research Database (Denmark)

    Bentin, Thomas

    2012-01-01

    A DNA capsule fitted with aptamer controlled target sensing has been "woven" using a 7308-base single-stranded DNA "thread" and 196 staple oligonucleotides. The capsule enables logic-gated molecular cargo delivery to targeted cell surfaces.......A DNA capsule fitted with aptamer controlled target sensing has been "woven" using a 7308-base single-stranded DNA "thread" and 196 staple oligonucleotides. The capsule enables logic-gated molecular cargo delivery to targeted cell surfaces....

  19. The Dictyostelium prestalk inducer DIF-1 directs phosphorylation of a bZIP transcription factor.

    Science.gov (United States)

    Yamada, Yoko; Kubohara, Yuzuru; Kikuchi, Haruhisa; Oshima, Yoshiteru; Wang, Hong-Yu; Ross, Susan; Williams, Jeffrey G

    2013-01-01

    DIF-1, a chlorinated hexaphenone produced by developing Dictyostelium cells, induces prestalk differentiation. DimB is a bZIP transcription factor that accumulates in the nucleus upon exposure to DIF-1, where it directly activates transcription of DIF-responsive genes. The signaling steps upstream of DimB and downstream of DIF-1 are entirely unknown. Analysis by mass spectrometry shows that incubation with DIF-1 rapidly stimulates phosphorylation at several sites in DimB. We characterize the most highly responsive site, S590, which is located very close to the C terminus. A point mutation in this site, S590A, does not inhibit DimB nuclear accumulation in response to DIF. However, this seems likely to reflect functional redundancy with other sites; because a panel of chemical variants on the structure of DIF-1 show a correlation between their potencies as inducers of DimB nuclear accumulation and their potencies as inducers of phosphorylation at S590. Furthermore, the S590A mutant is fully active in mutant rescue of a dimB null strain, arguing against an alternative role in transcriptional activation of target genes. We conclude that i) DIF-1 directs phosphorylation at S590, ii) although it is not essential for nuclear accumulation in response to DIF-1 correlative evidence, based upon a panel of DIF-1 related molecules, suggests that this modification may play a redundant role in the process. iii) We also present evidence that the kinase activity, which phosphorylates S590, is non-nuclear and that this signalling pathway is, in part at least, independent of the DIF-regulated STATc activation pathway.

  20. DNA-based machines.

    Science.gov (United States)

    Wang, Fuan; Willner, Bilha; Willner, Itamar

    2014-01-01

    The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications.

  1. Voltage-gated Proton Channels

    Science.gov (United States)

    DeCoursey, Thomas E.

    2014-01-01

    Voltage-gated proton channels, HV1, have vaulted from the realm of the esoteric into the forefront of a central question facing ion channel biophysicists, namely the mechanism by which voltage-dependent gating occurs. This transformation is the result of several factors. Identification of the gene in 2006 revealed that proton channels are homologues of the voltage-sensing domain of most other voltage-gated ion channels. Unique, or at least eccentric, properties of proton channels include dimeric architecture with dual conduction pathways, perfect proton selectivity, a single-channel conductance ~103 smaller than most ion channels, voltage-dependent gating that is strongly modulated by the pH gradient, ΔpH, and potent inhibition by Zn2+ (in many species) but an absence of other potent inhibitors. The recent identification of HV1 in three unicellular marine plankton species has dramatically expanded the phylogenetic family tree. Interest in proton channels in their own right has increased as important physiological roles have been identified in many cells. Proton channels trigger the bioluminescent flash of dinoflagellates, facilitate calcification by coccolithophores, regulate pH-dependent processes in eggs and sperm during fertilization, secrete acid to control the pH of airway fluids, facilitate histamine secretion by basophils, and play a signaling role in facilitating B-cell receptor mediated responses in B lymphocytes. The most elaborate and best-established functions occur in phagocytes, where proton channels optimize the activity of NADPH oxidase, an important producer of reactive oxygen species. Proton efflux mediated by HV1 balances the charge translocated across the membrane by electrons through NADPH oxidase, minimizes changes in cytoplasmic and phagosomal pH, limits osmotic swelling of the phagosome, and provides substrate H+ for the production of H2O2 and HOCl, reactive oxygen species crucial to killing pathogens. PMID:23798303

  2. Compound list: amphotericin B [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available amphotericin B AMB 00157 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/amphot...at/in_vivo/Liver/Single/amphotericin_B.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-...tggates/LATEST/Rat/in_vivo/Liver/Repeat/amphotericin_B.Rat.in_vivo.Liver.Repeat.z...ip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/amphotericin_B.Rat.in_vi...vo.Kidney.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Repeat/amphotericin_B.Rat.in_vivo.Kidney.Repeat.zip ...

  3. Compound list: puromycin aminonucleoside [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available puromycin aminonucleoside PAN 00143 ftp://ftp.biosciencedbc.jp/archive/open-tggates.../LATEST/Rat/in_vitro/puromycin_aminonucleoside.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/ope...n-tggates/LATEST/Rat/in_vivo/Liver/Single/puromycin_aminonucleoside.Rat.in_vivo.Liver.Single.zip ftp://ftp.b...iosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/puromycin_aminonu...o/Kidney/Single/puromycin_aminonucleoside.Rat.in_vivo.Kidney.Single.zip ftp://ftp.biosciencedbc.jp/archive/o

  4. Compound list: valproic acid [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available valproic acid VPA 00005 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/valproic_acid....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/valproic_acid..._vivo/Liver/Single/valproic_acid.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscienc...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/valproic_acid.Rat.in_vivo.Liver.Repeat.zip ftp:...//ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/valproic_acid.Rat.in_vivo.Kidne

  5. Compound list: cyclosporine A [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available cyclosporine A CSA 00142 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/cyclosporine..._A.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/cyclosporine.../in_vivo/Liver/Single/cyclosporine_A.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosc...iencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/cyclosporine_A.Rat.in_vivo.Liver.Repeat.zip... ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/cyclosporine_A.Rat.in_vivo

  6. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  7. Engineering of a novel zipFv using leucine zipper motif against rabies virus glycoprotein G with improved protection potency in vivo.

    Science.gov (United States)

    Xi, Hualong; Zhang, Kaixin; Yin, Yanchun; Gu, Tiejun; Sun, Qing; Li, Zhuang; Cheng, Yue; Jiang, Chunlai; Kong, Wei; Wu, Yongge

    2017-06-01

    Rabies is an acute zoonotic infectious disease with a high fatality rate but is preventable with vaccination and rabies immunoglobulin (RIG). The single-chain Fv fragment (scFv), a small engineered antigen-binding protein derived from antibody variable heavy (V H ) and light (V L ) chains connected by a peptide linker, can potentially be used to replace RIG. Here, we produced two peptides V H -JUN-HIS and V L -FOS-HA separately in Escherichia coli and assembled them to form zipFv successfully in vitro. The new zipFv utilizes FOS and JUN leucine zippers to form an antibody structure similar to the IgG counterpart with two free N-terminal ends of V H and V L . The zipFv protein showed notable improvement in binding ability and affinity over its corresponding scFv. The zipFv also demonstrated greater stability in serum and the same protective rate as RIG against challenge with a standard rabies virus (CVS-24) in mice. Our results indicated zipFv as a novel and efficient antibody form with enhanced neutralizing potency. Copyright © 2017. Published by Elsevier B.V.

  8. Hydration induced stress on DNA monolayers grafted on microcantilevers.

    Science.gov (United States)

    Domínguez, Carmen M; Kosaka, Priscila M; Mokry, Guillermo; Pini, Valerio; Malvar, Oscar; del Rey, Mercedes; Ramos, Daniel; San Paulo, Alvaro; Tamayo, Javier; Calleja, Montserrat

    2014-09-16

    Surface tethered single-stranded DNA films are relevant biorecognition layers for oligonucleotide sequence identification. Also, hydration induced effects on these films have proven useful for the nanomechanical detection of DNA hybridization. Here, we apply nanomechanical sensors and atomic force microscopy to characterize in air and upon varying relative humidity conditions the swelling and deswelling of grafted single stranded and double stranded DNA films. The combination of these techniques validates a two-step hybridization process, where complementary strands first bind to the surface tethered single stranded DNA probes and then slowly proceed to a fully zipped configuration. Our results also demonstrate that, despite the slow hybridization kinetics observed for grafted DNA onto microcantilever surfaces, ex situ sequence identification does not require hybridization times typically longer than 1 h, while quantification is a major challenge.

  9. UbiGate: a synthetic biology toolbox to analyse ubiquitination.

    Science.gov (United States)

    Kowarschik, Kathrin; Hoehenwarter, Wolfgang; Marillonnet, Sylvestre; Trujillo, Marco

    2018-03-01

    Ubiquitination is mediated by an enzymatic cascade that results in the modification of substrate proteins, redefining their fate. This post-translational modification is involved in most cellular processes, yet its analysis faces manifold obstacles due to its complex and ubiquitous nature. Reconstitution of the ubiquitination cascade in bacterial systems circumvents several of these problems and was shown to faithfully recapitulate the process. Here, we present UbiGate - a synthetic biology toolbox, together with an inducible bacterial expression system - to enable the straightforward reconstitution of the ubiquitination cascades of different organisms in Escherichia coli by 'Golden Gate' cloning. This inclusive toolbox uses a hierarchical modular cloning system to assemble complex DNA molecules encoding the multiple genetic elements of the ubiquitination cascade in a predefined order, to generate polycistronic operons for expression. We demonstrate the efficiency of UbiGate in generating a variety of expression elements to reconstitute autoubiquitination by different E3 ligases and the modification of their substrates, as well as its usefulness for dissecting the process in a time- and cost-effective manner. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  10. Cognitive mechanisms associated with auditory sensory gating

    Science.gov (United States)

    Jones, L.A.; Hills, P.J.; Dick, K.M.; Jones, S.P.; Bright, P.

    2016-01-01

    Sensory gating is a neurophysiological measure of inhibition that is characterised by a reduction in the P50 event-related potential to a repeated identical stimulus. The objective of this work was to determine the cognitive mechanisms that relate to the neurological phenomenon of auditory sensory gating. Sixty participants underwent a battery of 10 cognitive tasks, including qualitatively different measures of attentional inhibition, working memory, and fluid intelligence. Participants additionally completed a paired-stimulus paradigm as a measure of auditory sensory gating. A correlational analysis revealed that several tasks correlated significantly with sensory gating. However once fluid intelligence and working memory were accounted for, only a measure of latent inhibition and accuracy scores on the continuous performance task showed significant sensitivity to sensory gating. We conclude that sensory gating reflects the identification of goal-irrelevant information at the encoding (input) stage and the subsequent ability to selectively attend to goal-relevant information based on that previous identification. PMID:26716891

  11. Compound list: imatinib, methanesulfonate salt [Open TG-GATEs

    Lifescience Database Archive (English)

    Full Text Available imatinib, methanesulfonate salt IMA 00186 ftp://ftp.biosciencedbc.jp/archive/open-t...ggates/LATEST/Rat/in_vivo/Liver/Single/imatinib%2C_methanesulfonate_salt.Rat.in_vivo.Liver.Single.zip ...

  12. MCP gated x-ray framing camera

    Science.gov (United States)

    Cai, Houzhi; Liu, Jinyuan; Niu, Lihong; Liao, Hua; Zhou, Junlan

    2009-11-01

    A four-frame gated microchannel plate (MCP) camera is described in this article. Each frame photocathode coated with gold on the MCP is part of a transmission line with open circuit end driven by the gating electrical pulse. The gating pulse is 230 ps in width and 2.5 kV in amplitude. The camera is tested by illuminating its photocathode with ultraviolet laser pulses, 266 nm in wavelength, which shows exposure time as short as 80 ps.

  13. Gating-ML: XML-based gating descriptions in flow cytometry.

    Science.gov (United States)

    Spidlen, Josef; Leif, Robert C; Moore, Wayne; Roederer, Mario; Brinkman, Ryan R

    2008-12-01

    The lack of software interoperability with respect to gating due to lack of a standardized mechanism for data exchange has traditionally been a bottleneck, preventing reproducibility of flow cytometry (FCM) data analysis and the usage of multiple analytical tools. To facilitate interoperability among FCM data analysis tools, members of the International Society for the Advancement of Cytometry (ISAC) Data Standards Task Force (DSTF) have developed an XML-based mechanism to formally describe gates (Gating-ML). Gating-ML, an open specification for encoding gating, data transformations and compensation, has been adopted by the ISAC DSTF as a Candidate Recommendation. Gating-ML can facilitate exchange of gating descriptions the same way that FCS facilitated for exchange of raw FCM data. Its adoption will open new collaborative opportunities as well as possibilities for advanced analyses and methods development. The ISAC DSTF is satisfied that the standard addresses the requirements for a gating exchange standard.

  14. Effects of Voltage-Gated K+ Channel on Cell Proliferation in Multiple Myeloma

    Directory of Open Access Journals (Sweden)

    Wei Wang

    2014-01-01

    Full Text Available Objective. To study the effects and underlying mechanisms of voltage-gated K+ channels on the proliferation of multiple myeloma cells. Methods. RPMI-8226 MM cell line was used for the experiments. Voltage-gated K+ currents and the resting potential were recorded by whole-cell patch-clamp technique. RT-PCR detected Kv channel mRNA expression. Cell viability was analyzed with MTT assay. Cell counting system was employed to monitor cell proliferation. DNA contents and cell volume were analyzed by flow cytometry. Results. Currents recorded in RPMI-8226 cells were confirmed to be voltage-gated K+ channels. A high level of Kv1.3 mRNA was detected but no Kv3.1 mRNA was detected in RPMI-8226 cells. Voltage-gated K+ channel blocker 4-aminopyridine (4-AP (2 mM depolarized the resting potential from −42 ± 1.7 mV to −31.8 ± 2.8 mV (P0.05. Conclusions. In RPMI-8226, voltage-gated K+ channels are involved in proliferation and cell cycle progression its influence on the resting potential and cell volume may be responsible for this process; the inhibitory effect of the voltage-gated K+ channel blocker on RPMI-8226 cell proliferation is a phase-specific event.

  15. Identification of Candidate Iron Transporters From the ZIP/ZnT Gene Families in the Mosquito Aedes aegypti

    Directory of Open Access Journals (Sweden)

    Hitoshi Tsujimoto

    2018-04-01

    Full Text Available Mosquito-transmitted viral pathogens, such as dengue and Zika, afflict tens of thousands of people every year. These viruses are transmitted during the blood-feeding process that is required for mosquito reproduction, the most important vector being Aedes aegypti. While vertebrate blood is rich in protein, its high iron content is potentially toxic to mosquitoes. Although iron transport and sequestration are essential in the reproduction of vector mosquitoes, we discovered that culicine mosquitoes lack homologs of the common iron transporter NRAMP. Using a novel cell-based screen, we identified two ZIP and one ZnT genes as candidate iron transporters in the mosquito A. aegypti, the vector of dengue, Zika, and chikungunya. We determined the organ-specific expression pattern of these genes at critical time points in early reproduction. The result indicates modulation of these genes upon blood feeding, especially a ZIP13 homolog that is highly up-regulated after blood feeding, suggesting its importance in iron mobilization during blood digestion and reproduction. Gene silencing resulted in differential iron accumulation in the midgut and ovaries. This study sets a foundation for further investigation of iron transport and control strategies of this viral vector.

  16. Why Your ZIP Code Matters More Than Your Genetic Code: Promoting Healthy Outcomes from Mother to Child.

    Science.gov (United States)

    Graham, Garth N

    2016-10-01

    Health equity has long been the dominant theme in the work of the Aetna Foundation. Recent data have focused on disparities through another lens, particularly the correlation between where people live (i.e., ZIP code) and their quality-and length-of life. In various cities across America, average life expectancies in certain communities are 20-30 years shorter than those mere miles away. In general, health disparities are founded on a complex interplay of racial, economic, educational, and other social factors. For example, breastfeeding rates in the United States differ significantly depending upon the race and income of the mother. Government policy makers are acutely aware of these disparities, but recent health system reforms have focused predominately on the processes used to administer, finance, and deliver care. What is needed is an approach that considers the health and wellness of all people in a geographic area, beyond established patients, and that measures more than clinical factors-such as genetics, environmental health, social circumstances, and individual behaviors. Solutions also must extend beyond the traditional healthcare arena. In particular, novel technological innovations show promise to bridge gaps between our healthcare capabilities and the needs of underserved populations. Digital tools are poised to revolutionize measurement, diagnostics, treatment, and global aspect of our healthcare system. The Aetna Foundation views technology as a core strategy in reducing health inequities through an approach that addresses both clinical and social factors in populations to dismantle the persistent paradigm of ZIP code as personal health destiny.

  17. Instant Oracle GoldenGate

    CERN Document Server

    Bruzzese, Tony

    2013-01-01

    Filled with practical, step-by-step instructions and clear explanations for the most important and useful tasks. Get the job done and learn as you go. A how-To book with practical recipes accompanied with rich screenshots for easy comprehension.This is a Packt Instant How-to guide, which provides concise and clear recipes for performing the core task of replication using Oracle GoldenGate.The book is aimed at DBAs from any of popular RDBMS systems such as Oracle, SQL Server, Teradata, Sybase, and so on. The level of detail provides quick applicability to beginners and a handy review for more a

  18. Time complexity and gate complexity

    International Nuclear Information System (INIS)

    Koike, Tatsuhiko; Okudaira, Yosuke

    2010-01-01

    We formulate and investigate the simplest version of time-optimal quantum computation theory (TO-QCT), where the computation time is defined by the physical one and the Hamiltonian contains only one- and two-qubit interactions. This version of TO-QCT is also considered as optimality by sub-Riemannian geodesic length. The work has two aims: One is to develop a TO-QCT itself based on a physically natural concept of time, and the other is to pursue the possibility of using TO-QCT as a tool to estimate the complexity in conventional gate-optimal quantum computation theory (GO-QCT). In particular, we investigate to what extent is true the following statement: Time complexity is polynomial in the number of qubits if and only if gate complexity is also. In the analysis, we relate TO-QCT and optimal control theory (OCT) through fidelity-optimal computation theory (FO-QCT); FO-QCT is equivalent to TO-QCT in the limit of unit optimal fidelity, while it is formally similar to OCT. We then develop an efficient numerical scheme for FO-QCT by modifying Krotov's method in OCT, which has a monotonic convergence property. We implemented the scheme and obtained solutions of FO-QCT and of TO-QCT for the quantum Fourier transform and a unitary operator that does not have an apparent symmetry. The former has a polynomial gate complexity and the latter is expected to have an exponential one which is based on the fact that a series of generic unitary operators has an exponential gate complexity. The time complexity for the former is found to be linear in the number of qubits, which is understood naturally by the existence of an upper bound. The time complexity for the latter is exponential in the number of qubits. Thus, both the targets seem to be examples satisfyng the preceding statement. The typical characteristics of the optimal Hamiltonians are symmetry under time reversal and constancy of one-qubit operation, which are mathematically shown to hold in fairly general situations.

  19. Slowing DNA Translocation in a Nanofluidic Field-Effect Transistor.

    Science.gov (United States)

    Liu, Yifan; Yobas, Levent

    2016-04-26

    Here, we present an experimental demonstration of slowing DNA translocation across a nanochannel by modulating the channel surface charge through an externally applied gate bias. The experiments were performed on a nanofluidic field-effect transistor, which is a monolithic integrated platform featuring a 50 nm-diameter in-plane alumina nanocapillary whose entire length is surrounded by a gate electrode. The field-effect transistor behavior was validated on the gating of ionic conductance and protein transport. The gating of DNA translocation was subsequently studied by measuring discrete current dips associated with single λ-DNA translocation events under a source-to-drain bias of 1 V. The translocation speeds under various gate bias conditions were extracted by fitting event histograms of the measured translocation time to the first passage time distributions obtained from a simple 1D biased diffusion model. A positive gate bias was observed to slow the translocation of single λ-DNA chains markedly; the translocation speed was reduced by an order of magnitude from 18.4 mm/s obtained under a floating gate down to 1.33 mm/s under a positive gate bias of 9 V. Therefore, a dynamic and flexible regulation of the DNA translocation speed, which is vital for single-molecule sequencing, can be achieved on this device by simply tuning the gate bias. The device is realized in a conventional semiconductor microfabrication process without the requirement of advanced lithography, and can be potentially further developed into a compact electronic single-molecule sequencer.

  20. Boolean gates on actin filaments

    Energy Technology Data Exchange (ETDEWEB)

    Siccardi, Stefano, E-mail: ssiccardi@2ssas.it [The Unconventional Computing Centre, University of the West of England, Bristol (United Kingdom); Tuszynski, Jack A., E-mail: jackt@ualberta.ca [Department of Oncology, University of Alberta, Edmonton, Alberta (Canada); Adamatzky, Andrew, E-mail: andrew.adamatzky@uwe.ac.uk [The Unconventional Computing Centre, University of the West of England, Bristol (United Kingdom)

    2016-01-08

    Actin is a globular protein which forms long polar filaments in the eukaryotic cytoskeleton. Actin networks play a key role in cell mechanics and cell motility. They have also been implicated in information transmission and processing, memory and learning in neuronal cells. The actin filaments have been shown to support propagation of voltage pulses. Here we apply a coupled nonlinear transmission line model of actin filaments to study interactions between voltage pulses. To represent digital information we assign a logical TRUTH value to the presence of a voltage pulse in a given location of the actin filament, and FALSE to the pulse's absence, so that information flows along the filament with pulse transmission. When two pulses, representing Boolean values of input variables, interact, then they can facilitate or inhibit further propagation of each other. We explore this phenomenon to construct Boolean logical gates and a one-bit half-adder with interacting voltage pulses. We discuss implications of these findings on cellular process and technological applications. - Highlights: • We simulate interaction between voltage pulses using on actin filaments. • We use a coupled nonlinear transmission line model. • We design Boolean logical gates via interactions between the voltage pulses. • We construct one-bit half-adder with interacting voltage pulses.

  1. A gate drive circuit for gate-turn-off (GTO) devices in series stack

    International Nuclear Information System (INIS)

    Despe, O.

    1999-01-01

    A gate-turn-off (GTO) switch is under development at the Advanced Photon Source as a replacement for a thyratron switch in high power pulsed application. The high voltage in the application requires multiple GTOs connected in series. One component that is critical to the success of GTO operation is the gate drive circuit. The gate drive circuit has to provide fast high-current pulses to the GTO gate for fast turn-on and turn-off. It also has to be able to operate while floating at high voltage. This paper describes a gate drive circuit that meets these requirements

  2. Terahertz amplification in RTD-gated HEMTs with a grating-gate wave coupling topology

    Energy Technology Data Exchange (ETDEWEB)

    Condori Quispe, Hugo O.; Sensale-Rodriguez, Berardi [The University of Utah, Salt Lake City, Utah 84112 (United States); Encomendero-Risco, Jimy J.; Xing, Huili Grace [University of Notre Dame, Notre Dame, Indiana 46556 (United States); Cornell University, Ithaca, New York 14853 (United States)

    2016-08-08

    We theoretically analyze the operation of a terahertz amplifier consisting of a resonant-tunneling-diode gated high-electron-mobility transistor (RTD-gated HEMT) in a grating-gate topology. In these devices, the key element enabling substantial power gain is the efficient coupling of terahertz waves into and out of plasmons in the RTD-gated HEMT channel, i.e., the gain medium, via the grating-gate itself, part of the active device, rather than by an external antenna structure as discussed in previous works, therefore potentially enabling terahertz amplification with associated power gains >40 dB.

  3. Gates Auto Door Car With Lights Modulated

    OpenAIRE

    Lina Carolina; Luyung Dinani, Skom, MMSi

    2002-01-01

    In scientific writing wi ll be explained about automatic gates with modulated headlights, where to find the car lights were adjusted by the relative frequency darker because of this background that the author alleviate human task in performing daily activities by using an automatic gate with the car lights modulated.

  4. Protected gates for topological quantum field theories

    Science.gov (United States)

    Beverland, Michael E.; Buerschaper, Oliver; Koenig, Robert; Pastawski, Fernando; Preskill, John; Sijher, Sumit

    2016-02-01

    We study restrictions on locality-preserving unitary logical gates for topological quantum codes in two spatial dimensions. A locality-preserving operation is one which maps local operators to local operators — for example, a constant-depth quantum circuit of geometrically local gates, or evolution for a constant time governed by a geometrically local bounded-strength Hamiltonian. Locality-preserving logical gates of topological codes are intrinsically fault tolerant because spatially localized errors remain localized, and hence sufficiently dilute errors remain correctable. By invoking general properties of two-dimensional topological field theories, we find that the locality-preserving logical gates are severely limited for codes which admit non-abelian anyons, in particular, there are no locality-preserving logical gates on the torus or the sphere with M punctures if the braiding of anyons is computationally universal. Furthermore, for Ising anyons on the M-punctured sphere, locality-preserving gates must be elements of the logical Pauli group. We derive these results by relating logical gates of a topological code to automorphisms of the Verlinde algebra of the corresponding anyon model, and by requiring the logical gates to be compatible with basis changes in the logical Hilbert space arising from local F-moves and the mapping class group.

  5. Protected gates for topological quantum field theories

    Energy Technology Data Exchange (ETDEWEB)

    Beverland, Michael E.; Pastawski, Fernando; Preskill, John [Institute for Quantum Information and Matter, California Institute of Technology, Pasadena, California 91125 (United States); Buerschaper, Oliver [Dahlem Center for Complex Quantum Systems, Freie Universität Berlin, 14195 Berlin (Germany); Koenig, Robert [Institute for Advanced Study and Zentrum Mathematik, Technische Universität München, 85748 Garching (Germany); Sijher, Sumit [Institute for Quantum Computing and Department of Applied Mathematics, University of Waterloo, Waterloo, Ontario N2L 3G1 (Canada)

    2016-02-15

    We study restrictions on locality-preserving unitary logical gates for topological quantum codes in two spatial dimensions. A locality-preserving operation is one which maps local operators to local operators — for example, a constant-depth quantum circuit of geometrically local gates, or evolution for a constant time governed by a geometrically local bounded-strength Hamiltonian. Locality-preserving logical gates of topological codes are intrinsically fault tolerant because spatially localized errors remain localized, and hence sufficiently dilute errors remain correctable. By invoking general properties of two-dimensional topological field theories, we find that the locality-preserving logical gates are severely limited for codes which admit non-abelian anyons, in particular, there are no locality-preserving logical gates on the torus or the sphere with M punctures if the braiding of anyons is computationally universal. Furthermore, for Ising anyons on the M-punctured sphere, locality-preserving gates must be elements of the logical Pauli group. We derive these results by relating logical gates of a topological code to automorphisms of the Verlinde algebra of the corresponding anyon model, and by requiring the logical gates to be compatible with basis changes in the logical Hilbert space arising from local F-moves and the mapping class group.

  6. Multi-gated field emitters for a micro-column

    International Nuclear Information System (INIS)

    Mimura, Hidenori; Kioke, Akifumi; Aoki, Toru; Neo, Yoichiro; Yoshida, Tomoya; Nagao, Masayoshi

    2011-01-01

    We have developed a multi-gated field emitter (FE) such as a quadruple-gated FE with a three-stacked electrode lens and a quintuple-gated FE with a four-stacked electrode lens. Both the FEs can focus the electron beam. However, the quintuple-gated FE has a stronger electron convergence than the quadruple-gated FE, and a beam crossover is clearly observed for the quintuple-gated FE.

  7. Dedicated Searches for Low and High Mass Wimps with the SuperCDMS Soudan iZIP Detectors

    Energy Technology Data Exchange (ETDEWEB)

    Welliver, Bradford [Florida State Univ., Tallahassee, FL (United States)

    2016-01-01

    Recent cosmological evidence suggests most of the mass of the universe takes the form of a type of particle that we have not been able to directly detect. Nearly 80 years that have elapsed since the rst hints of this dark matter started to appear from astronomers without any direct detection. The high precision era of cosmology and unifying models of particle physics developed in the 20 th century have presented us with an exciting mystery at the intersection of these two elds that needs to be solved. SuperCDMS Soudan operates specialized germanium detectors (iZIPs) that are cooled to milliKelvin temperatures deep underground in the Soudan Underground Laboratory with the hope of detecting a rare collision between dark matter and a nucleus. A search for low-mass dark matter comes with multiple unique challenges since the background discrimination abilities of these detectors becomes less powerful at the low energies needed to probe low-mass dark matter since the signal to noise ratio deteriorates. Using a sophisticated background model via a pulse rescaling technique, SuperCDMS Soudan was able to produce a world leading exclusion limit on low-mass dark matter. Effort is to extend the analysis to higher masses require long running times during which many aspects of the detectors or the environment can change. Additional challenges are offered by the powerful background discrimination ability of the iZIP. The background distributions are well separated from the signal region, meaning most of the leakage arises from low-probability tails of the background distributions. In the absence of an enormous dataset, extrapolations from the bulk of the distribution are required. While attempting to obtain a model of gamma induced electron-recoils leaking into the signal region of the detector from high radius a curious asymmetry between the sides of the detectors was discovered potentially indicating an electronics or detector design problem. This thesis describes the physics

  8. Top-gate pentacene-based organic field-effect transistor with amorphous rubrene gate insulator

    Science.gov (United States)

    Hiroki, Mizuha; Maeda, Yasutaka; Ohmi, Shun-ichiro

    2018-02-01

    The scaling of organic field-effect transistors (OFETs) is necessary for high-density integration and for this, OFETs with a top-gate configuration are required. There have been several reports of damageless lithography processes for organic semiconductor or insulator layers. However, it is still difficult to fabricate scaled OFETs with a top-gate configuration. In this study, the lift-off process and the device characteristics of the OFETs with a top-gate configuration utilizing an amorphous (α) rubrene gate insulator were investigated. We have confirmed that α-rubrene shows an insulating property, and its extracted linear mobility was 2.5 × 10‑2 cm2/(V·s). The gate length and width were 10 and 60 µm, respectively. From these results, the OFET with a top-gate configuration utilizing an α-rubrene gate insulator is promising for the high-density integration of scaled OFETs.

  9. The Populus Class III HD ZIP, popREVOLUTA, Influences Cambium Initiation and Patterning of Woody Stems1[W][OA

    Science.gov (United States)

    Robischon, Marcel; Du, Juan; Miura, Eriko; Groover, Andrew

    2011-01-01

    The secondary growth of a woody stem requires the formation of a vascular cambium at an appropriate position and proper patterning of the vascular tissues derived from the cambium. Class III homeodomain-leucine zipper (HD ZIP) transcription factors have been implicated in polarity determination and patterning in lateral organs and primary vascular tissues and in the initiation and function of shoot apical meristems. We report here the functional characterization of a Populus class III HD ZIP gene, popREVOLUTA (PRE), that demonstrates another role for class III HD ZIPs in regulating the development of cambia and secondary vascular tissues. PRE is orthologous to Arabidopsis (Arabidopsis thaliana) REVOLUTA and is expressed in both the shoot apical meristem and in the cambial zone and secondary vascular tissues. Transgenic Populus expressing a microRNA-resistant form of PRE presents unstable phenotypic abnormalities affecting both primary and secondary growth. Surprisingly, phenotypic changes include abnormal formation of cambia within cortical parenchyma that can produce secondary vascular tissues in reverse polarity. Genes misexpressed in PRE mutants include transcription factors and auxin-related genes previously implicated in class III HD ZIP functions during primary growth. Together, these results suggest that PRE plays a fundamental role in the initiation of the cambium and in regulating the patterning of secondary vascular tissues. PMID:21205615

  10. Materials Fundamentals of Gate Dielectrics

    CERN Document Server

    Demkov, Alexander A

    2006-01-01

    This book presents materials fundamentals of novel gate dielectrics that are being introduced into semiconductor manufacturing to ensure the continuous scalling of the CMOS devices. This is a very fast evolving field of research so we choose to focus on the basic understanding of the structure, thermodunamics, and electronic properties of these materials that determine their performance in device applications. Most of these materials are transition metal oxides. Ironically, the d-orbitals responsible for the high dielectric constant cause sever integration difficulties thus intrinsically limiting high-k dielectrics. Though new in the electronics industry many of these materials are wel known in the field of ceramics, and we describe this unique connection. The complexity of the structure-property relations in TM oxides makes the use of the state of the art first-principles calculations necessary. Several chapters give a detailed description of the modern theory of polarization, and heterojunction band discont...

  11. Effects of superglue fuming on materials characterization of zip-lock polyethylene bags for route forensic analyses

    International Nuclear Information System (INIS)

    Koester, C.J.; Grant, P.M.; Blankenship, J.F.

    2013-01-01

    Using cyanoacrylate or 'superglue' fuming to develop latent dermatoglyphic prints significantly altered the volatile and semivolatile compounds within the material of polyethylene zip-lock bags. Comparisons of SPME-GC/MS analyses of poly bags obtained before and after application of a glue fuming fingermark-developing technique resulted in markedly different material profiles of the bags. Not only were species added to the chemical composition of a bag, but other compounds that had been initially present were removed. These effects are particularly important for nuclear forensic investigations in the realm of route (pathway) analyses, and may also be of general interest to criminalistics laboratories that examine illicit drugs and their packaging. (author)

  12. Functional footprinting of regulatory DNA.

    Science.gov (United States)

    Vierstra, Jeff; Reik, Andreas; Chang, Kai-Hsin; Stehling-Sun, Sandra; Zhou, Yuanyue; Hinkley, Sarah J; Paschon, David E; Zhang, Lei; Psatha, Nikoletta; Bendana, Yuri R; O'Neil, Colleen M; Song, Alexander H; Mich, Andrea K; Liu, Pei-Qi; Lee, Gary; Bauer, Daniel E; Holmes, Michael C; Orkin, Stuart H; Papayannopoulou, Thalia; Stamatoyannopoulos, George; Rebar, Edward J; Gregory, Philip D; Urnov, Fyodor D; Stamatoyannopoulos, John A

    2015-10-01

    Regulatory regions harbor multiple transcription factor (TF) recognition sites; however, the contribution of individual sites to regulatory function remains challenging to define. We describe an approach that exploits the error-prone nature of genome editing-induced double-strand break repair to map functional elements within regulatory DNA at nucleotide resolution. We demonstrate the approach on a human erythroid enhancer, revealing single TF recognition sites that gate the majority of downstream regulatory function.

  13. Pepper CabZIP63 acts as a positive regulator during Ralstonia solanacearum or high temperature–high humidity challenge in a positive feedback loop with CaWRKY40

    Science.gov (United States)

    Shen, Lei; Liu, Zhiqin; Yang, Sheng; Yang, Tong; Liang, Jiaqi; Wen, Jiayu; Liu, Yanyan; Li, Jiazhi; Shi, Lanping; Tang, Qian; Shi, Wei; Hu, Jiong; Liu, Cailing; Zhang, Yangwen; Lin, Wei; Wang, Rongzhang; Yu, Huanxin; Mou, Shaoliang; Hussain, Ansar; Cheng, Wei; Cai, Hanyang; He, Li; Guan, Deyi; Wu, Yang; He, Shuilin

    2016-01-01

    CaWRKY40 is known to act as a positive regulator in the response of pepper (Capsicum annuum) to Ralstonia solanacearum inoculation (RSI) or high temperature–high humidity (HTHH), but the underlying mechanism remains elusive. Herein, we report that CabZIP63, a pepper bZIP family member, participates in this process by regulating the expression of CaWRKY40. CabZIP63 was found to localize in the nuclei, be up-regulated by RSI or HTHH, bind to promoters of both CabZIP63 (pCabZIP63) and CaWRKY40 (pCaWRKY40), and activate pCabZIP63- and pCaWRKY40-driven β-glucuronidase expression in a C- or G-box-dependent manner. Silencing of CabZIP63 by virus-induced gene silencing (VIGS) in pepper plants significantly attenuated their resistance to RSI and tolerance to HTHH, accompanied by down-regulation of immunity- or thermotolerance-associated CaPR1, CaNPR1, CaDEF1, and CaHSP24. Hypersensitive response-mediated cell death and expression of the tested immunity- and thermotolerance-associated marker genes were induced by transient overexpression (TOE) of CabZIP63, but decreased by that of CabZIP63-SRDX. Additionally, binding of CabZIP63 to pCaWRKY40 was up-regulated by RSI or HTHH, and the transcript level of CaWRKY40 and binding of CaWRKY40 to the promoters of CaPR1, CaNPR1, CaDEF1 and CaHSP24 were up-regulated by TOE of CabZIP63. On the other hand, CabZIP63 was also up-regulated transcriptionally by TOE of CaWRKY40. The data suggest collectively that CabZIP63 directly or indirectly regulates the expression of CaWRKY40 at both the transcriptional and post-transcriptional level, forming a positive feedback loop with CaWRKY40 during pepper’s response to RSI or HTHH. Altogether, our data will help to elucidate the underlying mechanism of crosstalk between pepper’s response to RSI and HTHH. PMID:26936828

  14. Calibration of submerged multi-sluice gates

    Directory of Open Access Journals (Sweden)

    Mohamed F. Sauida

    2014-09-01

    The main objective of this work is to study experimentally and verify empirically the different parameters affecting the discharge through submerged multiple sluice gates (i.e., the expansion ratios, gates operational management, etc.. Using multiple regression analysis of the experimental results, a general equation for discharge coefficient is developed. The results show, that the increase in the expansion ratio and the asymmetric operation of gates, give higher values for the discharge coefficient. The obtained predictions of the discharge coefficient using the developed equations are compared to the experimental data. The present developed equations showed good consistency and high accuracy.

  15. A class of quantum gate entanglers

    International Nuclear Information System (INIS)

    Heydari, Hoshang

    2010-01-01

    We construct quantum gate entanglers for different classes of multipartite states based on the definition of W and GHZ concurrence classes. First, we review the basic construction of concurrence classes based on the orthogonal complement of a positive operator valued measure (POVM) on quantum phase. Then, we construct quantum gate entanglers for different classes of multi-qubit states. In particular, we show that these operators can entangle multipartite states if they satisfy some conditions for W and GHZ classes of states. Finally, we explicitly give the W class and GHZ classes of quantum gate entanglers for four-qubit states.

  16. Resonantly driven CNOT gate for electron spins

    Science.gov (United States)

    Zajac, D. M.; Sigillito, A. J.; Russ, M.; Borjans, F.; Taylor, J. M.; Burkard, G.; Petta, J. R.

    2018-01-01

    To build a universal quantum computer—the kind that can handle any computational task you throw at it—an essential early step is to demonstrate the so-called CNOT gate, which acts on two qubits. Zajac et al. built an efficient CNOT gate by using electron spin qubits in silicon quantum dots, an implementation that is especially appealing because of its compatibility with existing semiconductor-based electronics (see the Perspective by Schreiber and Bluhm). To showcase the potential, the authors used the gate to create an entangled quantum state called the Bell state.

  17. Stay vane and wicket gate relationship study

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    2005-01-19

    This report evaluates potential environmental and performance gains that can be achieved in a Kaplan turbine through non-structural modifications to stay vane and wicket gate assemblies. This summary is based primarily on data and conclusions drawn from models and studies of Lower Granite Dam. Based on this investigation, the study recommends (1) a proof of concept at Lower Granite Dam to establish predicted improvements for the existing turbine and to further refine the stay vane wicket gate designs for fish passage; and (2) consideration of the stay vane wicket gate systems in any future turbine rehabilitation studies.

  18. Gate A: changes to opening hours

    CERN Multimedia

    2015-01-01

    Due to maintenance work, the opening hours of Gate A (near Reception) will be modified between Monday, 13 and Friday, 17 April 2015.   During this period, the gate will be open to vehicles between 7 a.m. and 9.30 a.m., then between 4.30 p.m. and 7 p.m. It will be completely closed to traffic between 9.30 a.m. and 4.30 p.m. Pedestrians and cyclists may continue to use the gate. We apologise for any inconvenience and thank you for your understanding.

  19. Getting started with FortiGate

    CERN Document Server

    Fabbri, Rosato

    2013-01-01

    This book is a step-by-step tutorial that will teach you everything you need to know about the deployment and management of FortiGate, including high availability, complex routing, various kinds of VPN working, user authentication, security rules and controls on applications, and mail and Internet access.This book is intended for network administrators, security managers, and IT pros. It is a great starting point if you have to administer or configure a FortiGate unit, especially if you have no previous experience. For people that have never managed a FortiGate unit, the book helpfully walks t

  20. Abstractions for DNA circuit design

    Science.gov (United States)

    Lakin, Matthew R.; Youssef, Simon; Cardelli, Luca; Phillips, Andrew

    2012-01-01

    DNA strand displacement techniques have been used to implement a broad range of information processing devices, from logic gates, to chemical reaction networks, to architectures for universal computation. Strand displacement techniques enable computational devices to be implemented in DNA without the need for additional components, allowing computation to be programmed solely in terms of nucleotide sequences. A major challenge in the design of strand displacement devices has been to enable rapid analysis of high-level designs while also supporting detailed simulations that include known forms of interference. Another challenge has been to design devices capable of sustaining precise reaction kinetics over long periods, without relying on complex experimental equipment to continually replenish depleted species over time. In this paper, we present a programming language for designing DNA strand displacement devices, which supports progressively increasing levels of molecular detail. The language allows device designs to be programmed using a common syntax and then analysed at varying levels of detail, with or without interference, without needing to modify the program. This allows a trade-off to be made between the level of molecular detail and the computational cost of analysis. We use the language to design a buffered architecture for DNA devices, capable of maintaining precise reaction kinetics for a potentially unbounded period. We test the effectiveness of buffered gates to support long-running computation by designing a DNA strand displacement system capable of sustained oscillations. PMID:21775321

  1. EduGATE - basic examples for educative purpose using the GATE simulation platform.

    Science.gov (United States)

    Pietrzyk, Uwe; Zakhnini, Abdelhamid; Axer, Markus; Sauerzapf, Sophie; Benoit, Didier; Gaens, Michaela

    2013-02-01

    EduGATE is a collection of basic examples to introduce students to the fundamental physical aspects of medical imaging devices. It is based on the GATE platform, which has received a wide acceptance in the field of simulating medical imaging devices including SPECT, PET, CT and also applications in radiation therapy. GATE can be configured by commands, which are, for the sake of simplicity, listed in a collection of one or more macro files to set up phantoms, multiple types of sources, detection device, and acquisition parameters. The aim of the EduGATE is to use all these helpful features of GATE to provide insights into the physics of medical imaging by means of a collection of very basic and simple GATE macros in connection with analysis programs based on ROOT, a framework for data processing. A graphical user interface to define a configuration is also included. Copyright © 2012. Published by Elsevier GmbH.

  2. Mechanosensitive gating of Kv channels.

    Directory of Open Access Journals (Sweden)

    Catherine E Morris

    Full Text Available K-selective voltage-gated channels (Kv are multi-conformation bilayer-embedded proteins whose mechanosensitive (MS Popen(V implies that at least one conformational transition requires the restructuring of the channel-bilayer interface. Unlike Morris and colleagues, who attributed MS-Kv responses to a cooperative V-dependent closed-closed expansion↔compaction transition near the open state, Mackinnon and colleagues invoke expansion during a V-independent closed↔open transition. With increasing membrane tension, they suggest, the closed↔open equilibrium constant, L, can increase >100-fold, thereby taking steady-state Popen from 0→1; "exquisite sensitivity to small…mechanical perturbations", they state, makes a Kv "as much a mechanosensitive…as…a voltage-dependent channel". Devised to explain successive gK(V curves in excised patches where tension spontaneously increased until lysis, their L-based model falters in part because of an overlooked IK feature; with recovery from slow inactivation factored in, their g(V datasets are fully explained by the earlier model (a MS V-dependent closed-closed transition, invariant L≥4. An L-based MS-Kv predicts neither known Kv time courses nor the distinctive MS responses of Kv-ILT. It predicts Kv densities (hence gating charge per V-sensor several-fold different from established values. If opening depended on elevated tension (L-based model, standard gK(V operation would be compromised by animal cells' membrane flaccidity. A MS V-dependent transition is, by contrast, unproblematic on all counts. Since these issues bear directly on recent findings that mechanically-modulated Kv channels subtly tune pain-related excitability in peripheral mechanoreceptor neurons we undertook excitability modeling (evoked action potentials. Kvs with MS V-dependent closed-closed transitions produce nuanced mechanically-modulated excitability whereas an L-based MS-Kv yields extreme, possibly excessive

  3. C-V Test Structures for Metal Gate CMOS

    NARCIS (Netherlands)

    Bankras, R.G.; Tiggelman, M.P.J.; Negara, M. Adi; Sasse, G.T.; Schmitz, Jurriaan

    2006-01-01

    Gate leakage has complicated the layout and measurement of C-V test structures. In this paper the impact of metal gate introduction to C-V test structure design is discussed. The metal gate allows for wider-gate structures and for the application of n+-p+ diffusion edges. We show, both theoretically

  4. Nanomechanical DNA origami 'single-molecule beacons' directly imaged by atomic force microscopy

    Science.gov (United States)

    Kuzuya, Akinori; Sakai, Yusuke; Yamazaki, Takahiro; Xu, Yan; Komiyama, Makoto

    2011-01-01

    DNA origami involves the folding of long single-stranded DNA into designed structures with the aid of short staple strands; such structures may enable the development of useful nanomechanical DNA devices. Here we develop versatile sensing systems for a variety of chemical and biological targets at molecular resolution. We have designed functional nanomechanical DNA origami devices that can be used as 'single-molecule beacons', and function as pinching devices. Using 'DNA origami pliers' and 'DNA origami forceps', which consist of two levers ~170 nm long connected at a fulcrum, various single-molecule inorganic and organic targets ranging from metal ions to proteins can be visually detected using atomic force microscopy by a shape transition of the origami devices. Any detection mechanism suitable for the target of interest, pinching, zipping or unzipping, can be chosen and used orthogonally with differently shaped origami devices in the same mixture using a single platform. PMID:21863016

  5. Greening the Golden Gate National Recreation Area

    Science.gov (United States)

    The Golden Gate National Recreation Area was recognized a 2016 Federal Green Challenge Award for making significant strides to reduce its carbon footprint with the goal of becoming a carbon neutral park.

  6. Active gated imaging in driver assistance system

    Science.gov (United States)

    Grauer, Yoav

    2014-04-01

    In this paper, we shall present the active gated imaging system (AGIS) in relation to the automotive field. AGIS is based on a fast-gated camera and pulsed illuminator, synchronized in the time domain to record images of a certain range of interest. A dedicated gated CMOS imager sensor and near infra-red (NIR) pulsed laser illuminator, is presented in this paper to provide active gated technology. In recent years, we have developed these key components and learned the system parameters, which are most beneficial to nighttime (in all weather conditions) driving in terms of field of view, illumination profile, resolution, and processing power. We shall present our approach of a camera-based advanced driver assistance systems (ADAS) named BrightEye™, which makes use of the AGIS technology in the automotive field.

  7. Golden Gate and Pt. Reyes Acoustic Detections

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset contains detections of acoustic tagged fish from two general locations: Golden Gate (east and west line) and Pt. Reyes. Several Vemco 69khz acoustic...

  8. Extending Double Optical Gating to the Midinfrared

    Science.gov (United States)

    Gorman, Timothy; Camper, Antoine; Agostini, Pierre; Dimauro, Louis

    2015-05-01

    In the past decade there has been great interest in creating broadband isolated attosecond pulses (IAPs). Primarily these IAPs have been generated using Ti:Sapphire 800nm short pulses, namely through spatiotemporal gating with the attosecond lighthouse technique, amplitude gating, polarization gating, and double optical gating (DOG). Here we present theoretical calculations and experimental investigations into extending DOG to using a 2 μm driving wavelength, the benefits of which include extended harmonic cutoff and longer input driving pulse durations. It is proposed that broadband IAPs with cutoffs extending up to 250 eV can be generated in Argon by using >30 fs pulses from the passively-CEP stabilized 2 μm idler out of an optical parametric amplifier combined with a collinear DOG experimental setup.

  9. Ultrathin gate valve for high vacuum operation

    Science.gov (United States)

    Ugiansky, R. J.

    1971-01-01

    Thin, compact, high-vacuum gate valve used to join two vacuum systems together demonstrates multiple operation reliability. Valve measurements and non-protruding handle make valve usable in confined areas.

  10. 2010 ARRA Lidar: Golden Gate (CA)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Golden Gate LiDAR Project is a cooperative project sponsored by the US Geological Survey (USGS) and San Francisco State University (SFSU) that has resulted in...

  11. GATING SYSTEMS FOR PRODUCTION OF HYDRODISTRIBUTORS

    Directory of Open Access Journals (Sweden)

    D. A. Volkov

    2010-01-01

    Full Text Available Gating systems of the first group of special ways of casting into shell molds, casting in lined chill mold as more effective for production of hydrodistributors were developed and studied.

  12. Smart gating membranes with in situ self-assembled responsive nanogels as functional gates

    Science.gov (United States)

    Luo, Feng; Xie, Rui; Liu, Zhuang; Ju, Xiao-Jie; Wang, Wei; Lin, Shuo; Chu, Liang-Yin

    2015-01-01

    Smart gating membranes, inspired by the gating function of ion channels across cell membranes, are artificial membranes composed of non-responsive porous membrane substrates and responsive gates in the membrane pores that are able to dramatically regulate the trans-membrane transport of substances in response to environmental stimuli. Easy fabrication, high flux, significant response and strong mechanical strength are critical for the versatility of such smart gating membranes. Here we show a novel and simple strategy for one-step fabrication of smart gating membranes with three-dimensionally interconnected networks of functional gates, by self-assembling responsive nanogels on membrane pore surfaces in situ during a vapor-induced phase separation process for membrane formation. The smart gating membranes with in situ self-assembled responsive nanogels as functional gates show large flux, significant response and excellent mechanical property simultaneously. Because of the easy fabrication method as well as the concurrent enhancement of flux, response and mechanical property, the proposed smart gating membranes will expand the scope of membrane applications, and provide ever better performances in their applications. PMID:26434387

  13. Crystalline silicotitanate gate review analysis

    International Nuclear Information System (INIS)

    Schlahta, S.N.; Carreon, R.; Gentilucci, J.A.

    1997-11-01

    Crystalline silicotitanate (CST) is an ion-exchange method for removing radioactive cesium from tank waste to allow the separation of the waste into high- and low-level fractions. The CST, originally developed Sandia National Laboratories personnel in association with Union Oil Products Corporation, has both a high affinity and selectivity for sorbing cesium-137 from highly alkaline or acidic solutions. For several years now, the U.S. Department of Energy has funded work to investigate applying CST to large-scale removal of cesium-137 from radioactive tank wastes. In January 1997, an expert panel sponsored by the Tanks Focus Area met to review the current state of the technology and to determine whether it was ready for routine use. The review also sought to identify any technical issues that must be resolved or additional CST development that must occur before full implementation by end-users. The CST Gate Review Group concluded that sufficient work has been done to close developmental work on CST and turn the remaining site-specific tasks over to the users. This report documents the review group''s findings, issues, concerns, and recommendations as well as responses from the Tanks Focus Area expert staff to specific pretreatment and immobilization issues

  14. Range gated strip proximity sensor

    Science.gov (United States)

    McEwan, T.E.

    1996-12-03

    A range gated strip proximity sensor uses one set of sensor electronics and a distributed antenna or strip which extends along the perimeter to be sensed. A micro-power RF transmitter is coupled to the first end of the strip and transmits a sequence of RF pulses on the strip to produce a sensor field along the strip. A receiver is coupled to the second end of the strip, and generates a field reference signal in response to the sequence of pulse on the line combined with received electromagnetic energy from reflections in the field. The sensor signals comprise pulses of radio frequency signals having a duration of less than 10 nanoseconds, and a pulse repetition rate on the order of 1 to 10 MegaHertz or less. The duration of the radio frequency pulses is adjusted to control the range of the sensor. An RF detector feeds a filter capacitor in response to received pulses on the strip line to produce a field reference signal representing the average amplitude of the received pulses. When a received pulse is mixed with a received echo, the mixing causes a fluctuation in the amplitude of the field reference signal, providing a range-limited Doppler type signature of a field disturbance. 6 figs.

  15. Boolean gates on actin filaments

    Science.gov (United States)

    Siccardi, Stefano; Tuszynski, Jack A.; Adamatzky, Andrew

    2016-01-01

    Actin is a globular protein which forms long polar filaments in the eukaryotic cytoskeleton. Actin networks play a key role in cell mechanics and cell motility. They have also been implicated in information transmission and processing, memory and learning in neuronal cells. The actin filaments have been shown to support propagation of voltage pulses. Here we apply a coupled nonlinear transmission line model of actin filaments to study interactions between voltage pulses. To represent digital information we assign a logical TRUTH value to the presence of a voltage pulse in a given location of the actin filament, and FALSE to the pulse's absence, so that information flows along the filament with pulse transmission. When two pulses, representing Boolean values of input variables, interact, then they can facilitate or inhibit further propagation of each other. We explore this phenomenon to construct Boolean logical gates and a one-bit half-adder with interacting voltage pulses. We discuss implications of these findings on cellular process and technological applications.

  16. Induced Cavities for Photonic Quantum Gates

    Science.gov (United States)

    Lahad, Ohr; Firstenberg, Ofer

    2017-09-01

    Effective cavities can be optically induced in atomic media and employed to strengthen optical nonlinearities. Here we study the integration of induced cavities with a photonic quantum gate based on Rydberg blockade. Accounting for loss in the atomic medium, we calculate the corresponding finesse and gate infidelity. Our analysis shows that the conventional limits imposed by the blockade optical depth are mitigated by the induced cavity in long media, thus establishing the total optical depth of the medium as a complementary resource.

  17. Entanglement and Quantum Logical Gates. Part I.

    Science.gov (United States)

    Freytes, H.; Giuntini, R.; Leporini, R.; Sergioli, G.

    2015-12-01

    Is it possible to give a logical characterization of entanglement and of entanglement-measures in terms of the probabilistic behavior of some gates? This question admits different (positive or negative) answers in the case of different systems of gates and in the case of different classes of density operators. In the first part of this article we investigate possible relations between entanglement-measures and the probabilistic behavior of quantum computational conjunctions.

  18. Dual-gated volumetric modulated arc therapy

    International Nuclear Information System (INIS)

    Fahimian, Benjamin; Wu, Junqing; Wu, Huanmei; Geneser, Sarah; Xing, Lei

    2014-01-01

    Gated Volumetric Modulated Arc Therapy (VMAT) is an emerging radiation therapy modality for treatment of tumors affected by respiratory motion. However, gating significantly prolongs the treatment time, as delivery is only activated during a single respiratory phase. To enhance the efficiency of gated VMAT delivery, a novel dual-gated VMAT (DG-VMAT) technique, in which delivery is executed at both exhale and inhale phases in a given arc rotation, is developed and experimentally evaluated. Arc delivery at two phases is realized by sequentially interleaving control points consisting of MUs, MLC sequences, and angles of VMAT plans generated at the exhale and inhale phases. Dual-gated delivery is initiated when a respiration gating signal enters the exhale window; when the exhale delivery concludes, the beam turns off and the gantry rolls back to the starting position for the inhale window. The process is then repeated until both inhale and exhale arcs are fully delivered. DG-VMAT plan delivery accuracy was assessed using a pinpoint chamber and diode array phantom undergoing programmed motion. DG-VMAT delivery was experimentally implemented through custom XML scripting in Varian’s TrueBeam™ STx Developer Mode. Relative to single gated delivery at exhale, the treatment time was improved by 95.5% for a sinusoidal breathing pattern. The pinpoint chamber dose measurement agreed with the calculated dose within 0.7%. For the DG-VMAT delivery, 97.5% of the diode array measurements passed the 3%/3 mm gamma criterion. The feasibility of DG-VMAT delivery scheme has been experimentally demonstrated for the first time. By leveraging the stability and natural pauses that occur at end-inspiration and end-exhalation, DG-VMAT provides a practical method for enhancing gated delivery efficiency by up to a factor of two

  19. Phosphorylation of the parsley bZIP transcription factor CPRF2 is regulated by light.

    Science.gov (United States)

    Wellmer, F; Kircher, S; Rügner, A; Frohnmeyer, H; Schäfer, E; Harter, K

    1999-10-08

    The analysis of the complex network of signal transduction chains has demonstrated the importance of transcription factor activities for the control of gene expression. To understand how transcription factor activities in plants are regulated in response to light, we analyzed the common plant regulatory factor 2 (CPRF2) from parsley (Petroselinum crispum L.) that interacts with promoter elements of light-regulated genes. Here, we demonstrate that CPRF2 is a phosphoprotein in vivo and that its phosphorylation state is rapidly increased in response to light. Phosphorylation in vitro as well as in vivo occurs primarily within the C-terminal half of the factor, and is caused by a cytosolic 40-kDa protein serine kinase. In contrast to other plant basic leucine-zipper motif factors, phosphorylation of CPRF2 does not alter its DNA binding activity. Therefore, we discuss alternative functions of the light-dependent phosphorylation of CPRF2 including the regulation of its nucleocytoplasmic partitioning.

  20. DNA computation in mammalian cells: microRNA logic operations.

    Science.gov (United States)

    Hemphill, James; Deiters, Alexander

    2013-07-17

    DNA computation can utilize logic gates as modules to create molecular computers with biological inputs. Modular circuits that recognize nucleic acid inputs through strand hybridization activate computation cascades to produce controlled outputs. This allows for the construction of synthetic circuits that can be interfaced with cellular environments. We have engineered oligonucleotide AND gates to respond to specific microRNA (miRNA) inputs in live mammalian cells. Both single and dual-sensing miRNA-based computation devices were synthesized for the cell-specific identification of endogenous miR-21 and miR-122. A logic gate response was observed with miRNA expression regulators, exhibiting molecular recognition of miRNA profile changes. Nucleic acid logic gates that are functional in a cellular environment and recognize endogenous inputs significantly expand the potential of DNA computation to monitor, image, and respond to cell-specific markers.

  1. Cognitive mechanisms associated with auditory sensory gating.

    Science.gov (United States)

    Jones, L A; Hills, P J; Dick, K M; Jones, S P; Bright, P

    2016-02-01

    Sensory gating is a neurophysiological measure of inhibition that is characterised by a reduction in the P50 event-related potential to a repeated identical stimulus. The objective of this work was to determine the cognitive mechanisms that relate to the neurological phenomenon of auditory sensory gating. Sixty participants underwent a battery of 10 cognitive tasks, including qualitatively different measures of attentional inhibition, working memory, and fluid intelligence. Participants additionally completed a paired-stimulus paradigm as a measure of auditory sensory gating. A correlational analysis revealed that several tasks correlated significantly with sensory gating. However once fluid intelligence and working memory were accounted for, only a measure of latent inhibition and accuracy scores on the continuous performance task showed significant sensitivity to sensory gating. We conclude that sensory gating reflects the identification of goal-irrelevant information at the encoding (input) stage and the subsequent ability to selectively attend to goal-relevant information based on that previous identification. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  2. Sensory gating deficits in parents of schizophrenics

    Energy Technology Data Exchange (ETDEWEB)

    Waldo, M.; Madison, A.; Freedman, R. [Univ. of Colorado Health Sciences Center, Denver, CO (United States)] [and others

    1995-12-18

    Although schizophrenia clusters in families, it is not inherited in Mendelian fashion. This suggests that there may be alternative phenotypic expressions of genes that convey risk for schizophrenia, such as more elementary physiological or biochemical defects. One proposed phenotype is impaired inhibitory gating of the auditory evoked potential to repeated stimuli. Normally, the amplitude of the P50 response to the second stimulus is significantly less than the response to the first, but this gating of response is generally impaired in schizophrenia. Clinically unaffected individuals within a pedigree who have both an ancestral and descendant history of schizophrenia may be useful for studying whether this physiological defect is a possible alternative phenotype. We have studied inhibitory gating of the auditory P50 response to pairs of auditory stimuli in 17 nuclear families. In 11, there was one parent who had another relative with a chronic psychotic illness, in addition to the schizophrenic proband. AR of the parents with family histories of schizophrenia had gating of the P50 response similar to their schizophrenia offspring, whereas only 7% of the parents without family history had gating of the P50 response in the abnormal range. These results support loss of gating of the auditory P50 wave as an inherited deficit related to schizophrenia and suggest that studies of parents may help elucidate the neurobiological expression of genes that convey risk for schizophrenia. 36 refs., 2 figs., 2 tabs.

  3. VKCDB: Voltage-gated potassium channel database

    Directory of Open Access Journals (Sweden)

    Gallin Warren J

    2004-01-01

    Full Text Available Abstract Background The family of voltage-gated potassium channels comprises a functionally diverse group of membrane proteins. They help maintain and regulate the potassium ion-based component of the membrane potential and are thus central to many critical physiological processes. VKCDB (Voltage-gated potassium [K] Channel DataBase is a database of structural and functional data on these channels. It is designed as a resource for research on the molecular basis of voltage-gated potassium channel function. Description Voltage-gated potassium channel sequences were identified by using BLASTP to search GENBANK and SWISSPROT. Annotations for all voltage-gated potassium channels were selectively parsed and integrated into VKCDB. Electrophysiological and pharmacological data for the channels were collected from published journal articles. Transmembrane domain predictions by TMHMM and PHD are included for each VKCDB entry. Multiple sequence alignments of conserved domains of channels of the four Kv families and the KCNQ family are also included. Currently VKCDB contains 346 channel entries. It can be browsed and searched using a set of functionally relevant categories. Protein sequences can also be searched using a local BLAST engine. Conclusions VKCDB is a resource for comparative studies of voltage-gated potassium channels. The methods used to construct VKCDB are general; they can be used to create specialized databases for other protein families. VKCDB is accessible at http://vkcdb.biology.ualberta.ca.

  4. A novel Glycine soja homeodomain-leucine zipper (HD-Zip) I gene, Gshdz4, positively regulates bicarbonate tolerance and responds to osmotic stress in Arabidopsis.

    Science.gov (United States)

    Cao, Lei; Yu, Yang; DuanMu, Huizi; Chen, Chao; Duan, Xiangbo; Zhu, Pinghui; Chen, Ranran; Li, Qiang; Zhu, Yanming; Ding, Xiaodong

    2016-08-24

    Wild soybean (Glycine soja) is a highly adaptive plant species which can grow well in saline-alkaline soils. In soybean genome, there exist about 140 HD-Zip (Homeodomain-leucine Zipper) genes. HD-Zip transcription factor family is one of the largest plant specific superfamilies and plays important roles in response to abiotic stresses. Although HD-Zip transcription factors have been broadly reported to be involved in plant resistance to abiotic stresses like salt and drought, their roles in response to bicarbonate stress is largely unknown. From our previous transcriptome profile analysis of wild soybean treated by 50 mM NaHCO3, we identified an HD-Zip gene (Gshdz4) which showed high response to the alkaline stress. Our result of qRT-PCR showed that the expression of Gshdz4 was induced by alkaline stress (NaHCO3) in both leaves and roots of wild soybean. Overexpression of Gshdz4 in Arabidopsis resulted in enhanced tolerance to NaHCO3 and KHCO3 during the process of plant growth and development. However, the growths of transgenic and WT plants were not significantly different on the medium with high pH adjusted by KOH, implicating Gshdz4 is only responsible for resisting HCO3 (-) but not high pH. The transgenic plants had less MDA contents but higher POD activities and chlorophyll contents than the WT plants. Moreover, the transcript levels of stress-related genes, such as NADP-ME, H (+) -Ppase, RD29B and KIN1 were increased with greater extent in the transgenic plants than the wild plants. On the contrary, Gshdz4 overexpression lines were much sensitive to osmotic stress at seed germination and stocking stages compared to the wild plants. We revealed that the important and special roles of Gshdz4 in enhancing bicarbonate tolerance and responding to osmotic stress. It is the first time to elucidate these novel functions of HD-ZIP transcription factors. All the evidences broaden our understanding of functions of HD-Zip family and provide clues for uncovering the

  5. A bio-inspired, sensitive, and selective ionic gate driven by silver (I) ions.

    Science.gov (United States)

    Gao, Loujun; Li, Pei; Zhang, Yuqi; Xiao, Kai; Ma, Jie; Xie, Ganhua; Hou, Guanglei; Zhang, Zhen; Wen, Liping; Jiang, Lei

    2015-02-04

    By grafting specific response DNA on the interior surface of ion track-etched conical nanochannels, a highly sensitive and selective ionic gate that can be driven by silver (I) ions is demonstrated. The switches between the OFF-state and the ON-state are mainly dependent on silver (I) ions and cysteine. Such a biomimetic nanodevice shows potential for application in sensing, pharmaceuticals, and sterilization. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases.

    Science.gov (United States)

    Laponogov, Ivan; Sohi, Maninder K; Veselkov, Dennis A; Pan, Xiao-Su; Sawhney, Ritica; Thompson, Andrew W; McAuley, Katherine E; Fisher, L Mark; Sanderson, Mark R

    2009-06-01

    Type II topoisomerases alter DNA topology by forming a covalent DNA-cleavage complex that allows DNA transport through a double-stranded DNA break. We present the structures of cleavage complexes formed by the Streptococcus pneumoniae ParC breakage-reunion and ParE TOPRIM domains of topoisomerase IV stabilized by moxifloxacin and clinafloxacin, two antipneumococcal fluoroquinolones. These structures reveal two drug molecules intercalated at the highly bent DNA gate and help explain antibacterial quinolone action and resistance.

  7. Gallium arsenide processing for gate array logic

    Science.gov (United States)

    Cole, Eric D.

    1989-01-01

    The development of a reliable and reproducible GaAs process was initiated for applications in gate array logic. Gallium Arsenide is an extremely important material for high speed electronic applications in both digital and analog circuits since its electron mobility is 3 to 5 times that of silicon, this allows for faster switching times for devices fabricated with it. Unfortunately GaAs is an extremely difficult material to process with respect to silicon and since it includes the arsenic component GaAs can be quite dangerous (toxic) especially during some heating steps. The first stage of the research was directed at developing a simple process to produce GaAs MESFETs. The MESFET (MEtal Semiconductor Field Effect Transistor) is the most useful, practical and simple active device which can be fabricated in GaAs. It utilizes an ohmic source and drain contact separated by a Schottky gate. The gate width is typically a few microns. Several process steps were required to produce a good working device including ion implantation, photolithography, thermal annealing, and metal deposition. A process was designed to reduce the total number of steps to a minimum so as to reduce possible errors. The first run produced no good devices. The problem occurred during an aluminum etch step while defining the gate contacts. It was found that the chemical etchant attacked the GaAs causing trenching and subsequent severing of the active gate region from the rest of the device. Thus all devices appeared as open circuits. This problem is being corrected and since it was the last step in the process correction should be successful. The second planned stage involves the circuit assembly of the discrete MESFETs into logic gates for test and analysis. Finally the third stage is to incorporate the designed process with the tested circuit in a layout that would produce the gate array as a GaAs integrated circuit.

  8. The zygomatic implant perforated (ZIP) flap: a new technique for combined surgical reconstruction and rapid fixed dental rehabilitation following low-level maxillectomy

    OpenAIRE

    Butterworth, C. J.; Rogers, S. N.

    2017-01-01

    This aim of this report is to describe the development and evolution of a new surgical technique for the immediate surgical reconstruction and rapid post-operative prosthodontic rehabilitation with a fixed dental prosthesis following low-level maxillectomy for malignant disease. The technique involves the use of a zygomatic oncology implant perforated micro-vascular soft tissue flap (ZIP flap) for the primary management of maxillary malignancy with surgical closure of the resultant maxillary ...

  9. Single-molecule Förster resonance energy transfer (FRET) analysis discloses the dynamics of the DNA-topoisomerase II (Top2) interaction in the presence of TOP2-targeting agents.

    Science.gov (United States)

    Huang, Wan-Chen; Lee, Chun-Ying; Hsieh, Tao-Shih

    2017-07-28

    Topoisomerases play crucial roles in DNA replication, transcription, and recombination. For instance, topoisomerase II (Top2) is critically important for resolving DNA tangles during cell division, and as such, it is a broad anticancer drug target. Top2 regulates DNA topology by transiently breaking one double-stranded DNA molecule (cleavage), allowing a second double strand to pass through the opened DNA gate (opening), and then closing the gate by rejoining the broken ends. Drugs that modulate Top2 catalysis may therefore affect enzymatic activity at several different steps. Previous studies have focused on examining DNA cleavage and ligation; however, the dynamic opening and closing of the DNA gate has been less explored. Here, we used the single-molecule Förster resonance energy transfer (smFRET) method to observe the open and closed state of the DNA gate and to measure dwell times in each state. Our results show that Top2 binds and bends DNA to increase the energy transfer efficiency ( E FRET ), and ATP treatment further induces the fluctuation of E FRET , representing the gate opening and closing. Additionally, our results demonstrate that both types of Top2-targeting anticancer drugs, the catalytic inhibitor dexrazoxane (ICRF187) and mechanistic poison teniposide (VM26), can interfere with DNA gate dynamics and shorten the dwell time in the closed state. Moreover, Top2 bound to the nonhydrolyzable ATP analog 5'-adenylyl-β,γ-imidodiphosphate exhibits altered DNA gate dynamics, but the DNA gate appears to open and close even after N-gate closure. In summary, we have utilized single-molecule detection to unravel Top2 DNA gate dynamics and reveal previously unknown effects of Top2 drugs on these dynamics. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. A realistic 3-D gated cardiac phantom for quality control of gated myocardial perfusion SPET: the Amsterdam gated (AGATE) cardiac phantom

    NARCIS (Netherlands)

    Visser, Jacco J. N.; Sokole, Ellinor Busemann; Verberne, Hein J.; Habraken, Jan B. A.; van de Stadt, Huybert J. F.; Jaspers, Joris E. N.; Shehata, Morgan; Heeman, Paul M.; van Eck-Smit, Berthe L. F.

    2004-01-01

    A realistic 3-D gated cardiac phantom with known left ventricular (LV) volumes and ejection fractions (EFs) was produced to evaluate quantitative measurements obtained from gated myocardial single-photon emission tomography (SPET). The 3-D gated cardiac phantom was designed and constructed to fit

  11. Palladium gates for reproducible quantum dots in silicon.

    Science.gov (United States)

    Brauns, Matthias; Amitonov, Sergey V; Spruijtenburg, Paul-Christiaan; Zwanenburg, Floris A

    2018-04-09

    We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack.

  12. Environmental regulation of lateral root emergence in Medicago truncatula requires the HD-Zip I transcription factor HB1.

    Science.gov (United States)

    Ariel, Federico; Diet, Anouck; Verdenaud, Marion; Gruber, Véronique; Frugier, Florian; Chan, Raquel; Crespi, Martin

    2010-07-01

    The adaptation of root architecture to environmental constraints is a major agricultural trait, notably in legumes, the third main crop worldwide. This root developmental plasticity depends on the formation of lateral roots (LRs) emerging from primary roots. In the model legume Medicago truncatula, the HD-Zip I transcription factor HB1 is expressed in primary and lateral root meristems and induced by salt stress. Constitutive expression of HB1 in M. truncatula roots alters their architecture, whereas hb1 TILLING mutants showed increased lateral root emergence. Electrophoretic mobility shift assay, promoter mutagenesis, and chromatin immunoprecipitation-PCR assays revealed that HB1 directly recognizes a CAATAATTG cis-element present in the promoter of a LOB-like (for Lateral Organ Boundaries) gene, LBD1, transcriptionally regulated by auxin. Expression of these genes in response to abscisic acid and auxin and their behavior in hb1 mutants revealed an HB1-mediated repression of LBD1 acting during LR emergence. M. truncatula HB1 regulates an adaptive developmental response to minimize the root surface exposed to adverse environmental stresses.

  13. Nuclear Import of the Parsley bZIP Transcription Factor CPRF2 Is Regulated by Phytochrome Photoreceptors

    Science.gov (United States)

    Kircher, Stefan; Wellmer, Frank; Nick, Peter; Rügner, Alexander; Schäfer, Eberhard; Harter, Klaus

    1999-01-01

    In plants, light perception by photoreceptors leads to differential expression of an enormous number of genes. An important step for differential gene expression is the regulation of transcription factor activities. To understand these processes in light signal transduction we analyzed the three well-known members of the common plant regulatory factor (CPRF) family from parsley (Petroselinum crispum). Here, we demonstrate that these CPRFs, which belong to the basic- region leucine-zipper (bZIP) domain-containing transcription factors, are differentially distributed within parsley cells, indicating different regulatory functions within the regulatory networks of the plant cell. In particular, we show by cell fractionation and immunolocalization approaches that CPRF2 is transported from the cytosol into the nucleus upon irradiation due to action of phytochrome photoreceptors. Two NH2-terminal domains responsible for cytoplasmic localization of CPRF2 in the dark were characterized by deletion analysis using a set of CPRF2-green fluorescent protein (GFP) gene fusion constructs transiently expressed in parsley protoplasts. We suggest that light-induced nuclear import of CPRF2 is an essential step in phytochrome signal transduction. PMID:9922448

  14. JUNGBRUNNEN1 Confers Drought Tolerance Downstream of the HD-Zip I Transcription Factor AtHB13

    Directory of Open Access Journals (Sweden)

    Saghar Ebrahimian-Motlagh

    2017-12-01

    Full Text Available Low water availability is the major environmental factor limiting growth and productivity of plants and crops and is therefore considered of high importance for agriculture affected by climate change. Identifying regulatory components controlling the response and tolerance to drought stress is thus of major importance. The NAC transcription factor (TF JUNGBRUNNEN1 (JUB1 from Arabidopsis thaliana extends leaf longevity under non-stress growth conditions, lowers cellular hydrogen peroxide (H2O2 level, and enhances tolerance against heat stress and salinity. Here, we additionally find that JUB1 strongly increases tolerance to drought stress in Arabidopsis when expressed from both, a constitutive (CaMV 35S and an abiotic stress-induced (RD29A promoter. Employing a yeast one-hybrid screen we identified HD-Zip class I TF AtHB13 as an upstream regulator of JUB1. AtHB13 has previously been reported to act as a positive regulator of drought tolerance. AtHB13 and JUB1 thereby establish a joint drought stress control module.

  15. Development of T cell lymphoma in HTLV-1 bZIP factor and Tax double transgenic mice.

    Science.gov (United States)

    Zhao, Tiejun; Satou, Yorifumi; Matsuoka, Masao

    2014-07-01

    Adult T-cell leukemia (ATL) is an aggressive T-cell malignancy caused by human T-cell leukemia virus type 1 (HTLV-1). ATL cells possess a CD4+ CD25+ phenotype, similar to that of regulatory T cells (Tregs). Tax has been reported to play a crucial role in the leukemogenesis of HTLV-1. The HTLV-1 bZIP factor (HBZ), which is encoded by the minus strand of the viral genomic RNA, is expressed in all ATL cases and induces neoplastic and inflammatory disease in vivo. To test whether HBZ and Tax are both required for T cell malignancy, we generated HBZ/Tax double transgenic mice in which HBZ and Tax are expressed exclusively in CD4+ T cells. Survival was much reduced in HBZ/Tax double-transgenic mice compared with wild type littermates. Transgenic expression of HBZ and Tax induced skin lesions and T-cell lymphoma in mice, resembling diseases observed in HTLV-1 infected individuals. However, Tax single transgenic mice did not develop major health problems. In addition, memory CD4+ T cells and Foxp3+ Treg cells counts were increased in HBZ/Tax double transgenic mice, and their proliferation was enhanced. There was very little difference between HBZ single and HBZ/Tax double transgenic mice. Taken together, these results show that HBZ, in addition to Tax, plays a critical role in T-cell lymphoma arising from HTLV-1 infection.

  16. Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway.

    Science.gov (United States)

    McEwan, Deborah L; Feinbaum, Rhonda L; Stroustrup, Nicholas; Haas, Wilhelm; Conery, Annie L; Anselmo, Anthony; Sadreyev, Ruslan; Ausubel, Frederick M

    2016-12-07

    Many pathogens secrete toxins that target key host processes resulting in the activation of immune pathways. The secreted Pseudomonas aeruginosa toxin Exotoxin A (ToxA) disrupts intestinal protein synthesis, which triggers the induction of a subset of P. aeruginosa-response genes in the nematode Caenorhabditis elegans. We show here that one ToxA-induced C. elegans gene, the Tribbles pseudokinase ortholog nipi-3, is essential for host survival following exposure to P. aeruginosa or ToxA. We find that NIPI-3 mediates the post-developmental expression of intestinal immune genes and proteins and primarily functions in parallel to known immune pathways, including p38 MAPK signaling. Through mutagenesis screening, we identify mutants of the bZIP C/EBP transcription factor cebp-1 that suppress the hypersusceptibility defects of nipi-3 mutants. NIPI-3 is a negative regulator of CEBP-1, which in turn negatively regulates protective immune mechanisms. This pathway represents a previously unknown innate immune signaling pathway in intestinal epithelial cells that is involved in the surveillance of cellular homeostasis. Because NIPI-3 and CEBP-1 are also essential for C. elegans development, NIPI-3 is analogous to other key innate immune signaling molecules such as the Toll receptors in Drosophila that have an independent role during development.

  17. BnaA.bZIP1 Negatively Regulates a Novel Small Peptide Gene, BnaC.SP6, Involved in Pollen Activity

    Directory of Open Access Journals (Sweden)

    Xuanpeng Wang

    2017-12-01

    Full Text Available Small peptides secreted to the extracellular matrix control many aspects of the plant’s physiological activities which were identified in Arabidopsis thaliana, called ATSPs. Here, we isolated and characterized the small peptide gene Bna.SP6 from Brassica napus. The BnaC.SP6 promoter was cloned and identified. Promoter deletion analysis suggested that the -447 to -375 and -210 to -135 regions are crucial for the silique septum and pollen expression of BnaC.SP6, respectively. Furthermore, the minimal promoter region of p158 (-210 to -52 was sufficient for driving gene expression specifically in pollen and highly conserved in Brassica species. In addition, BnaA.bZIP1 was predominantly expressed in anthers where BnaC.SP6 was also expressed, and was localized to the nuclei. BnaA.bZIP1 possessed transcriptional activation activity in yeast and protoplast system. It could specifically bind to the C-box in p158 in vitro, and negatively regulate p158 activity in vivo. BnaA.bZIP1 functions as a transcriptional repressor of BnaC.SP6 in pollen activity. These results provide novel insight into the transcriptional regulation of BnaC.SP6 in pollen activity and the pollen/anther-specific promoter regions of BnaC.SP6 may have their potential agricultural application for new male sterility line generation.

  18. Instantons in Self-Organizing Logic Gates

    Science.gov (United States)

    Bearden, Sean R. B.; Manukian, Haik; Traversa, Fabio L.; Di Ventra, Massimiliano

    2018-03-01

    Self-organizing logic is a recently suggested framework that allows the solution of Boolean truth tables "in reverse"; i.e., it is able to satisfy the logical proposition of gates regardless to which terminal(s) the truth value is assigned ("terminal-agnostic logic"). It can be realized if time nonlocality (memory) is present. A practical realization of self-organizing logic gates (SOLGs) can be done by combining circuit elements with and without memory. By employing one such realization, we show, numerically, that SOLGs exploit elementary instantons to reach equilibrium points. Instantons are classical trajectories of the nonlinear equations of motion describing SOLGs and connect topologically distinct critical points in the phase space. By linear analysis at those points, we show that these instantons connect the initial critical point of the dynamics, with at least one unstable direction, directly to the final fixed point. We also show that the memory content of these gates affects only the relaxation time to reach the logically consistent solution. Finally, we demonstrate, by solving the corresponding stochastic differential equations, that, since instantons connect critical points, noise and perturbations may change the instanton trajectory in the phase space but not the initial and final critical points. Therefore, even for extremely large noise levels, the gates self-organize to the correct solution. Our work provides a physical understanding of, and can serve as an inspiration for, models of bidirectional logic gates that are emerging as important tools in physics-inspired, unconventional computing.

  19. Iron Gates Natural Park - Administration and Management

    Directory of Open Access Journals (Sweden)

    Sînziana Pauliuc

    2016-11-01

    Full Text Available This paper analyzes the management and administration of one of the largest, beautiful and complex natural parks from Romania, the Iron Gates Natural Park. The management plan is a frame of integration of the biodiversity conservation problems and protection of the natural and cultural environment that also supports socio-economic development of Iron Gates Natural Park. It is also an instrument of dialog between the institutions which coordinate this area. The management plan is a document approved by H.G 1048/2013 and it resulted after consulting the interested factors of the area (city halls, local and central authorities, civil society. The administration of Iron Gates Natural Park has a new structure, founded in 2003 and is working as a subunit of Forest-National Administration (Romsilva, which assures the necessary personal and equipment for administrating the area. The area has the status of: Natural Park, Natura 2000 and Ramsar site. The forest represents 65% of the total area, 98% being a state property. Analysing Iron Gates Natural Park documents (Iron Gates Natural Park management plan, scientific council and park administration documents, visits and observations within park, we can conclude that the park has a good administration leaded by the scientific councils, who also achieved many successful European projects.

  20. The pollution of the 'iron gate' reservoir

    International Nuclear Information System (INIS)

    Babic-Mladenovic, M.; Varga, S; Popovic, L.; Damjanovic, M.

    2002-01-01

    The paper presents the characteristics of the Iron Gate I (the Djerdap) Water Power and Navigational System, one of the largest in Europe (completed in 1972 by joint efforts of Yugoslavia and Romania). In this paper the attention is devoted to review of the sediment monitoring program and impacts of reservoir sedimentation, as well as to the investigations of water and sediment quality. Special consideration is paid to the issue of sediment pollution research needs. Namely, the hot spot of the 'Iron Gate' sedimentation represents a scarcely known pollution of sediment deposits. The present pollution probably is considerable, since the 'Iron Gate' reservoir drains about 577000 km 2 , with over 80 million inhabitants, and developed municipal and industrial infrastructure. Therefore, in the thirty-year reservoir life various types of sediment-bound pollutants entered and deposited within it. Especially severe incidents happened during 1999 (as a result of NATO bombing campaign) and 2000 (two accidental pollutions in the Tisza river catchment). The study of the 'Iron Gate' reservoir pollution should be prepared in order to enlighten the present state of reservoir sedimentation and pollution. The main objectives of the study are to enhance the government and public awareness of the present environmental state of the 'Iron Gate' reservoir and to serve as a baseline for all future actions. (author)

  1. Noisy signaling through promoter logic gates.

    Science.gov (United States)

    Gerstung, Moritz; Timmer, Jens; Fleck, Christian

    2009-01-01

    We study the influence of noisy transcription factor signals on cis-regulatory promoter elements. These elements process the probability of binary binding events analogous to computer logic gates. At equilibrium, this probability is given by the so-called input function. We show that transcription factor noise causes deviations from the equilibrium value due to the nonlinearity of the input function. For a single binding site, the correction is always negative resulting in an occupancy below the mean-field level. Yet for more complex promoters it depends on the correlation of the transcription factor signals and the geometry of the input function. We present explicit solutions for the basic types of AND and OR gates. The correction size varies among these different types of gates and signal types, mainly being larger in AND gates and for correlated fluctuations. In all cases we find excellent agreement between the analytical results and numerical simulations. We also study the E. coli Lac operon as an example of an AND NOR gate. We present a consistent mathematical method that allows one to separate different sources of noise and quantifies their effect on promoter occupation. A surprising result of our analysis is that Poissonian molecular fluctuations, in contrast to external fluctuations, do no contribute to the correction.

  2. Activator Protein-1: redox switch controlling structure and DNA-binding

    Energy Technology Data Exchange (ETDEWEB)

    Yin, Zhou; Machius, Mischa; Nestler, Eric J.; Rudenko, Gabby (Texas-MED); (Icahn)

    2017-09-07

    The transcription factor, activator protein-1 (AP-1), binds to cognate DNA under redox control; yet, the underlying mechanism has remained enigmatic. A series of crystal structures of the AP-1 FosB/JunD bZIP domains reveal ordered DNA-binding regions in both FosB and JunD even in absence DNA. However, while JunD is competent to bind DNA, the FosB bZIP domain must undergo a large conformational rearrangement that is controlled by a ‘redox switch’ centered on an inter-molecular disulfide bond. Solution studies confirm that FosB/JunD cannot undergo structural transition and bind DNA when the redox-switch is in the ‘OFF’ state, and show that the mid-point redox potential of the redox switch affords it sensitivity to cellular redox homeostasis. The molecular and structural studies presented here thus reveal the mechanism underlying redox-regulation of AP-1 Fos/Jun transcription factors and provide structural insight for therapeutic interventions targeting AP-1 proteins.

  3. Activator Protein-1: redox switch controlling structure and DNA-binding.

    Science.gov (United States)

    Yin, Zhou; Machius, Mischa; Nestler, Eric J; Rudenko, Gabby

    2017-11-02

    The transcription factor, activator protein-1 (AP-1), binds to cognate DNA under redox control; yet, the underlying mechanism has remained enigmatic. A series of crystal structures of the AP-1 FosB/JunD bZIP domains reveal ordered DNA-binding regions in both FosB and JunD even in absence DNA. However, while JunD is competent to bind DNA, the FosB bZIP domain must undergo a large conformational rearrangement that is controlled by a 'redox switch' centered on an inter-molecular disulfide bond. Solution studies confirm that FosB/JunD cannot undergo structural transition and bind DNA when the redox-switch is in the 'OFF' state, and show that the mid-point redox potential of the redox switch affords it sensitivity to cellular redox homeostasis. The molecular and structural studies presented here thus reveal the mechanism underlying redox-regulation of AP-1 Fos/Jun transcription factors and provide structural insight for therapeutic interventions targeting AP-1 proteins. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. HTLV-1 bZIP factor induces inflammation through labile Foxp3 expression.

    Directory of Open Access Journals (Sweden)

    Nanae Yamamoto-Taguchi

    2013-09-01

    Full Text Available Human T-cell leukemia virus type 1 (HTLV-1 causes both a neoplastic disease and inflammatory diseases, including HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP. The HTLV-1 basic leucine zipper factor (HBZ gene is encoded in the minus strand of the proviral DNA and is constitutively expressed in infected cells and ATL cells. HBZ increases the number of regulatory T (Treg cells by inducing the Foxp3 gene transcription. Recent studies have revealed that some CD4⁺Foxp3⁺ T cells are not terminally differentiated but have a plasticity to convert to other T-cell subsets. Induced Treg (iTreg cells tend to lose Foxp3 expression, and may acquire an effector phenotype accompanied by the production of inflammatory cytokines, such as interferon-γ (IFN-γ. In this study, we analyzed a pathogenic mechanism of chronic inflammation related with HTLV-1 infection via focusing on HBZ and Foxp3. Infiltration of lymphocytes was observed in the skin, lung and intestine of HBZ-Tg mice. As mechanisms, adhesion and migration of HBZ-expressing CD4⁺ T cells were enhanced in these mice. Foxp3⁻CD4⁺ T cells produced higher amounts of IFN-γ compared to those from non-Tg mice. Expression of Helios was reduced in Treg cells from HBZ-Tg mice and HAM/TSP patients, indicating that iTreg cells are predominant. Consistent with this finding, the conserved non-coding sequence 2 region of the Foxp3 gene was hypermethylated in Treg cells of HBZ-Tg mice, which is a characteristic of iTreg cells. Furthermore, Treg cells in the spleen of HBZ-transgenic mice tended to lose Foxp3 expression and produced an excessive amount of IFN-γ, while Foxp3 expression was stable in natural Treg cells of the thymus. HBZ enhances the generation of iTreg cells, which likely convert to Foxp3⁻T cells producing IFN-γ. The HBZ-mediated proinflammatory phenotype of CD4⁺ T cells is implicated in the pathogenesis of HTLV-1-associated inflammation.

  5. Four-gate transistor analog multiplier circuit

    Science.gov (United States)

    Mojarradi, Mohammad M. (Inventor); Blalock, Benjamin (Inventor); Cristoloveanu, Sorin (Inventor); Chen, Suheng (Inventor); Akarvardar, Kerem (Inventor)

    2011-01-01

    A differential output analog multiplier circuit utilizing four G.sup.4-FETs, each source connected to a current source. The four G.sup.4-FETs may be grouped into two pairs of two G.sup.4-FETs each, where one pair has its drains connected to a load, and the other par has its drains connected to another load. The differential output voltage is taken at the two loads. In one embodiment, for each G.sup.4-FET, the first and second junction gates are each connected together, where a first input voltage is applied to the front gates of each pair, and a second input voltage is applied to the first junction gates of each pair. Other embodiments are described and claimed.

  6. TOURISM IN THE TOURIST AREA "IRON GATES"

    Directory of Open Access Journals (Sweden)

    DINU LOREDANA

    2015-12-01

    Full Text Available This paper wants to highlight the trends of tourist demanding from the touristic area Iron Gates. We will see that the future of tourism include new forms such as those caused by the increased interest in areas with agritourism attractions or areas and portions of parks and nature reserves, which will raise the attractiveness of Danube, putting in a new pole of attraction area. Thus, we conducted a research based on survey among visitors on the tourist area "Iron Gates". The main endpoint based on survey was highlighting the motivation that determined the choice of the tourist area "Iron Gates", but also knowledge of consumer satisfaction for the tourists to the visited area (tourist product studied. The main objectives were, of course, linked with socio - economic and demographic characteristics of tourists to form a clearer picture of the motivational factors involved.

  7. Active gated imaging for automotive safety applications

    Science.gov (United States)

    Grauer, Yoav; Sonn, Ezri

    2015-03-01

    The paper presents the Active Gated Imaging System (AGIS), in relation to the automotive field. AGIS is based on a fast gated-camera equipped with a unique Gated-CMOS sensor, and a pulsed Illuminator, synchronized in the time domain to record images of a certain range of interest which are then processed by computer vision real-time algorithms. In recent years we have learned the system parameters which are most beneficial to night-time driving in terms of; field of view, illumination profile, resolution and processing power. AGIS provides also day-time imaging with additional capabilities, which enhances computer vision safety applications. AGIS provides an excellent candidate for camera-based Advanced Driver Assistance Systems (ADAS) and the path for autonomous driving, in the future, based on its outstanding low/high light-level, harsh weather conditions capabilities and 3D potential growth capabilities.

  8. The Airport Gate Assignment Problem: A Survey

    Science.gov (United States)

    Ghaleb, Mageed A.; Salem, Ahmed M.

    2014-01-01

    The airport gate assignment problem (AGAP) is one of the most important problems operations managers face daily. Many researches have been done to solve this problem and tackle its complexity. The objective of the task is assigning each flight (aircraft) to an available gate while maximizing both conveniences to passengers and the operational efficiency of airport. This objective requires a solution that provides the ability to change and update the gate assignment data on a real time basis. In this paper, we survey the state of the art of these problems and the various methods to obtain the solution. Our survey covers both theoretical and real AGAP with the description of mathematical formulations and resolution methods such as exact algorithms, heuristic algorithms, and metaheuristic algorithms. We also provide a research trend that can inspire researchers about new problems in this area. PMID:25506074

  9. Hematology - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ivo tests. Data file File name: open_tggates_hematology.zip File URL: ftp://ftp.biosciencedbc.jp/archive/ope...n-tggates/LATEST/open_tggates_hematology.zip File size: 636 KB Simple search URL ...http://togodb.biosciencedbc.jp/togodb/view/open_tggates_hematology#en Data acquisition method - Data analysi

  10. Biochemistry - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available tests. Data file File name: open_tggates_biochemistry.zip File URL: ftp://ftp.biosciencedbc.jp/archive/open-...tggates/LATEST/open_tggates_biochemistry.zip File size: 666 KB Simple search URL ...http://togodb.biosciencedbc.jp/togodb/view/open_tggates_biochemistry#en Data acquisition method - Data analy

  11. Pathological items - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available . Data file File name: open_tggates_pathology.zip File URL: ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/open_tggates_patho...b.biosciencedbc.jp/togodb/view/open_tggates_pathology#en Data acquisition method We prepared hematoxylin-eos...logy.zip File size: 89 KB Simple search URL http://togod

  12. Pressure Sensitive Insulated Gate Field Effect Transistor

    Science.gov (United States)

    Suminto, James Tjan-Meng

    A pressure sensitive insulated gate field effect transistor has been developed. The device is an elevated gate field-effect-transistor. It consists of a p-type silicon substrate in which two n^+ region, the source and drain, are formed. The gate electrode is a metal film sandwiched in an insulated micro-diaphragm resembling a pill-box which covers the gate oxide, drain, and source. The space between the gate electrode and the oxide is vacuum or an air-gap. When pressure is applied on the diaphragm it deflects and causes a change in the gate capacitance, and thus modulates the conductance of the channel between source and drain. A general theory dealing with the characteristic of this pressure sensitive insulated gate field effect transistor has been derived, and the device fabricated. The fabrication process utilizes the standard integrated circuit fabrication method. It features a batch fabrication of field effect devices followed by the batch fabrication of the deposited diaphragm on top of each field effect device. The keys steps of the diaphragm fabrication are the formation of spacer layer, formation of the diaphragm layer, and the subsequent removal of the spacer layer. The chip size of the device is 600 μm x 1050 mum. The diaphragm size is 200 μm x 200 mum. Characterization of the device has been performed. The current-voltage characteristics with pressure as parameters have been demonstrated and the current-pressure transfer curves obtained. They show non-linear characteristics as those of conventional capacitive pressure sensors. The linearity of threshold voltage versus pressure transfer curves has been demonstrated. The temperature effect on the device performances has been tested. The temperature coefficient of threshold voltage, rather than the electron mobility, has dominated the temperature coefficient of the device. Two temperature compensation schemes have been tested: one method is by connecting two identical PSIGFET in a differential amplifier

  13. Ge /Si heteronanocrystal floating gate memory

    Science.gov (United States)

    Li, Bei; Liu, Jianlin; Liu, G. F.; Yarmoff, J. A.

    2007-09-01

    Metal oxide semiconductor field effect transistor memories with Ge /Si heteronanocrystals (HNCs) as floating gate were fabricated and characterized. Ge /Si HNCs with density of 5×1011cm-2 were grown on n-type Si (100) substrate with thin tunnel oxide on the top. Enhanced device performances including longer retention time, faster programming speed, and higher charge storage capability are demonstrated compared with Si nanocrystal (NC) memories. The erasing speed and endurance performance of Ge /Si HNC memories are similar to that of Si NC devices. The results suggest that Ge /Si HNCs may be an alternative to make further floating gate memory scaling down possible.

  14. Gate-Controlled WSe2Transistors Using a Buried Triple-Gate Structure.

    Science.gov (United States)

    Müller, M R; Salazar, R; Fathipour, S; Xu, H; Kallis, K; Künzelmann, U; Seabaugh, A; Appenzeller, J; Knoch, J

    2016-12-01

    In the present paper, we show tungsten diselenide (WSe 2 ) devices that can be tuned to operate as n-type and p-type field-effect transistors (FETs) as well as band-to-band tunnel transistors on the same flake. Source, channel, and drain areas of the WSe 2 flake are adjusted, using buried triple-gate substrates with three independently controllable gates. The device characteristics found in the tunnel transistor configuration are determined by the particular geometry of the buried triple-gate structure, consistent with a simple estimation of the expected off-state behavior.

  15. Determination of prospective displacement-based gate threshold for respiratory-gated radiation delivery from retrospective phase-based gate threshold selected at 4D CT simulation

    International Nuclear Information System (INIS)

    Vedam, S.; Archambault, L.; Starkschall, G.; Mohan, R.; Beddar, S.

    2007-01-01

    Four-dimensional (4D) computed tomography (CT) imaging has found increasing importance in the localization of tumor and surrounding normal structures throughout the respiratory cycle. Based on such tumor motion information, it is possible to identify the appropriate phase interval for respiratory gated treatment planning and delivery. Such a gating phase interval is determined retrospectively based on tumor motion from internal tumor displacement. However, respiratory-gated treatment is delivered prospectively based on motion determined predominantly from an external monitor. Therefore, the simulation gate threshold determined from the retrospective phase interval selected for gating at 4D CT simulation may not correspond to the delivery gate threshold that is determined from the prospective external monitor displacement at treatment delivery. The purpose of the present work is to establish a relationship between the thresholds for respiratory gating determined at CT simulation and treatment delivery, respectively. One hundred fifty external respiratory motion traces, from 90 patients, with and without audio-visual biofeedback, are analyzed. Two respiratory phase intervals, 40%-60% and 30%-70%, are chosen for respiratory gating from the 4D CT-derived tumor motion trajectory. From residual tumor displacements within each such gating phase interval, a simulation gate threshold is defined based on (a) the average and (b) the maximum respiratory displacement within the phase interval. The duty cycle for prospective gated delivery is estimated from the proportion of external monitor displacement data points within both the selected phase interval and the simulation gate threshold. The delivery gate threshold is then determined iteratively to match the above determined duty cycle. The magnitude of the difference between such gate thresholds determined at simulation and treatment delivery is quantified in each case. Phantom motion tests yielded coincidence of simulation

  16. Gate errors in solid-state quantum-computer architectures

    International Nuclear Information System (INIS)

    Hu Xuedong; Das Sarma, S.

    2002-01-01

    We theoretically consider possible errors in solid-state quantum computation due to the interplay of the complex solid-state environment and gate imperfections. In particular, we study two examples of gate operations in the opposite ends of the gate speed spectrum, an adiabatic gate operation in electron-spin-based quantum dot quantum computation and a sudden gate operation in Cooper-pair-box superconducting quantum computation. We evaluate quantitatively the nonadiabatic operation of a two-qubit gate in a two-electron double quantum dot. We also analyze the nonsudden pulse gate in a Cooper-pair-box-based quantum-computer model. In both cases our numerical results show strong influences of the higher excited states of the system on the gate operation, clearly demonstrating the importance of a detailed understanding of the relevant Hilbert-space structure on the quantum-computer operations

  17. Improved Classical Simulation of Quantum Circuits Dominated by Clifford Gates

    Science.gov (United States)

    Bravyi, Sergey; Gosset, David

    2016-06-01

    We present a new algorithm for classical simulation of quantum circuits over the Clifford+T gate set. The runtime of the algorithm is polynomial in the number of qubits and the number of Clifford gates in the circuit but exponential in the number of T gates. The exponential scaling is sufficiently mild that the algorithm can be used in practice to simulate medium-sized quantum circuits dominated by Clifford gates. The first demonstrations of fault-tolerant quantum circuits based on 2D topological codes are likely to be dominated by Clifford gates due to a high implementation cost associated with logical T gates. Thus our algorithm may serve as a verification tool for near-term quantum computers which cannot in practice be simulated by other means. To demonstrate the power of the new method, we performed a classical simulation of a hidden shift quantum algorithm with 40 qubits, a few hundred Clifford gates, and nearly 50 T gates.

  18. A novel trench gate MOSFET with a multiple-layered gate oxide for high-reliability operation

    International Nuclear Information System (INIS)

    Kim, Sang Gi; Kah, Dong Ha; Na, Kyoung Il; Yang, Yil Suk; Koo, Jin Gun; Kim, Jong Dae; Lee, Jin Ho; Park, Hoon Soo

    2012-01-01

    Gate dielectrics in trench structures for trench gate metal oxide semiconductor field-effect transistor (MOSFET) power devices are very important to realize excellent characteristics. In this paper we describe multiple-layer gate dielectrics for trench gate MOSFETs with both thermal and chemical vapor deposition (CVD) gate oxides that exhibit excellent gate oxide properties and surface roughness. Through various trench etching experiments for better surface conditions in the trench, the optimum etching gas chemistry and etch conditions were found. The destruction of gate dielectric in trench gate MOSFET occurs at the top and the bottom trench corner edges. The structure of the gate electrode is pulled out with the polysilicon layer which is buried in the trench. Thus, high electric field operation is inevitable at the gate between source diffusion and the gate polysilicon. Moreover, the trench corner oxide suffers from the high electric field. We propose a multiple-gate dielectric structure of a thermal oxide and CVD oxide for highly reliable operation of the device. This enables trench surface smoothing and low thermal stress at the trench corners and provides the oxide thickness uniformity, giving superior device characteristics of high breakdown voltage and low leakage current. These improvements are caused by the excellent quality of the gate oxide and the good thickness uniformity that is formed at the inner trench with a specific geometrical factor.

  19. Overexpression of the transporters AtZIP1 and AtMTP1 in cassava changes zinc accumulation and partitioning

    Directory of Open Access Journals (Sweden)

    Eliana eGaitan-Solis

    2015-07-01

    Full Text Available Zinc deficiency in humans is a serious problem worldwide with an estimated one third of populations at risk for insufficient zinc in diet which leads to impairment of cognitive abilities and immune system function. The goal of this research was to increase the bioavailable zinc in the edible portion of cassava roots to improve the overall zinc nutrition of populations that rely on cassava as a dietary staple. To increase zinc concentrations, two A. thaliana genes coding for ZIP1 and MTP1 were overexpressed with a tuber-specific or constitutive promoter. Eighteen transgenic events from four constructs, out of a total of 73 events generated, showed significantly higher zinc concentrations in the edible portion of the storage root compared to the non-transgenic controls. The zinc content in the transgenic lines ranged from 4 - 73 mg/Kg Dry Weight (DW as compared to the non-transgenic control which contained 8 mg/Kg. Striking changes in whole plant phenotype such as smaller plant size and chlorotic leaves were observed in transgenic lines that over accumulated zinc. In a confined field trial five transgenic events grown for 12 months showed a range of zinc concentrations from 18 – 217 mg/Kg DW. Although the overexpression of zinc transporters was successful in increasing the zinc concentrations in 25% of the transgenic lines generated, it also resulted in a decrease in plant and tuber size and overall yield due to what appears to be zinc deficiency in the aerial parts of the plant.

  20. zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.

    Science.gov (United States)

    Sand, Andreas; Kristiansen, Martin; Pedersen, Christian N S; Mailund, Thomas

    2013-11-22

    Hidden Markov models are widely used for genome analysis as they combine ease of modelling with efficient analysis algorithms. Calculating the likelihood of a model using the forward algorithm has worst case time complexity linear in the length of the sequence and quadratic in the number of states in the model. For genome analysis, however, the length runs to millions or billions of observations, and when maximising the likelihood hundreds of evaluations are often needed. A time efficient forward algorithm is therefore a key ingredient in an efficient hidden Markov model library. We have built a software library for efficiently computing the likelihood of a hidden Markov model. The library exploits commonly occurring substrings in the input to reuse computations in the forward algorithm. In a pre-processing step our library identifies common substrings and builds a structure over the computations in the forward algorithm which can be reused. This analysis can be saved between uses of the library and is independent of concrete hidden Markov models so one preprocessing can be used to run a number of different models.Using this library, we achieve up to 78 times shorter wall-clock time for realistic whole-genome analyses with a real and reasonably complex hidden Markov model. In one particular case the analysis was performed in less than 8 minutes compared to 9.6 hours for the previously fastest library. We have implemented the preprocessing procedure and forward algorithm as a C++ library, zipHMM, with Python bindings for use in scripts. The library is available at http://birc.au.dk/software/ziphmm/.

  1. ATF3, an HTLV-1 bZip factor binding protein, promotes proliferation of adult T-cell leukemia cells

    Directory of Open Access Journals (Sweden)

    Ohshima Koichi

    2011-03-01

    Full Text Available Abstract Background Adult T-cell leukemia (ATL is an aggressive malignancy of CD4+ T-cells caused by human T-cell leukemia virus type 1 (HTLV-1. The HTLV-1 bZIP factor (HBZ gene, which is encoded by the minus strand of the viral genome, is expressed as an antisense transcript in all ATL cases. By using yeast two-hybrid screening, we identified activating transcription factor 3 (ATF3 as an HBZ-interacting protein. ATF3 has been reported to be expressed in ATL cells, but its biological significance is not known. Results Immunoprecipitation analysis confirmed that ATF3 interacts with HBZ. Expression of ATF3 was upregulated in ATL cell lines and fresh ATL cases. Reporter assay revealed that ATF3 could interfere with the HTLV-1 Tax's transactivation of the 5' proviral long terminal repeat (LTR, doing so by affecting the ATF/CRE site, as well as HBZ. Suppressing ATF3 expression inhibited proliferation and strongly reduced the viability of ATL cells. As mechanisms of growth-promoting activity of ATF3, comparative expression profiling of ATF3 knockdown cells identified candidate genes that are critical for the cell cycle and cell death, including cell division cycle 2 (CDC2 and cyclin E2. ATF3 also enhanced p53 transcriptional activity, but this activity was suppressed by HBZ. Conclusions Thus, ATF3 expression has positive and negative effects on the proliferation and survival of ATL cells. HBZ impedes its negative effects, leaving ATF3 to promote proliferation of ATL cells via mechanisms including upregulation of CDC2 and cyclin E2. Both HBZ and ATF3 suppress Tax expression, which enables infected cells to escape the host immune system.

  2. Reliability study of refractory gate gallium arsenide MESFETS

    Science.gov (United States)

    Yin, J. C. W.; Portnoy, W. M.

    1981-01-01

    Refractory gate MESFET's were fabricated as an alternative to aluminum gate devices, which have been found to be unreliable as RF power amplifiers. In order to determine the reliability of the new structures, statistics of failure and information about mechanisms of failure in refractory gate MESFET's are given. Test transistors were stressed under conditions of high temperature and forward gate current to enhance failure. Results of work at 150 C and 275 C are reported.

  3. Dynamic Power Reduction of Digital Circuits by ClockGating

    OpenAIRE

    Varsha Dewre; Rakesh Mandliya

    2017-01-01

    In this paper we have presented clock gating process for low power VLSI (very large scale integration) circuit design. Clock gating is one of the most quite often used systems in RTL to shrink dynamic power consumption without affecting the performance of the design. One process involves inserting gating requisites in the RTL, which the synthesis tool translates to clock gating cells in the clock-path of a register bank. This helps to diminish the switching activity on the clock network, ther...

  4. Tunable pulse-shaping with gated graphene nanoribbons

    DEFF Research Database (Denmark)

    Prokopeva, Ludmila; Emani, Naresh K.; Boltasseva, Alexandra

    2014-01-01

    We propose a pulse-shaper made of gated graphene nanoribbons. Simulations demonstrate tunable control over the shapes of transmitted and reflected pulses using the gating bias. Initial fabrication and characterization of graphene elements is also discussed.......We propose a pulse-shaper made of gated graphene nanoribbons. Simulations demonstrate tunable control over the shapes of transmitted and reflected pulses using the gating bias. Initial fabrication and characterization of graphene elements is also discussed....

  5. Self-gated fat-suppressed cardiac cine MRI.

    Science.gov (United States)

    Ingle, R Reeve; Santos, Juan M; Overall, William R; McConnell, Michael V; Hu, Bob S; Nishimura, Dwight G

    2015-05-01

    To develop a self-gated alternating repetition time balanced steady-state free precession (ATR-SSFP) pulse sequence for fat-suppressed cardiac cine imaging. Cardiac gating is computed retrospectively using acquired magnetic resonance self-gating data, enabling cine imaging without the need for electrocardiogram (ECG) gating. Modification of the slice-select rephasing gradients of an ATR-SSFP sequence enables the acquisition of a one-dimensional self-gating readout during the unused short repetition time (TR). Self-gating readouts are acquired during every TR of segmented, breath-held cardiac scans. A template-matching algorithm is designed to compute cardiac trigger points from the self-gating signals, and these trigger points are used for retrospective cine reconstruction. The proposed approach is compared with ECG-gated ATR-SSFP and balanced steady-state free precession in 10 volunteers and five patients. The difference of ECG and self-gating trigger times has a variability of 13 ± 11 ms (mean ± SD). Qualitative reviewer scoring and ranking indicate no statistically significant differences (P > 0.05) between self-gated and ECG-gated ATR-SSFP images. Quantitative blood-myocardial border sharpness is not significantly different among self-gated ATR-SSFP ( 0.61±0.15 mm -1), ECG-gated ATR-SSFP ( 0.61±0.15 mm -1), or conventional ECG-gated balanced steady-state free precession cine MRI ( 0.59±0.15 mm -1). The proposed self-gated ATR-SSFP sequence enables fat-suppressed cardiac cine imaging at 1.5 T without the need for ECG gating and without decreasing the imaging efficiency of ATR-SSFP. © 2014 Wiley Periodicals, Inc.

  6. Corner Office Interview: Gates Foundation's Deborah Jacobs

    Science.gov (United States)

    Miller, Rebecca

    2010-01-01

    U.S. libraries gave the world a top talent when Deborah Jacobs left her transformational role as City Librarian of Seattle in 2008 to head the Bill & Melinda Gates Foundation's Global Libraries program, the international sibling to the U.S. Libraries program. The initiative fosters national-scale projects with grantees in transitioning countries…

  7. An electronically controlled automatic security access gate

    Directory of Open Access Journals (Sweden)

    Jonathan A. ENOKELA

    2014-11-01

    Full Text Available The security challenges being encountered in many places require electronic means of controlling access to communities, recreational centres, offices, and homes. The electronically controlled automated security access gate being proposed in this work helps to prevent an unwanted access to controlled environments. This is achieved mainly through the use of a Radio Frequency (RF transmitter-receiver pair. In the design a microcontroller is programmed to decode a given sequence of keys that is entered on a keypad and commands a transmitter module to send out this code as signal at a given radio frequency. Upon reception of this RF signal by the receiver module, another microcontroller activates a driver circuitry to operate the gate automatically. The codes for the microcontrollers were written in C language and were debugged and compiled using the KEIL Micro vision 4 integrated development environment. The resultant Hex files were programmed into the memories of the microcontrollers with the aid of a universal programmer. Software simulation was carried out using the Proteus Virtual System Modeling (VSM version 7.7. A scaled-down prototype of the system was built and tested. The electronically controlled automated security access gate can be useful in providing security for homes, organizations, and automobile terminals. The four-character password required to operate the gate gives the system an increased level of security. Due to its standalone nature of operation the system is cheaper to maintain in comparison with a manually operated type.

  8. Angular momentum gated neutron evaporation studies

    International Nuclear Information System (INIS)

    Banerjee, K.; Kundu, S.; Rana, T.K.; Bhattacharya, C.; Mukherjee, G.; Gohil, M.; Meena, J.K.; Pandey, R.; Pai, H.; Dey, A.; Biswas, M.; Mukhopadhyay, S.; Pandit, D.; Pal, S.; Banerjee, S.R.; Bhattacharya, S.; Bandhopadhyay, T.

    2010-01-01

    The inverse level density parameter k (k = A/a, where A is the mass number of the compound nucleus)is investigated as a function of angular momentum by measuring γ-ray fold gated neutron evaporation spectrum in 4 He + 115 In fusion reaction using 35 MeV 4 He ion beam from VECC K130 cyclotron

  9. Sensorimotor gating deficits in multiple system atrophy

    DEFF Research Database (Denmark)

    Zoetmulder, Marielle; Biernat, Heidi Bryde; Nikolic, Miki

    2014-01-01

    Prepulse inhibition (PPI) of the auditory blink reflex is a measure of sensorimotor gating, which reflects an organism's ability to filter out irrelevant sensory information. PPI has never been studied in patients with multiple system atrophy (MSA), although sensorimotor deficits are frequently...

  10. Comparison of gate capacitance extraction methodologies

    NARCIS (Netherlands)

    Kazmi, S.N.R.; Schmitz, Jurriaan

    2008-01-01

    In recent years, many new capacitance-voltage measurement approaches have been presented in literature. New approaches became necessary with the rapidly increasing gate current density in newer CMOS generations. Here we present a simulation platform using Silvaco software, to describe the full chain

  11. Optical Co-Incidence Gate | Srinivasulu | African Journal of Science ...

    African Journals Online (AJOL)

    The paper explains Optical co-incidence gate, realized using Unijunction transistors (UJT), Light emitting diodes (LED) and Photo-resistors (LDR), which works on 1.8Vdc instead of 3Vdc. The power dissipation of the designed gate is only 3 mW. This optical gate finds application in the field of Mechatronics, Instrumentation ...

  12. Online junction temperature measurement using peak gate current

    DEFF Research Database (Denmark)

    Baker, Nick; Munk-Nielsen, Stig; Iannuzzo, Francesco

    2015-01-01

    A new method for junction temperature measurement of MOS-gated power semiconductor switches is presented. The measurement method involves detecting the peak voltage over the external gate resistor of an IGBT or MOSFET during turn-on. This voltage is directly proportional to the peak gate current...

  13. Gate Engineering in SOI LDMOS for Device Reliability

    Directory of Open Access Journals (Sweden)

    Aanand

    2016-01-01

    Full Text Available A linearly graded doping drift region with step gate structure, used for improvement of reduced surface field (RESURF SOI LDMOS transistor performance has been simulated with 0.35µm technology in this paper. The proposed device has one poly gate and double metal gate arranged in a stepped manner, from channel to drift region. The first gate uses n+ poly (near source where as other two gates of aluminium. The first gate with thin gate oxide has good control over the channel charge. The third gate with thick gate oxide at drift region reduce gate to drain capacitance. The arrangement of second and third gates in a stepped manner in drift region spreads the electric field uniformly. Using two dimensional device simulations, the proposed SOI LDMOS is compared with conventional structure and the extended metal structure. We demonstrate that the proposed device exhibits significant enhancement in linearity, breakdown voltage, on-resistance and HCI. Double metal gate reduces the impact ionization area which helps to improve the Hot Carrier Injection effect..

  14. Normal p50 gating in unmedicated schizophrenia outpatients

    DEFF Research Database (Denmark)

    Arnfred, Sidse M; Chen, Andrew C.N.; Glenthøj, Birte Y

    2003-01-01

    The hypothesis of a sensory gating defect in schizophrenia has been supported by studies demonstrating deficient auditory P50 gating in patients. P50 gating is the relative attenuation of P50 amplitude in the auditory evoked potential following the second auditory stimulus of a stimulus pair....

  15. Gate-Keeping and Feedback as Determinants of the Translation ...

    African Journals Online (AJOL)

    Mrs Afam

    Abstract. Based on a theoretical perspective and a critical documentary analysis, this paper seeks to locate the two ... Gate-Keeping and Feedback in the Process of (Mass) Communication. Gate-keeping and feedback ... fact, gatekeepers exist in large numbers in all mass communication organisations. Gate-keeping in this ...

  16. Application of optical logic gates | Srinivasulu | Zede Journal

    African Journals Online (AJOL)

    This paper proposes optical NOT. AND, and NOR gates using unijunction transistor (UJT), light emitting diode (LED), and light dependent resistor (LDR). Efforts are made to extend the development of these gates using LDR, LED, and UJT to work at 1.8V instead of 3V. These optical gates find their application in the field of ...

  17. High frequency MOSFET gate drivers technologies and applications

    CERN Document Server

    Zhang, Zhiliang

    2017-01-01

    This book describes high frequency power MOSFET gate driver technologies, including gate drivers for GaN HEMTs, which have great potential in the next generation of switching power converters. Gate drivers serve as a critical role between control and power devices.

  18. Allosteric gating mechanism underlies the flexible gating of KCNQ1 potassium channels

    Science.gov (United States)

    Osteen, Jeremiah D.; Barro-Soria, Rene; Robey, Seth; Sampson, Kevin J.; Kass, Robert S.; Larsson, H. Peter

    2012-01-01

    KCNQ1 (Kv7.1) is a unique member of the superfamily of voltage-gated K+ channels in that it displays a remarkable range of gating behaviors tuned by coassembly with different β subunits of the KCNE family of proteins. To better understand the basis for the biophysical diversity of KCNQ1 channels, we here investigate the basis of KCNQ1 gating in the absence of β subunits using voltage-clamp fluorometry (VCF). In our previous study, we found the kinetics and voltage dependence of voltage-sensor movements are very similar to those of the channel gate, as if multiple voltage-sensor movements are not required to precede gate opening. Here, we have tested two different hypotheses to explain KCNQ1 gating: (i) KCNQ1 voltage sensors undergo a single concerted movement that leads to channel opening, or (ii) individual voltage-sensor movements lead to channel opening before all voltage sensors have moved. Here, we find that KCNQ1 voltage sensors move relatively independently, but that the channel can conduct before all voltage sensors have activated. We explore a KCNQ1 point mutation that causes some channels to transition to the open state even in the absence of voltage-sensor movement. To interpret these results, we adopt an allosteric gating scheme wherein KCNQ1 is able to transition to the open state after zero to four voltage-sensor movements. This model allows for widely varying gating behavior, depending on the relative strength of the opening transition, and suggests how KCNQ1 could be controlled by coassembly with different KCNE family members. PMID:22509038

  19. LIFE CYCLE ASSESSMENT FOR OIL PALM BASED PLYWOOD: A GATE-TO-GATE CASE STUDY

    OpenAIRE

    M. Shamim Ahmad; Vijaya Subramaniam; Halimah Mohammad; Anis Mokhtar; B. S. Ismail

    2014-01-01

    Life Cycle Assessment (LCA) is an important tool for identifying potential environmental impacts associated with the production of palm based plywood. This study is to make available the life cycle inventory for gate-to-gate data so that the environmental impact posed by oil palm based plywood production can be assessed. Conducting an LCA on the palm based plywood that are derived from the wastes of the oil palm industry is a first step towards performing green environmental product. Therefor...

  20. Low-power DRAM-compatible Replacement Gate High-k/Metal Gate Stacks

    Science.gov (United States)

    Ritzenthaler, R.; Schram, T.; Bury, E.; Spessot, A.; Caillat, C.; Srividya, V.; Sebaai, F.; Mitard, J.; Ragnarsson, L.-Å.; Groeseneken, G.; Horiguchi, N.; Fazan, P.; Thean, A.

    2013-06-01

    In this work, the possibility of integration of High-k/Metal Gate (HKMG), Replacement Metal Gate (RMG) gate stacks for low power DRAM compatible transistors is studied. First, it is shown that RMG gate stacks used for Logic applications need to be seriously reconsidered, because of the additional anneal(s) needed in a DRAM process. New solutions are therefore developed. A PMOS stack HfO2/TiN with TiN deposited in three times combined with Work Function metal oxidations is demonstrated, featuring a very good Work Function of 4.95 eV. On the other hand, the NMOS side is shown to be a thornier problem to solve: a new solution based on the use of oxidized Ta as a diffusion barrier is proposed, and a HfO2/TiN/TaOX/TiAl/TiN/TiN gate stack featuring an aggressive Work Function of 4.35 eV (allowing a Work Function separation of 600 mV between NMOS and PMOS) is demonstrated. This work paves the way toward the integration of gate-last options for DRAM periphery transistors.

  1. A programming language for composable DNA circuits.

    Science.gov (United States)

    Phillips, Andrew; Cardelli, Luca

    2009-08-06

    Recently, a range of information-processing circuits have been implemented in DNA by using strand displacement as their main computational mechanism. Examples include digital logic circuits and catalytic signal amplification circuits that function as efficient molecular detectors. As new paradigms for DNA computation emerge, the development of corresponding languages and tools for these paradigms will help to facilitate the design of DNA circuits and their automatic compilation to nucleotide sequences. We present a programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism. The language includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure. The language is used to model and simulate a variety of circuits, including an entropy-driven catalytic gate, a simple gate motif for synthesizing large-scale circuits and a scheme for implementing an arbitrary system of chemical reactions. The language is a first step towards the design of modelling and simulation tools for DNA strand displacement, which complements the emergence of novel implementation strategies for DNA computing.

  2. Mitochondrial DNA.

    Science.gov (United States)

    Wright, Russell G.; Bottino, Paul J.

    1986-01-01

    Provides background information for teachers on mitochondrial DNA, pointing out that it may have once been a free-living organism. Includes a ready-to-duplicate exercise titled "Using Microchondrial DNA to Measure Evolutionary Distance." (JN)

  3. Cloning and Molecular Analysis of HlbZip1 and HlbZip2 Transcription Factors Putatively Involved in the Regulation of the Lupulin Metabolome in Hop (Humulus lupulus L.)

    Czech Academy of Sciences Publication Activity Database

    Matoušek, Jaroslav; Kocábek, Tomáš; Patzak, J.; Stehlík, Jan; Füssy, Zoltán; Krofta, K.; Heyerick, A.; Roldán-Ruiz, I.; Maloukh, L.; De Keukeleire, D.

    2010-01-01

    Roč. 58, č. 2 (2010), s. 902-912 ISSN 0021-8561 R&D Projects: GA ČR GA521/08/0740; GA MZe QH81052; GA MŠk ME 940 Institutional research plan: CEZ:AV0Z50510513 Keywords : secondary metabolites transcriptional regulation * cDNA-AFLP analysis * hop cDNA library screening * Nicotiana benthamiana * Petunia hybrida Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.816, year: 2010

  4. Ant Colony Algorithm and Simulation for Robust Airport Gate Assignment

    Directory of Open Access Journals (Sweden)

    Hui Zhao

    2014-01-01

    Full Text Available Airport gate assignment is core task for airport ground operations. Due to the fact that the departure and arrival time of flights may be influenced by many random factors, the airport gate assignment scheme may encounter gate conflict and many other problems. This paper aims at finding a robust solution for airport gate assignment problem. A mixed integer model is proposed to formulate the problem, and colony algorithm is designed to solve this model. Simulation result shows that, in consideration of robustness, the ability of antidisturbance for airport gate assignment scheme has much improved.

  5. The analysis of injection molding defects caused by gate vestiges

    Directory of Open Access Journals (Sweden)

    T. Tabi

    2015-04-01

    Full Text Available Issues of product safety are the most serious problems of an injection molded product due to their risk to human health. Such a safety problem can be the needle-shaped vestige at the gate zone of injection molded products, called a gate vestige. Only observations of the formation of gate vestiges can be found in the literature, but the processing parameters influencing their dimensions, especially their height have not been studied yet. Our goal was to study the effect of various injection molding processing parameters and gate constructions on gate vestige formation.

  6. Edge-on gating effect in molecular wires.

    Science.gov (United States)

    Lo, Wai-Yip; Bi, Wuguo; Li, Lianwei; Jung, In Hwan; Yu, Luping

    2015-02-11

    This work demonstrates edge-on chemical gating effect in molecular wires utilizing the pyridinoparacyclophane (PC) moiety as the gate. Different substituents with varied electronic demands are attached to the gate to simulate the effect of varying gating voltages similar to that in field-effect transistor (FET). It was observed that the orbital energy level and charge carrier's tunneling barriers can be tuned by changing the gating group from strong electron acceptors to strong electron donors. The single molecule conductance and current-voltage characteristics of this molecular system are truly similar to those expected for an actual single molecular transistor.

  7. Modeling DNA

    Science.gov (United States)

    Robertson, Carol

    2016-01-01

    Deoxyribonucleic acid (DNA) is life's most amazing molecule. It carries the genetic instructions that almost every organism needs to develop and reproduce. In the human genome alone, there are some three billion DNA base pairs. The most difficult part of teaching DNA structure, however, may be getting students to visualize something as small as a…

  8. Impedance characterization of DNA-functionalization layers on AlGaN/GaN high electron mobility transistors

    OpenAIRE

    Espinosa, N.; Schwarz, S.U.; Cimalla, V.; Podolska, A.; Ambacher, O.

    2015-01-01

    Characterization and optimization for biosensor implementation with open gate AlGaN/GaN transistors is described. Probe-DNA was immobilized on the gate. As target, complementary DNA at 10-12-10-7mol/L was added. To investigate the impedimetric properties of the sensing area, electrochemical impedance spectroscopy was used. For very low frequencies, the bio-functionalization layer was modeled as a membrane with a charge transfer resistor in series with a Warburg element. This component present...

  9. Synthesis of multivalued quantum logic circuits by elementary gates

    Science.gov (United States)

    Di, Yao-Min; Wei, Hai-Rui

    2013-01-01

    We propose the generalized controlled X (gcx) gate as the two-qudit elementary gate, and based on Cartan decomposition, we also give the one-qudit elementary gates. Then we discuss the physical implementation of these elementary gates and show that it is feasible with current technology. With these elementary gates many important qudit quantum gates can be synthesized conveniently. We provide efficient methods for the synthesis of various kinds of controlled qudit gates and greatly simplify the synthesis of existing generic multi-valued quantum circuits. Moreover, we generalize the quantum Shannon decomposition (QSD), the most powerful technique for the synthesis of generic qubit circuits, to the qudit case. A comparison of ququart (d=4) circuits and qubit circuits reveals that using ququart circuits may have an advantage over the qubit circuits in the synthesis of quantum circuits.

  10. Double-gated spectral snapshots for biomolecular fluorescence

    International Nuclear Information System (INIS)

    Nakamura, Ryosuke; Hamada, Norio; Ichida, Hideki; Tokunaga, Fumio; Kanematsu, Yasuo

    2007-01-01

    A versatile method to take femtosecond spectral snapshots of fluorescence has been developed based on a double gating technique in the combination of an optical Kerr gate and an image intensifier as an electrically driven gate set in front of a charge-coupled device detector. The application of a conventional optical-Kerr-gate method is limited to molecules with the short fluorescence lifetime up to a few hundred picoseconds, because long-lifetime fluorescence itself behaves as a source of the background signal due to insufficiency of the extinction ratio of polarizers employed for the Kerr gate. By using the image intensifier with the gate time of 200 ps, we have successfully suppressed the background signal and overcome the application limit of optical-Kerr-gate method. The system performance has been demonstrated by measuring time-resolved fluorescence spectra for laser dye solution and the riboflavin solution as a typical sample of biomolecule

  11. Reduction of the reversible circuits gate complexity without using the equivalent replacement tables for the gate compositions

    Directory of Open Access Journals (Sweden)

    D. V. Zakablukov

    2014-01-01

    Full Text Available The subject of study of this paper is reversible logic circuits. The irreversibility of computation can lead in the future to significant energy loss during the calculation process. Reversible circuits can be widely used in devices operating under conditions of limited computational resources.Presently, the problem of reversible logic synthesis is widely studied. The task a synthesis algorithm can face with is to reduce the gate complexity of synthesized circuit. One way to solve this problem is to use equivalent replacement tables for the gate compositions. The disadvantage of this approach is that it is necessary to build replacement tables, it takes a long time to find the replacement in the table, and there is no way to build an appropriate universal replacement table for arbitrary reversible circuit. The aim of this paper is to develop the solution for the problem of gate complexity reduction for the reversible circuits without using equivalent replacement tables for the gate compositions.This paper makes a generalization of the k-CNOT gate for the case of zero value at some of the gate control inputs. To describe such gates it suggests using a set of direct control inputs and a set of inverted ones. A definition of the independence of two reversible gates is introduced. Two independent gates standing next to each other in the circuit can be swapped without changing the circuit result transformation. Various conditions of the independence of two reversible gates are considered including conditions imposed to the set of direct control inputs and the set of inverted ones. It is proved that two gates are independent if there is, at least, one common control input, which differs only by the type (direct or inverted.Various equivalent replacements of two k-CNOT gates compositions and its conditions imposed to the set of direct control inputs and to the set of inverted ones are considered. The proof of correctness for such replacements is

  12. Rapid gated Thallium-201 perfusion SPECT - clinically feasible?

    International Nuclear Information System (INIS)

    Wadhwa, S.S.; Mansberg, R.; Fernandes, V.B.; Wilkinson, D.; Abatti, D.

    1998-01-01

    Full text: Standard dose energy window optimised Thallium-201 (Tl-201) SPECT has about half the counts of a standard dose from Technetium-99m Sestamibi (Tc99m-Mibi) gated perfusion SPECT. This study investigates the clinical feasibility of rapid energy window optimised Tl-201 gated perfusion SPECT (gated-TI) and compares quantitative left ventricular ejection fraction (LVEF) and visually assessed image quality for wall motion and thickening to analogous values obtained from Tc99m-Mibi gated perfusion SPECT (gated - mibi). Methods: We studied 60 patients with a rest gated Tl-201 SPECT (100 MBq, 77KeV peak, 34% window, 20 sec/projection) followed by a post stress gated Sestamibi SPECT (1GBq, 140KeV, 20% window, 20 sec/projection) separate dual isotope protocol. LVEF quantitation was performed using commercially available software (SPECTEF, General Electric). Visual grading of image quality for wall thickening and motion was performed using a three-point scale (excellent, good and poor). Results: LVEF for gated Tl-201 SPECT was 59.6 ± 12.0% (Mean ± SD). LVEF for gated Sestamibi SPECT was 60.4 ±11.4% (Mean ± SD). These were not significantly different (P=0.27, T-Test). There was good correlation (r=0.9) between gated-TI and gated-mibi LVEF values. The quality of gated-Tl images was ranked as excellent, good and poor in 12, 50 and 38% of the patients respectively. Image quality was better in gated-mibi SPECT, with ratings of 12, 62 and 26% respectively. Conclusion: Rapid gated Thallium-201 acquisition with energy window optimisation can be effectively performed on majority of patients and offers the opportunity to assess not only myocardial perfusion and function, as with Technetium based agents, but also viability using a single day one isotope protocol

  13. Identification and characterization of hydrophobic gate residues in TRP channels.

    Science.gov (United States)

    Zheng, Wang; Hu, Ruikun; Cai, Ruiqi; Hofmann, Laura; Hu, Qiaolin; Fatehi, Mohammad; Long, Wentong; Kong, Tim; Tang, Jingfeng; Light, Peter; Flockerzi, Veit; Cao, Ying; Chen, Xing-Zhen

    2018-02-01

    Transient receptor potential (TRP) channels, subdivided into 6 subfamilies in mammals, have essential roles in sensory physiology. They respond to remarkably diverse stimuli, comprising thermal, chemical, and mechanical modalities, through opening or closing of channel gates. In this study, we systematically substituted the hydrophobic residues within the distal fragment of pore-lining helix S6 with hydrophilic residues and, based on Xenopus oocyte and mammalian cell electrophysiology and a hydrophobic gate theory, identified hydrophobic gates in TRPV6/V5/V4/C4/M8. We found that channel activity drastically increased when TRPV6 Ala616 or Met617 or TRPV5 Ala576 or Met577 , but not any of their adjacent residues, was substituted with hydrophilic residues. Channel activity strongly correlated with the hydrophilicity of the residues at those sites, suggesting that consecutive hydrophobic residues TRPV6 Ala616-Met617 and TRPV5 Ala576-Met577 form a double-residue gate in each channel. By the same strategy, we identified a hydrophobic single-residue gate in TRPV4 Iso715 , TRPC4 Iso617 , and TRPM8 Val976 . In support of the hydrophobic gate theory, hydrophilic substitution at the gate site, which removes the hydrophobic gate seal, substantially increased the activity of TRP channels in low-activity states but had little effect on the function of activated channels. The double-residue gate channels were more sensitive to small changes in the gate's hydrophobicity or size than single-residue gate channels. The unconventional double-reside gating mechanism in TRP channels may have been evolved to respond especially to physiologic stimuli that trigger relatively small gate conformational changes.-Zheng, W., Hu, R., Cai, R., Hofmann, L., Hu, Q., Fatehi, M., Long, W., Kong, T., Tang, J., Light, P., Flockerzi, V., Cao, Y., Chen, X.-Z. Identification and characterization of hydrophobic gate residues in TRP channels.

  14. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  15. Zip Code Manager

    Data.gov (United States)

    Office of Personnel Management — The system used to associate what Federal Employees Health Benefits Program (FEHBP) and Federal Employees Dental/Vision Program (FEDVIP) health, dental, and vision...

  16. zipHMMlib:

    DEFF Research Database (Denmark)

    Sand, Andreas; Kristiansen, Martin; Pedersen, Christian Nørgaard Storm

    2013-01-01

    the computations in the forward algorithm which can be reused. This analysis can be saved between uses of the library and is independent of concrete hidden Markov models so one preprocessing can be used to run a number of different models. Using this library, we achieve up to 78 times shorter wall-clock time...... have built a software library for efficiently computing the likelihood of a hidden Markov model. The library exploits commonly occurring substrings in the input to reuse computations in the forward algorithm. In a pre-processing step our library identifies common substrings and builds a structure over...

  17. Zipping into fusion

    NARCIS (Netherlands)

    Zheng, Tingting

    2014-01-01

    Fusion of lipid bilayers in cells facilitates the active transport of chemicals. Non-viral membrane fusion is regulated by a cascade of proteins as the process is highly regulated both in space and time. In eukaryotic cells, the so-called SNARE protein complex is at the heart of fusion. However,

  18. A parallel computational model for GATE simulations.

    Science.gov (United States)

    Rannou, F R; Vega-Acevedo, N; El Bitar, Z

    2013-12-01

    GATE/Geant4 Monte Carlo simulations are computationally demanding applications, requiring thousands of processor hours to produce realistic results. The classical strategy of distributing the simulation of individual events does not apply efficiently for Positron Emission Tomography (PET) experiments, because it requires a centralized coincidence processing and large communication overheads. We propose a parallel computational model for GATE that handles event generation and coincidence processing in a simple and efficient way by decentralizing event generation and processing but maintaining a centralized event and time coordinator. The model is implemented with the inclusion of a new set of factory classes that can run the same executable in sequential or parallel mode. A Mann-Whitney test shows that the output produced by this parallel model in terms of number of tallies is equivalent (but not equal) to its sequential counterpart. Computational performance evaluation shows that the software is scalable and well balanced. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  19. Spin gated transistors for reprogrammable logic

    Science.gov (United States)

    Ciccarelli, Chiara; Gonzalez-Zalba, Fernando; Irvine, Andrew; Campion, Richard; Zarbo, Liviu; Gallagher, Brian; Ferguson, Andrew; Jungwirth, Tomas; Wunderlich, Joerg; Institute of Physics ASCR Collaboration; University of Nottingham Collaboration; Hitachi Cambridge Laboratory Team; Institute of Physics ASCR Collaboration; University of Nottingham Collaboration; University of Cambridge Team

    2014-03-01

    In spin-orbit coupled magnetic materials the chemical potential depends on the orientation of the magnetisation. By making the gate of a field effect transistor magnetic, it is possible to tune the channel conductance not only electrically but also magnetically. We show that these magnetic transistor can be used to realise non-volatile reprogrammable Boolean logic. The non-volatile reconfigurable capability resides in the magnetization-dependent band structure of the magnetic stack. A change in magnetization orientation produces a change in the electrochemical potential, which induces a charge accumulation in the correspondent gate electrode. This is readily sensed by a field-effect device such as standard field-effect transistors or more exotic single-electron transistors. We propose circuits for low power consumption applications that can be magnetically switched between NAND and OR logic functions and between NOR and AND logic functions.

  20. Gate Control Coefficient Effect on CNFET Characteristic

    International Nuclear Information System (INIS)

    Sanudin, Rahmat; Ma'Radzi, Ahmad Alabqari; Nayan, Nafarizal

    2009-01-01

    The development of carbon nanotube field-effect transistor (CNFET) as alternative to existing transistor technology has long been published and discussed. The emergence of this device offers new material and structure in building a transistor. This paper intends to do an analysis of gate control coefficient effect on CNFET performance. The analysis is based on simulation study of current-voltage (I-V) characteristic of ballistic CNFET. The simulation study used the MOSFET-like CNFET mathematical model to establish the device output characteristic. Based on the analysis of simulation result, it is found that the gate control coefficient contributes to a significant effect on the performance of CNFET. The result also shown the parameter could help to improve the device performance in terms of its output and response as well. Nevertheless, the characteristic of the carbon nanotube that acts as the channel is totally important in determining the performance of the transistor as a whole.

  1. Philosophy of voltage-gated proton channels.

    Science.gov (United States)

    DeCoursey, Thomas E; Hosler, Jonathan

    2014-03-06

    In this review, voltage-gated proton channels are considered from a mainly teleological perspective. Why do proton channels exist? What good are they? Why did they go to such lengths to develop several unique hallmark properties such as extreme selectivity and ΔpH-dependent gating? Why is their current so minuscule? How do they manage to be so selective? What is the basis for our belief that they conduct H(+) and not OH(-)? Why do they exist in many species as dimers when the monomeric form seems to work quite well? It is hoped that pondering these questions will provide an introduction to these channels and a way to logically organize their peculiar properties as well as to understand how they are able to carry out some of their better-established biological functions.

  2. Cascadable spatial-soliton logic gates.

    Science.gov (United States)

    Blair, S; Wagner, K

    2000-11-10

    The three-terminal spatial-soliton angular-deflection geometry provides the characteristics of an inverting logic gate with gain, and phase-insensitive implementations can be realized by a number of specific nonlinear interactions between orthogonally polarized waves. In particular, numerical simulations of spatial-soliton dragging and collision are used to calculate the transfer functions of inverter and multiple configurations of two-input nor gates and to address their cascadability. These transfer functions converge in cascaded operation and suggest that fan-out greater than 2 with a large noise margin is attainable in a system with standardized signal levels. These results are obtained with the material properties of fused silica and are representative of low-loss Kerr media.

  3. GATE V6: a major enhancement of the GATE simulation platform enabling modelling of CT and radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Jan, S; Becheva, E [DSV/I2BM/SHFJ, Commissariat a l' Energie Atomique, Orsay (France); Benoit, D; Rehfeld, N; Stute, S; Buvat, I [IMNC-UMR 8165 CNRS-Paris 7 and Paris 11 Universities, 15 rue Georges Clemenceau, 91406 Orsay Cedex (France); Carlier, T [INSERM U892-Cancer Research Center, University of Nantes, Nantes (France); Cassol, F; Morel, C [Centre de physique des particules de Marseille, CNRS-IN2P3 and Universite de la Mediterranee, Aix-Marseille II, 163, avenue de Luminy, 13288 Marseille Cedex 09 (France); Descourt, P; Visvikis, D [INSERM, U650, Laboratoire du Traitement de l' Information Medicale (LaTIM), CHU Morvan, Brest (France); Frisson, T; Grevillot, L; Guigues, L; Sarrut, D; Zahra, N [Universite de Lyon, CREATIS, CNRS UMR5220, Inserm U630, INSA-Lyon, Universite Lyon 1, Centre Leon Berard (France); Maigne, L; Perrot, Y [Laboratoire de Physique Corpusculaire, 24 Avenue des Landais, 63177 Aubiere Cedex (France); Schaart, D R [Delft University of Technology, Radiation Detection and Medical Imaging, Mekelweg 15, 2629 JB Delft (Netherlands); Pietrzyk, U, E-mail: buvat@imnc.in2p3.fr [Reseach Center Juelich, Institute of Neurosciences and Medicine and Department of Physics, University of Wuppertal (Germany)

    2011-02-21

    GATE (Geant4 Application for Emission Tomography) is a Monte Carlo simulation platform developed by the OpenGATE collaboration since 2001 and first publicly released in 2004. Dedicated to the modelling of planar scintigraphy, single photon emission computed tomography (SPECT) and positron emission tomography (PET) acquisitions, this platform is widely used to assist PET and SPECT research. A recent extension of this platform, released by the OpenGATE collaboration as GATE V6, now also enables modelling of x-ray computed tomography and radiation therapy experiments. This paper presents an overview of the main additions and improvements implemented in GATE since the publication of the initial GATE paper (Jan et al 2004 Phys. Med. Biol. 49 4543-61). This includes new models available in GATE to simulate optical and hadronic processes, novelties in modelling tracer, organ or detector motion, new options for speeding up GATE simulations, examples illustrating the use of GATE V6 in radiotherapy applications and CT simulations, and preliminary results regarding the validation of GATE V6 for radiation therapy applications. Upon completion of extensive validation studies, GATE is expected to become a valuable tool for simulations involving both radiotherapy and imaging.

  4. DNA Computing Systems Activated by Electrochemically-triggered DNA Release from a Polymer-brush-modified Electrode Array

    Science.gov (United States)

    Gamella, Maria; Zakharchenko, Andrey; Guz, Nataliia; Masi, Madeline; Minko, Sergiy; Kolpashchikov, Dmitry M.; Iken, Heiko; Poghossian, Arshak; Schöning, Michael J.; Katz, Evgeny

    2017-01-01

    An array of four independently wired indium tin oxide (ITO) electrodes was used for electrochemically stimulated DNA release and activation of DNA-based Identity, AND and XOR logic gates. Single-stranded DNA molecules were loaded on the mixed poly(N,N-di-methylaminoethyl methacrylate) (PDMAEMA)/poly-(methacrylic acid) (PMAA) brush covalently attached to the ITO electrodes. The DNA deposition was performed at pH 5.0 when the polymer brush is positively charged due to protonation of tertiary amino groups in PDMAE-MA, thus resulting in electrostatic attraction of the negatively charged DNA. By applying electrolysis at −1.0 V(vs. Ag/AgCl reference) electrochemical oxygen reduction resulted in the consumption of hydrogen ions and local pH increase near the electrode surface. The process resulted in recharging the polymer brush to the negative state due to dissociation of carboxylic groups of PMAA, thus repulsing the negatively charged DNA and releasing it from the electrode surface. The DNA release was performed in various combinations from different electrodes in the array assembly. The released DNA operated as input signals for activation of the Boolean logic gates. The developed system represents a step forward in DNA computing, combining for the first time DNA chemical processes with electronic input signals. PMID:29379265

  5. Molecular sensors and molecular logic gates

    International Nuclear Information System (INIS)

    Georgiev, N.; Bojinov, V.

    2013-01-01

    Full text: The rapid grow of nanotechnology field extended the concept of a macroscopic device to the molecular level. Because of this reason the design and synthesis of (supra)-molecular species capable of mimicking the functions of macroscopic devices are currently of great interest. Molecular devices operate via electronic and/or nuclear rearrangements and, like macroscopic devices, need energy to operate and communicate between their elements. The energy needed to make a device work can be supplied as chemical energy, electrical energy, or light. Luminescence is one of the most useful techniques to monitor the operation of molecular-level devices. This fact determinates the synthesis of novel fluorescence compounds as a considerable and inseparable part of nanoscience development. Further miniaturization of semiconductors in electronic field reaches their limit. Therefore the design and construction of molecular systems capable of performing complex logic functions is of great scientific interest now. In semiconductor devices the logic gates work using binary logic, where the signals are encoded as 0 and 1 (low and high current). This process is executable on molecular level by several ways, but the most common are based on the optical properties of the molecule switches encoding the low and high concentrations of the input guest molecules and the output fluorescent intensities with binary 0 and 1 respectively. The first proposal to execute logic operations at the molecular level was made in 1988, but the field developed only five years later when the analogy between molecular switches and logic gates was experimentally demonstrated by de Silva. There are seven basic logic gates: AND, OR, XOR, NOT, NAND, NOR and XNOR and all of them were achieved by molecules, the fluorescence switching as well. key words: fluorescence, molecular sensors, molecular logic gates

  6. Re-opening of Gate C

    CERN Multimedia

    TS-FM Group

    2006-01-01

    From 3rd April to 1st December 2006, Gate C (Satigny) will be open to pedestrians and vehicles (except delivery vehicles) from Monday to Friday, excluding official holidays, between 8.00 a.m. and 9.00 a.m. for those entering the site and between 5.00 p.m. and 6.00 p.m. for those leaving the site. TS-FM Group Reception and Access Control Service

  7. Re-opening of Gate C

    CERN Document Server

    2006-01-01

    From 3rd April to 1st December 2006, Gate C (Satigny) will be open to pedestrians and vehicles (except delivery vehicles) from Mondays to Fridays, excluding official holidays, between 8.00 a.m. and 9.00 a.m. for those entering the site and between 5.00 p.m. and 6.00 p.m. for those leaving the site. TS-FM Group Reception and Access Control Service

  8. Cluster computing software for GATE simulations

    International Nuclear Information System (INIS)

    Beenhouwer, Jan de; Staelens, Steven; Kruecker, Dirk; Ferrer, Ludovic; D'Asseler, Yves; Lemahieu, Ignace; Rannou, Fernando R.

    2007-01-01

    Geometry and tracking (GEANT4) is a Monte Carlo package designed for high energy physics experiments. It is used as the basis layer for Monte Carlo simulations of nuclear medicine acquisition systems in GEANT4 Application for Tomographic Emission (GATE). GATE allows the user to realistically model experiments using accurate physics models and time synchronization for detector movement through a script language contained in a macro file. The downside of this high accuracy is long computation time. This paper describes a platform independent computing approach for running GATE simulations on a cluster of computers in order to reduce the overall simulation time. Our software automatically creates fully resolved, nonparametrized macros accompanied with an on-the-fly generated cluster specific submit file used to launch the simulations. The scalability of GATE simulations on a cluster is investigated for two imaging modalities, positron emission tomography (PET) and single photon emission computed tomography (SPECT). Due to a higher sensitivity, PET simulations are characterized by relatively high data output rates that create rather large output files. SPECT simulations, on the other hand, have lower data output rates but require a long collimator setup time. Both of these characteristics hamper scalability as a function of the number of CPUs. The scalability of PET simulations is improved here by the development of a fast output merger. The scalability of SPECT simulations is improved by greatly reducing the collimator setup time. Accordingly, these two new developments result in higher scalability for both PET and SPECT simulations and reduce the computation time to more practical values

  9. Nanomechanical molecular devices made of DNA origami.

    Science.gov (United States)

    Kuzuya, Akinori; Ohya, Yuichi

    2014-06-17

    CONSPECTUS: Eight years have passed since the striking debut of the DNA origami technique ( Rothemund, P. W. K. Nature 2006 , 440 , 297 - 302 ), in which long single-stranded DNA is folded into a designed nanostructure, in either 2D or 3D, with the aid of many short staple strands. The number of proposals for new design principles for DNA origami structures seems to have already reached a peak. It is apparent that DNA origami study is now entering the second phase of creating practical applications. The development of functional nanomechanical molecular devices using the DNA origami technique is one such application attracting significant interest from researchers in the field. Nanomechanical DNA origami devices, which maintain the characteristics of DNA origami structures, have various advantages over conventional DNA nanomachines. Comparatively high assembly yield, relatively large size visible via atomic force microscopy (AFM) or transmission electron microscopy (TEM), and the capability to assemble multiple functional groups with precision using multiple staple strands are some of the advantages of the DNA origami technique for constructing sophisticated molecular devices. This Account describes the recent developments of such nanomechanical DNA origami devices and reviews the emerging target of DNA origami studies. First, simple "dynamic" DNA origami structures with transformation capability, such as DNA origami boxes and a DNA origami hatch with structure control, are briefly summarized. More elaborate nanomechanical DNA origami devices are then reviewed. The first example describes DNA origami pinching devices that can be used as "single-molecule" beacons to detect a variety of biorelated molecules, from metal ions at the size of a few tens of atomic mass number units to relatively gigantic proteins with a molecular mass greater than a hundred kilodaltons, all on a single platform. Clamshell-like DNA nanorobots equipped with logic gates can discriminate

  10. Opening of the New Gate E (Reminder)

    CERN Document Server

    Relations with the Host States Service

    2004-01-01

    Since 1 November 2004, members of the CERN personnel holding a legitimation document issued by the Swiss Federal Department of Foreign Affairs may use Gate E ("Charles de Gaulle Gate"), located at the West end of the Meyrin Site, from Monday to Friday, except on official CERN holidays, from 7.30 a.m. to 9.30 a.m. to enter the site and from 4.30 p.m. to 6.30 p.m. to leave the site. All persons using Gate E must automatically present for inspection by the Guard on duty: either their azure B-type CERN access card (the letter B precedes the identification number printed on the card); or, during a transitional period lasting until 17 December 2004, their blue C-type CERN access card (the letter C precedes the identification number printed on the card) and their legitimation document issued by the Swiss Federal Department of Foreign Affairs («Carte de légitimation» or «Attestation de fonctions»). The new azure B-type CERN access card is issued, where appropria...

  11. Engineering integrated photonics for heralded quantum gates.

    Science.gov (United States)

    Meany, Thomas; Biggerstaff, Devon N; Broome, Matthew A; Fedrizzi, Alessandro; Delanty, Michael; Steel, M J; Gilchrist, Alexei; Marshall, Graham D; White, Andrew G; Withford, Michael J

    2016-06-10

    Scaling up linear-optics quantum computing will require multi-photon gates which are compact, phase-stable, exhibit excellent quantum interference, and have success heralded by the detection of ancillary photons. We investigate the design, fabrication and characterisation of the optimal known gate scheme which meets these requirements: the Knill controlled-Z gate, implemented in integrated laser-written waveguide arrays. We show device performance to be less sensitive to phase variations in the circuit than to small deviations in the coupler reflectivity, which are expected given the tolerance values of the fabrication method. The mode fidelity is also shown to be less sensitive to reflectivity and phase errors than the process fidelity. Our best device achieves a fidelity of 0.931 ± 0.001 with the ideal 4 × 4 unitary circuit and a process fidelity of 0.680 ± 0.005 with the ideal computational-basis process.

  12. Optical parametrically gated microscopy in scattering media.

    Science.gov (United States)

    Zhao, Youbo; Adie, Steven G; Tu, Haohua; Liu, Yuan; Graf, Benedikt W; Chaney, Eric J; Marjanovic, Marina; Boppart, Stephen A

    2014-09-22

    High-resolution imaging in turbid media has been limited by the intrinsic compromise between the gating efficiency (removal of multiply-scattered light background) and signal strength in the existing optical gating techniques. This leads to shallow depths due to the weak ballistic signal, and/or degraded resolution due to the strong multiply-scattering background--the well-known trade-off between resolution and imaging depth in scattering samples. In this work, we employ a nonlinear optics based optical parametric amplifier (OPA) to address this challenge. We demonstrate that both the imaging depth and the spatial resolution in turbid media can be enhanced simultaneously by the OPA, which provides a high level of signal gain as well as an inherent nonlinear optical gate. This technology shifts the nonlinear interaction to an optical crystal placed in the detection arm (image plane), rather than in the sample, which can be used to exploit the benefits given by the high-order parametric process and the use of an intense laser field. The coherent process makes the OPA potentially useful as a general-purpose optical amplifier applicable to a wide range of optical imaging techniques.

  13. String method solution of the gating pathways for a pentameric ligand-gated ion channel

    Science.gov (United States)

    Lev, Bogdan; Murail, Samuel; Poitevin, Frédéric; Cromer, Brett A.; Delarue, Marc; Allen, Toby W.

    2017-01-01

    Pentameric ligand-gated ion channels control synaptic neurotransmission by converting chemical signals into electrical signals. Agonist binding leads to rapid signal transduction via an allosteric mechanism, where global protein conformational changes open a pore across the nerve cell membrane. We use all-atom molecular dynamics with a swarm-based string method to solve for the minimum free-energy gating pathways of the proton-activated bacterial GLIC channel. We describe stable wetted/open and dewetted/closed states, and uncover conformational changes in the agonist-binding extracellular domain, ion-conducting transmembrane domain, and gating interface that control communication between these domains. Transition analysis is used to compute free-energy surfaces that suggest allosteric pathways; stabilization with pH; and intermediates, including states that facilitate channel closing in the presence of an agonist. We describe a switching mechanism that senses proton binding by marked reorganization of subunit interface, altering the packing of β-sheets to induce changes that lead to asynchronous pore-lining M2 helix movements. These results provide molecular details of GLIC gating and insight into the allosteric mechanisms for the superfamily of pentameric ligand-gated channels. PMID:28487483

  14. Statistical Determination of the Gating Windows for Respiratory-Gated Radiotherapy Using a Visible Guiding System.

    Science.gov (United States)

    Oh, Se An; Yea, Ji Woon; Kim, Sung Kyu

    2016-01-01

    Respiratory-gated radiation therapy (RGRT) is used to minimize the radiation dose to normal tissue in lung-cancer patients. Although determining the gating window in the respiratory phase of patients is important in RGRT, it is not easy. Our aim was to determine the optimal gating window when using a visible guiding system for RGRT. Between April and October 2014, the breathing signals of 23 lung-cancer patients were recorded with a real-time position management (RPM) respiratory gating system (Varian, USA). We performed statistical analysis with breathing signals to find the optimal gating window for guided breathing in RGRT. When we compared breathing signals before and after the breathing training, 19 of the 23 patients showed statistically significant differences (p guiding system. RGRT was performed with the RPM system to confirm the usefulness of the visible guiding system. The RPM system and our visible guiding system improve the respiratory regularity, which in turn should improve the accuracy and efficiency of RGRT.

  15. Probing Dense Sprays with Gated, Picosecond, Digital Particle Field Holography

    Directory of Open Access Journals (Sweden)

    James Trolinger

    2011-12-01

    Full Text Available This paper describes work that demonstrated the feasibility of producing a gated digital holography system that is capable of producing high-resolution images of three-dimensional particle and structure details deep within dense particle fields of a spray. We developed a gated picosecond digital holocamera, using optical Kerr cell gating, to demonstrate features of gated digital holography that make it an exceptional candidate for this application. The Kerr cell gate shuttered the camera after the initial burst of ballistic and snake photons had been recorded, suppressing longer path, multiple scattered illumination. By starting with a CW laser without gating and then incorporating a picosecond laser and an optical Kerr gate, we were able to assess the imaging quality of the gated holograms, and determine improvement gained by gating. We produced high quality images of 50–200 μm diameter particles, hairs and USAF resolution charts from digital holograms recorded through turbid media where more than 98% of the light was scattered from the field. The system can gate pulses as short as 3 mm in pathlength (10 ps, enabling image-improving features of the system. The experiments lead us to the conclusion that this method has an excellent capability as a diagnostics tool in dense spray combustion research.

  16. An Agent-Based Model for Zip-Code Level Diffusion of Electric Vehicles and Electricity Consumption in New York City

    Directory of Open Access Journals (Sweden)

    Azadeh Ahkamiraad

    2018-03-01

    Full Text Available Current power grids in many countries are not fully prepared for high electric vehicle (EV penetration, and there is evidence that the construction of additional grid capacity is constantly outpaced by EV diffusion. If this situation continues, then it will compromise grid reliability and cause problems such as system overload, voltage and frequency fluctuations, and power losses. This is especially true for densely populated areas where the grid capacity is already strained with existing old infrastructure. The objective of this research is to identify the zip-code level electricity consumption that is associated with large-scale EV adoption in New York City, one of the most densely populated areas in the United States (U.S.. We fuse the Fisher and Pry diffusion model and Rogers model within the agent-based simulation to forecast zip-code level EV diffusion and the required energy capacity to satisfy the charging demand. The research outcomes will assist policy makers and grid operators in making better planning decisions on the locations and timing of investments during the transition to smarter grids and greener transportation.

  17. The zinc transporter SLC39A13/ZIP13 is required for connective tissue development; its involvement in BMP/TGF-beta signaling pathways.

    Directory of Open Access Journals (Sweden)

    Toshiyuki Fukada

    Full Text Available BACKGROUND: Zinc (Zn is an essential trace element and it is abundant in connective tissues, however biological roles of Zn and its transporters in those tissues and cells remain unknown. METHODOLOGY/PRINCIPAL FINDINGS: Here we report that mice deficient in Zn transporter Slc39a13/Zip13 show changes in bone, teeth and connective tissue reminiscent of the clinical spectrum of human Ehlers-Danlos syndrome (EDS. The Slc39a13 knockout (Slc39a13-KO mice show defects in the maturation of osteoblasts, chondrocytes, odontoblasts, and fibroblasts. In the corresponding tissues and cells, impairment in bone morphogenic protein (BMP and TGF-beta signaling were observed. Homozygosity for a SLC39A13 loss of function mutation was detected in sibs affected by a unique variant of EDS that recapitulates the phenotype observed in Slc39a13-KO mice. CONCLUSIONS/SIGNIFICANCE: Hence, our results reveal a crucial role of SLC39A13/ZIP13 in connective tissue development at least in part due to its involvement in the BMP/TGF-beta signaling pathways. The Slc39a13-KO mouse represents a novel animal model linking zinc metabolism, BMP/TGF-beta signaling and connective tissue dysfunction.

  18. De Novo Synthesis of Basal Bacterial Cell Division Proteins FtsZ, FtsA, and ZipA Inside Giant Vesicles.

    Science.gov (United States)

    Furusato, Takumi; Horie, Fumihiro; Matsubayashi, Hideaki T; Amikura, Kazuaki; Kuruma, Yutetsu; Ueda, Takuya

    2018-03-13

    Cell division is the most dynamic event in the cell cycle. Recently, efforts have been made to reconstruct it using the individual component proteins to obtain a better understanding of the process of self-reproduction of cells. However, such reconstruction studies are frequently hampered by difficulties in preparing membrane-associated proteins. Here we demonstrate a de novo synthesis approach based on a cell-free translation system. Genes for fundamental cell division proteins, FtsZ, FtsA, and ZipA, were expressed inside the lipid compartment of giant vesicles (GVs). The synthesized proteins showed polymerization, membrane localization, and eventually membrane deformation. Notably, we found that this morphological change of the vesicle is forced by only FtsZ and ZipA, which form clusters on the membrane at the vesicle interior. Our cell-free approach provides a platform for studying protein dynamics associated with lipid membrane and paves the way to create a synthetic cell that undergoes self-reproduction.

  19. Natural antioxidants exhibit chemopreventive characteristics through the regulation of CNC b-Zip transcription factors in estrogen-induced breast carcinogenesis.

    Science.gov (United States)

    Chatterjee, Anwesha; Ronghe, Amruta; Singh, Bhupendra; Bhat, Nimee K; Chen, Jie; Bhat, Hari K

    2014-12-01

    The objective of the present study was to characterize the role of resveratrol (Res) and vitamin C (VC) in prevention of estrogen-induced breast cancer through regulation of cap "n"collar (CNC) b-zip transcription factors. Human breast epithelial cell line MCF-10A was treated with 17β-estradiol (E2) and VC or Res with or without E2. mRNA and protein expression levels of CNC b-zip transcription factors nuclear factor erythroid 2-related factor 1 (Nrf1), nuclear factor erythroid 2 related factor 2 (Nrf2), nuclear factor erythroid 2 related factor 3 (Nrf3), and Nrf2-regulated antioxidant enzymes superoxide dismutase 3 (SOD3) and quinone oxidoreductase 1 (NQO1) were quantified. The treatment with E2 suppressed, whereas VC and Res prevented E2-mediated decrease in the expression levels of SOD3, NQO1, Nrf2 mRNA, and protein in MCF-10A cells. The treatment with E2, Res, or VC significantly increased mRNA and protein expression levels of Nrf1. 17β-Estradiol treatment significantly increased but VC or Res decreased Nrf3 mRNA and protein expression levels. Our studies demonstrate that estrogen-induced breast cancer might be prevented through upregulation of antioxidant enzymes via Nrf-dependent pathways. © 2014 Wiley Periodicals, Inc.

  20. The zygomatic implant perforated (ZIP) flap: a new technique for combined surgical reconstruction and rapid fixed dental rehabilitation following low-level maxillectomy.

    Science.gov (United States)

    Butterworth, C J; Rogers, S N

    2017-12-01

    This aim of this report is to describe the development and evolution of a new surgical technique for the immediate surgical reconstruction and rapid post-operative prosthodontic rehabilitation with a fixed dental prosthesis following low-level maxillectomy for malignant disease.The technique involves the use of a zygomatic oncology implant perforated micro-vascular soft tissue flap (ZIP flap) for the primary management of maxillary malignancy with surgical closure of the resultant maxillary defect and the installation of osseointegrated support for a zygomatic implant-supported maxillary fixed dental prosthesis.The use of this technique facilitates extremely rapid oral and dental rehabilitation within a few weeks of resective surgery, providing rapid return to function and restoring appearance following low-level maxillary resection, even in cases where radiotherapy is required as an adjuvant treatment post-operatively. The ZIP flap technique has been adopted as a standard procedure in the unit for the management of low-level maxillary malignancy, and this report provides a detailed step-by-step approach to treatment and discusses modifications developed over the treatment of an initial cohort of patients.

  1. The IRE1/bZIP60 pathway and bax inhibitor 1 suppress systemic accumulation of potyviruses and potexviruses in Arabidopsis and Nicotiana benthamiana Plants

    DEFF Research Database (Denmark)

    Gaguancela, Omar Arias; Zúñiga, Lizbeth Peña; Arias, Alexis Vela

    2016-01-01

    that regulates cell death in response to environmental assaults. The potyvirus 6K2 and potexvirus TGB3 proteins are known to reside in the ER, serving, respectively, as anchors for the viral replicase and movement protein complex. This study used green fluorescent protein (GFP)-tagged Turnip mosaic virus (Tu...... genes into plant cells activated bZIP60 and BI-1 expression in Arabidopsis thaliana, N. benthamiana, and S. tuberosum. Homozygous ire1a-2, ire1b-4, and ire1a-2/ire1b-4 mutant Arabidopsis plants were inoculated with TuMV-GFP or PlAMV-GFP. PlAMV accumulates to a higher level in ire1a-2 or ire1a-2/ire1b-4...... mutant plants than in ire1b-4 or wild-type plants. TuMV-GFP accumulates to a higher level in ire1a-2, ire1b-4, or ire1a-2/ire1b-4 compared with wild-type plants, suggesting that both isoforms contribute to TuMV-GFP infection. Gene silencing was used to knock down bZIP60 and BI-1 expression in N...

  2. A robust family of Golden Gate Agrobacterium vectors for plant synthetic biology

    Directory of Open Access Journals (Sweden)

    Shahram eEmami

    2013-09-01

    Full Text Available Tools that allow for rapid, accurate and inexpensive assembly of multi-component combinatorial libraries of DNA for transformation into plants will accelerate the progress of synthetic biology research. Recent progress in molecular cloning methods has vastly expanded the repertoire with which plant biologists can engineer a transgene. Here we describe a new set of binary vectors for use in Agrobacterium-mediated plant transformation that utilizes the Golden-Gate cloning approach. Our optimized protocol facilitates the rapid and inexpensive generation of multi-component transgenes for later introduction into plants.

  3. Free energy dissipation of the spontaneous gating of a single voltage-gated potassium channel

    Science.gov (United States)

    Wang, Jia-Zeng; Wang, Rui-Zhen

    2018-02-01

    Potassium channels mainly contribute to the resting potential and re-polarizations, with the potassium electrochemical gradient being maintained by the pump Na+/K+-ATPase. In this paper, we construct a stochastic model mimicking the kinetics of a potassium channel, which integrates temporal evolving of the membrane voltage and the spontaneous gating of the channel. Its stationary probability density functions (PDFs) are found to be singular at the boundaries, which result from the fact that the evolving rates of voltage are greater than the gating rates of the channel. We apply PDFs to calculate the power dissipations of the potassium current, the leakage, and the gating currents. On a physical perspective, the essential role of the system is the K+-battery charging the leakage (L-)battery. A part of power will inevitably be dissipated among the process. So, the efficiency of energy transference is calculated.

  4. Analysis of gate underlap channel double gate MOS transistor for electrical detection of bio-molecules

    Science.gov (United States)

    Ajay; Narang, Rakhi; Saxena, Manoj; Gupta, Mridula

    2015-12-01

    In this paper, an analytical model for gate drain underlap channel Double-Gate Metal-Oxide-Semiconductor Field-Effect Transistor (DG-MOSFET) for label free electrical detection of biomolecules has been proposed. The conformal mapping technique has been used to derive the expressions for surface potential, lateral electric field, energy bands (i.e. conduction and valence band) and threshold voltage (Vth). Subsequently a full drain current model to analyze the sensitivity of the biosensor has been developed. The shift in the threshold voltage and drain current (after the biomolecules interaction with the gate underlap channel region of the MOS transistor) has been used as a sensing metric. All the characteristic trends have been verified through ATLAS (SILVACO) device simulation results.

  5. Controlling charge current through a DNA based molecular transistor

    Energy Technology Data Exchange (ETDEWEB)

    Behnia, S., E-mail: s.behnia@sci.uut.ac.ir; Fathizadeh, S.; Ziaei, J.

    2017-01-05

    Molecular electronics is complementary to silicon-based electronics and may induce electronic functions which are difficult to obtain with conventional technology. We have considered a DNA based molecular transistor and study its transport properties. The appropriate DNA sequence as a central chain in molecular transistor and the functional interval for applied voltages is obtained. I–V characteristic diagram shows the rectifier behavior as well as the negative differential resistance phenomenon of DNA transistor. We have observed the nearly periodic behavior in the current flowing through DNA. It is reported that there is a critical gate voltage for each applied bias which above it, the electrical current is always positive. - Highlights: • Modeling a DNA based molecular transistor and studying its transport properties. • Choosing the appropriate DNA sequence using the quantum chaos tools. • Choosing the functional interval for voltages via the inverse participation ratio tool. • Detecting the rectifier and negative differential resistance behavior of DNA.

  6. Lighting up left-handed Z-DNA: photoluminescent carbon dots induce DNA B to Z transition and perform DNA logic operations.

    Science.gov (United States)

    Feng, Lingyan; Zhao, Andong; Ren, Jinsong; Qu, Xiaogang

    2013-09-01

    Left-handed Z-DNA has been identified as a transient structure occurred during transcription. DNA B-Z transition has attracted much attention because of not only Z-DNA biological importance but also their relation to disease and DNA nanotechnology. Recently, photoluminescent carbon dots, especially highly luminescent nitrogen-doped carbon dots, have attracted much attention on their applications to bioimaging and gene/drug delivery because of carbon dots with low toxicity, highly stable photoluminescence and controllable surface function. However, it is still unknown whether carbon dots can influence DNA conformation or structural transition, such as B-Z transition. Herein, based on our previous series work on DNA interactions with carbon nanotubes, we report the first example that photoluminescent carbon dots can induce right-handed B-DNA to left-handed Z-DNA under physiological salt conditions with sequence and conformation selectivity. Further studies indicate that carbon dots would bind to DNA major groove with GC preference. Inspired by carbon dots lighting up Z-DNA and DNA nanotechnology, several types of DNA logic gates have been designed and constructed based on fluorescence resonance energy transfer between photoluminescent carbon dots and DNA intercalators.

  7. Inversion gate capacitance of undoped single-gate and double-gate field-effect transistor geometries in the extreme quantum limit

    Energy Technology Data Exchange (ETDEWEB)

    Majumdar, Amlan, E-mail: amajumd@us.ibm.com [IBM Research Division, T. J. Watson Research Center, Yorktown Heights, New York 10598 (United States)

    2015-05-28

    We present first-principle analytical derivations and numerically modeled data to show that the gate capacitance per unit gate area C{sub G} of extremely thin undoped-channel single-gate and double-gate field-effect transistor geometries in the extreme quantum limit with single-subband occupancy can be written as 1/C{sub G} = 1/C{sub OX} + N{sub G}/C{sub DOS} + N{sub G}/ηC{sub WF}, where N{sub G} is the number of gates, C{sub OX} is the oxide capacitance per unit area, C{sub DOS} is the density-of-states capacitance per unit area, C{sub WF} is the wave function spreading capacitance per unit area, and η is a constant on the order of 1.

  8. Biotechnological mass production of DNA origami

    Science.gov (United States)

    Praetorius, Florian; Kick, Benjamin; Behler, Karl L.; Honemann, Maximilian N.; Weuster-Botz, Dirk; Dietz, Hendrik

    2017-12-01

    DNA nanotechnology, in particular DNA origami, enables the bottom-up self-assembly of micrometre-scale, three-dimensional structures with nanometre-precise features. These structures are customizable in that they can be site-specifically functionalized or constructed to exhibit machine-like or logic-gating behaviour. Their use has been limited to applications that require only small amounts of material (of the order of micrograms), owing to the limitations of current production methods. But many proposed applications, for example as therapeutic agents or in complex materials, could be realized if more material could be used. In DNA origami, a nanostructure is assembled from a very long single-stranded scaffold molecule held in place by many short single-stranded staple oligonucleotides. Only the bacteriophage-derived scaffold molecules are amenable to scalable and efficient mass production; the shorter staple strands are obtained through costly solid-phase synthesis or enzymatic processes. Here we show that single strands of DNA of virtually arbitrary length and with virtually arbitrary sequences can be produced in a scalable and cost-efficient manner by using bacteriophages to generate single-stranded precursor DNA that contains target strand sequences interleaved with self-excising ‘cassettes’, with each cassette comprising two Zn2+-dependent DNA-cleaving DNA enzymes. We produce all of the necessary single strands of DNA for several DNA origami using shaker-flask cultures, and demonstrate end-to-end production of macroscopic amounts of a DNA origami nanorod in a litre-scale stirred-tank bioreactor. Our method is compatible with existing DNA origami design frameworks and retains the modularity and addressability of DNA origami objects that are necessary for implementing custom modifications using functional groups. With all of the production and purification steps amenable to scaling, we expect that our method will expand the scope of DNA nanotechnology in

  9. SU-E-T-350: Verification of Gating Performance of a New Elekta Gating Solution: Response Kit and Catalyst System

    International Nuclear Information System (INIS)

    Xie, X; Cao, D; Housley, D; Mehta, V; Shepard, D

    2014-01-01

    Purpose: In this work, we have tested the performance of new respiratory gating solutions for Elekta linacs. These solutions include the Response gating and the C-RAD Catalyst surface mapping system.Verification measurements have been performed for a series of clinical cases. We also examined the beam on latency of the system and its impact on delivery efficiency. Methods: To verify the benefits of tighter gating windows, a Quasar Respiratory Motion Platform was used. Its vertical-motion plate acted as a respiration surrogate and was tracked by the Catalyst system to generate gating signals. A MatriXX ion-chamber array was mounted on its longitudinal-moving platform. Clinical plans are delivered to a stationary and moving Matrix array at 100%, 50% and 30% gating windows and gamma scores were calculated comparing moving delivery results to the stationary result. It is important to note that as one moves to tighter gating windows, the delivery efficiency will be impacted by the linac's beam-on latency. Using a specialized software package, we generated beam-on signals of lengths of 1000ms, 600ms, 450ms, 400ms, 350ms and 300ms. As the gating windows get tighter, one can expect to reach a point where the dose rate will fall to nearly zero, indicating that the gating window is close to beam-on latency. A clinically useful gating window needs to be significantly longer than the latency for the linac. Results: As expected, the use of tighter gating windows improved delivery accuracy. However, a lower limit of the gating window, largely defined by linac beam-on latency, exists at around 300ms. Conclusion: The Response gating kit, combined with the C-RAD Catalyst, provides an effective solution for respiratorygated treatment delivery. Careful patient selection, gating window design, even visual/audio coaching may be necessary to ensure both delivery quality and efficiency. This research project is funded by Elekta

  10. Gate replacement at the Upper Lake Falls development

    International Nuclear Information System (INIS)

    Chen, C.T.; Locke, A.E.; Brown, E.R.

    1998-01-01

    Nova Scotia Power's integrated approach to dam safety was discussed. One of the two intake gates at Unit 1 of the Upper Falls Power Plant on the Mersey River was replaced in 1997 as part of the Utility's upgrading program. In the event of governor failure or turbine runaway, the new roller gate will allow operators to close the original sliding gate first under a more-or-less balanced head condition, and then to close the new roller gate under a full-flow condition. The planning, design and construction of the new roller gate is described. One of the two head gates of Unit 2 at the same station will be replaced in a similar fashion in the fall of 1998. 4 refs., 7 figs

  11. Modeling and Simulating Airport Surface Operations with Gate Conflicts

    Science.gov (United States)

    Zelinski, Shannon; Windhorst, Robert

    2017-01-01

    The Surface Operations Simulator and Scheduler (SOSS) is a fast-time simulation platform used to develop and test future surface scheduling concepts such as NASAs Air Traffic Demonstration 2 of time-based surface metering at Charlotte Douglas International Airport (CLT). Challenges associated with CLT surface operations have driven much of SOSS development. Recently, SOSS functionality for modeling hardstand operations was developed to address gate conflicts, which occur when an arrival and departure wish to occupy the same gate at the same time. Because surface metering concepts such as ATD2 have the potential to increase gates conflicts as departure are held at their gates, it is important to study the interaction between surface metering and gate conflict management. Several approaches to managing gate conflicts with and without the use of hardstands were simulated and their effects on surface operations and scheduler performance compared.

  12. Double gated-integrator for shaping nuclear radiation detector signals

    International Nuclear Information System (INIS)

    Gal, J.

    2001-01-01

    A new shaper, the double gated-integrator, for shaping nuclear radiation detector signals is investigated both theoretically and experimentally. The double gated-integrator consists of a pre-filter and two cascaded gated integrators. Two kinds of pre-filters were considered: a rectangular one and an exponential one. The results of the theoretical calculation show that the best figure of demerit for the double gated-integrator with exponential pre-filter is 1.016. This means that its noise to signal ratio is only 1.6% worse than that it is for infinite cusp shaping. The practical realization of the exponential pre-filter and that of the double gated integrator, both in analogue and in digital way, is very simple. Therefore, the double gated-integrator with exponential pre-filter could be a promising solution for shaping nuclear radiation detector signals

  13. Biophysics, Pathophysiology and Pharmacology of Ion Channel Gating Pores

    Directory of Open Access Journals (Sweden)

    Adrien eMoreau

    2014-04-01

    Full Text Available Voltage sensor domain (VSDs are a feature of voltage gated ion channel (VGICs and voltage sensitive proteins. They are composed of four transmembrane (TM segments (S1 to S4. Currents leaking through VSDs are called omega or gating pore currents.Gating pores are caused by mutations of the highly conserved positively charged amino acids in the S4 segment that disrupt interactions between the S4 segment and the gating charge transfer center (GCTC. The GCTC separates the intracellular and extracellular water crevices. The disruption of S4–GCTC interactions allows these crevices to communicate and create a fast activating and non-inactivating alternative cation-selective permeation pathway of low conductance, or a gating pore.Gating pore currents have recently been shown to cause periodic paralysis phenotypes. There is also increasing evidence that gating pores are linked to several other familial diseases. For example, gating pores in Nav1.5 and Kv7.2 channels may underlie mixed arrhythmias associated with dilated cardiomyopathy (DCM phenotypes and peripheral nerve hyperexcitability (PNH respectively. There is little evidence for the existence of gating pore blockers. Moreover, it is known that a number of toxins bind to the VSD of a specific domain of Na+ channels. These toxins may thus modulate gating pore currents. This focus on the VSD motif opens up a new area of research centered on developing molecules to treat a number of cell excitability disorders such as epilepsy, cardiac arrhythmias, and pain.The purpose of the present review is to summarize existing knowledge of the pathophysiology, biophysics, and pharmacology of gating pore currents and to serve as a guide for future studies aimed at improving our understanding of gating pores and their pathophysiological roles.

  14. Screening for protein-DNA interactions by automatable DNA-protein interaction ELISA.

    Directory of Open Access Journals (Sweden)

    Luise H Brand

    Full Text Available DNA-binding proteins (DBPs, such as transcription factors, constitute about 10% of the protein-coding genes in eukaryotic genomes and play pivotal roles in the regulation of chromatin structure and gene expression by binding to short stretches of DNA. Despite their number and importance, only for a minor portion of DBPs the binding sequence had been disclosed. Methods that allow the de novo identification of DNA-binding motifs of known DBPs, such as protein binding microarray technology or SELEX, are not yet suited for high-throughput and automation. To close this gap, we report an automatable DNA-protein-interaction (DPI-ELISA screen of an optimized double-stranded DNA (dsDNA probe library that allows the high-throughput identification of hexanucleotide DNA-binding motifs. In contrast to other methods, this DPI-ELISA screen can be performed manually or with standard laboratory automation. Furthermore, output evaluation does not require extensive computational analysis to derive a binding consensus. We could show that the DPI-ELISA screen disclosed the full spectrum of binding preferences for a given DBP. As an example, AtWRKY11 was used to demonstrate that the automated DPI-ELISA screen revealed the entire range of in vitro binding preferences. In addition, protein extracts of AtbZIP63 and the DNA-binding domain of AtWRKY33 were analyzed, which led to a refinement of their known DNA-binding consensi. Finally, we performed a DPI-ELISA screen to disclose the DNA-binding consensus of a yet uncharacterized putative DBP, AtTIFY1. A palindromic TGATCA-consensus was uncovered and we could show that the GATC-core is compulsory for AtTIFY1 binding. This specific interaction between AtTIFY1 and its DNA-binding motif was confirmed by in vivo plant one-hybrid assays in protoplasts. Thus, the value and applicability of the DPI-ELISA screen for de novo binding site identification of DBPs, also under automatized conditions, is a promising approach for a

  15. Technical aspects of image-guided respiration-gated radiation therapy

    International Nuclear Information System (INIS)

    Jiang, Steve B.

    2006-01-01

    In this review article, we discuss various technical aspects of image-guided respiration-gated radiation therapy. We first review some basic concepts related to respiratory gating, including gating window, duty cycle, residual motion, internal/external gating, amplitude/phase gating, etc. We then discuss 2 implementations of image-guided respiration-gated treatment, i.e., the Mitsubishi/Hokkaido technique for internal gating and the MGH technique for external gating. Several existing problems related to respiratory gating, namely external gating mode (phase vs. amplitude), imaging dose for internal gating, gated treatment for lung cancer without implanted fiducial makers, as well as gated intensity-modulated radiation therapy issues, are also discussed along with potential solutions

  16. Electrochemical Single-Molecule Transistors with Optimized Gate Coupling

    DEFF Research Database (Denmark)

    Osorio, Henrry M.; Catarelli, Samantha; Cea, Pilar

    2015-01-01

    . These data are rationalized in terms of a two-step electrochemical model for charge transport across the redox bridge. In this model the gate coupling in the ionic liquid is found to be fully effective with a modeled gate coupling parameter, ξ, of unity. This compares to a much lower gate coupling parameter......Electrochemical gating at the single molecule level of viologen molecular bridges in ionic liquids is examined. Contrary to previous data recorded in aqueous electrolytes, a clear and sharp peak in the single molecule conductance versus electrochemical potential data is obtained in ionic liquids...

  17. Optimal length of decomposition sequences composed of imperfect gates

    Science.gov (United States)

    Nam, Y. S.; Blümel, R.

    2017-05-01

    Quantum error correcting circuitry is both a resource for correcting errors and a source for generating errors. A balance has to be struck between these two aspects. Perfect quantum gates do not exist in nature. Therefore, it is important to investigate how flaws in the quantum hardware affect quantum computing performance. We do this in two steps. First, in the presence of realistic, faulty quantum hardware, we establish how quantum error correction circuitry achieves reduction in the extent of quantum information corruption. Then, we investigate fault-tolerant gate sequence techniques that result in an approximate phase rotation gate, and establish the existence of an optimal length L_{ {opt}} of the length L of the decomposition sequence. The existence of L_{ {opt}} is due to the competition between the increase in gate accuracy with increasing L, but the decrease in gate performance due to the diffusive proliferation of gate errors due to faulty basis gates. We present an analytical formula for the gate fidelity as a function of L that is in satisfactory agreement with the results of our simulations and allows the determination of L_{ {opt}} via the solution of a transcendental equation. Our result is universally applicable since gate sequence approximations also play an important role, e.g., in atomic and molecular physics and in nuclear magnetic resonance.

  18. Heavy-ion-induced, gate-rupture in power MOSFETs

    International Nuclear Information System (INIS)

    Fischer, T.A.

    1987-01-01

    A new, heavy-ion-induced, burnout mechanism has been experimentally observed in power metal-oxide-semiconductor field-effect transistors (MOSFETs). This mechanism occurs when a heavy, charged particle passes through the gate oxide region of n- or p-channel devices having sufficient gate-to-source or gate-to-drain bias. The gate-rupture leads to significant permanent degradation of the device. A proposed failure mechanism is discussed and experimentally verified. In addition, the absolute immunity of p-channel devices to heavy-ion-induced, semiconductor burnout is demonstrated and discussed along with new, non-destructive, burnout testing methods

  19. Speed control system for an access gate

    Science.gov (United States)

    Bzorgi, Fariborz M [Knoxville, TN

    2012-03-20

    An access control apparatus for an access gate. The access gate typically has a rotator that is configured to rotate around a rotator axis at a first variable speed in a forward direction. The access control apparatus may include a transmission that typically has an input element that is operatively connected to the rotator. The input element is generally configured to rotate at an input speed that is proportional to the first variable speed. The transmission typically also has an output element that has an output speed that is higher than the input speed. The input element and the output element may rotate around a common transmission axis. A retardation mechanism may be employed. The retardation mechanism is typically configured to rotate around a retardation mechanism axis. Generally the retardation mechanism is operatively connected to the output element of the transmission and is configured to retard motion of the access gate in the forward direction when the first variable speed is above a control-limit speed. In many embodiments the transmission axis and the retardation mechanism axis are substantially co-axial. Some embodiments include a freewheel/catch mechanism that has an input connection that is operatively connected to the rotator. The input connection may be configured to engage an output connection when the rotator is rotated at the first variable speed in a forward direction and configured for substantially unrestricted rotation when the rotator is rotated in a reverse direction opposite the forward direction. The input element of the transmission is typically operatively connected to the output connection of the freewheel/catch mechanism.

  20. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  1. DNA Vaccines

    Indian Academy of Sciences (India)

    DNA vaccine, immune response, antibodies, infectious diseases. GENERAL I ARTICLE. DNA Vaccines. P N Rangarajan. History of Vaccine Development. The year 1996 marked the 200th anniversary of the first vaccine developed against smallpox by Edward Jenner. In the now- famous 1796 experiment, Jenner scratched ...

  2. Hyperstretching DNA

    NARCIS (Netherlands)

    Schakenraad, Koen; Biebricher, Andreas S.; Sebregts, Maarten; Ten Bensel, Brian; Peterman, Erwin J.G.; Wuite, Gijs J L; Heller, Iddo; Storm, Cornelis; Van Der Schoot, Paul

    2017-01-01

    The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely

  3. Temporary new opening hours for Gate C

    CERN Multimedia

    GS Department

    2010-01-01

    Please note the new temporary opening hours for the gate C as from 22 September 2010 until 29 October 2010 (working days): Morning: between 7:00 a.m. and 9:00 a.m. Lunch: between 12:00 and 2:00 p.m. Evening: between 5:00 pm and 7:00 p.m. Traffic flow will be permitted in both directions during this period. Please minimize your speed accordingly and respect all road signs. GS-SEM Group General Infrastructure Services Department

  4. Nano-CMOS gate dielectric engineering

    CERN Document Server

    Wong, Hei

    2011-01-01

    According to Moore's Law, not only does the number of transistors in an integrated circuit double every two years, but transistor size also decreases at a predictable rate. At the rate we are going, the downsizing of CMOS transistors will reach the deca-nanometer scale by 2020. Accordingly, the gate dielectric thickness will be shrunk to less than half-nanometer oxide equivalent thickness (EOT) to maintain proper operation of the transistors, leaving high-k materials as the only viable solution for such small-scale EOT. This comprehensive, up-to-date text covering the physics, materials, devic

  5. Visualization of neonatal coronary arteries on multidetector row CT: ECG-gated versus non-ECG-gated technique

    Energy Technology Data Exchange (ETDEWEB)

    Tsai, I.C.; Lee, Tain [Taichung Veterans General Hospital, Department of Radiology, Taichung (China); Medical College of Chung Shan Medical University, Faculty of Medicine, Taichung (China); National Yang Ming University, Department of Medicine and Institute of Clinical Medicine, Taipei (China); Chen, Min-Chi [Taichung Veterans General Hospital, Department of Radiology, Taichung (China); Fu, Yun-Ching [National Yang Ming University, Department of Medicine and Institute of Clinical Medicine, Taipei (China); Taichung Veterans General Hospital, Section of Paediatric Cardiology, Department of Paediatrics, Taichung (China); Jan, Sheng-Lin [Medical College of Chung Shan Medical University, Faculty of Medicine, Taichung (China); Taichung Veterans General Hospital, Section of Paediatric Cardiology, Department of Paediatrics, Taichung (China); Wang, Chung-Chi; Chang, Yen [Taichung Veterans General Hospital, Section of Cardiovascular Surgery, Department of Surgery, Taichung (China)

    2007-08-15

    Multidetector CT (MDCT) seems to be a promising tool for detection of neonatal coronary arteries, but whether the ECG-gated or non-ECG-gated technique should be used has not been established. To compare the detection rate and image quality of neonatal coronary arteries on MDCT using ECG-gated and non-ECG-gated techniques. Twelve neonates with complex congenital heart disease were included. The CT scan was acquired using an ECG-gated technique, and the most quiescent phase of the RR interval was selected to represent the ECG-gated images. The raw data were then reconstructed without the ECG signal to obtain non-ECG-gated images. The detection rate and image quality of nine coronary artery segments in the two sets of images were then compared. A two-tailed paired t test was used with P values <0.05 considered as statistically significant. In all coronary segments the ECG-gated technique had a better detection rate and produced images of better quality. The difference between the two techniques ranged from 25% in the left main coronary artery to 100% in the distal right coronary artery. For neonates referred for MDCT, if evaluation of coronary artery anatomy is important for the clinical management or surgical planning, the ECG-gated technique should be used because it can reliably detect the coronary arteries. (orig.)

  6. A spatially localized architecture for fast and modular DNA computing

    Science.gov (United States)

    Chatterjee, Gourab; Dalchau, Neil; Muscat, Richard A.; Phillips, Andrew; Seelig, Georg

    2017-09-01

    Cells use spatial constraints to control and accelerate the flow of information in enzyme cascades and signalling networks. Synthetic silicon-based circuitry similarly relies on spatial constraints to process information. Here, we show that spatial organization can be a similarly powerful design principle for overcoming limitations of speed and modularity in engineered molecular circuits. We create logic gates and signal transmission lines by spatially arranging reactive DNA hairpins on a DNA origami. Signal propagation is demonstrated across transmission lines of different lengths and orientations and logic gates are modularly combined into circuits that establish the universality of our approach. Because reactions preferentially occur between neighbours, identical DNA hairpins can be reused across circuits. Co-localization of circuit elements decreases computation time from hours to minutes compared to circuits with diffusible components. Detailed computational models enable predictive circuit design. We anticipate our approach will motivate using spatial constraints for future molecular control circuit designs.

  7. Diminished auditory sensory gating during active auditory verbal hallucinations.

    Science.gov (United States)

    Thoma, Robert J; Meier, Andrew; Houck, Jon; Clark, Vincent P; Lewine, Jeffrey D; Turner, Jessica; Calhoun, Vince; Stephen, Julia

    2017-10-01

    Auditory sensory gating, assessed in a paired-click paradigm, indicates the extent to which incoming stimuli are filtered, or "gated", in auditory cortex. Gating is typically computed as the ratio of the peak amplitude of the event related potential (ERP) to a second click (S2) divided by the peak amplitude of the ERP to a first click (S1). Higher gating ratios are purportedly indicative of incomplete suppression of S2 and considered to represent sensory processing dysfunction. In schizophrenia, hallucination severity is positively correlated with gating ratios, and it was hypothesized that a failure of sensory control processes early in auditory sensation (gating) may represent a larger system failure within the auditory data stream; resulting in auditory verbal hallucinations (AVH). EEG data were collected while patients (N=12) with treatment-resistant AVH pressed a button to indicate the beginning (AVH-on) and end (AVH-off) of each AVH during a paired click protocol. For each participant, separate gating ratios were computed for the P50, N100, and P200 components for each of the AVH-off and AVH-on states. AVH trait severity was assessed using the Psychotic Symptoms Rating Scales AVH Total score (PSYRATS). The results of a mixed model ANOVA revealed an overall effect for AVH state, such that gating ratios were significantly higher during the AVH-on state than during AVH-off for all three components. PSYRATS score was significantly and negatively correlated with N100 gating ratio only in the AVH-off state. These findings link onset of AVH with a failure of an empirically-defined auditory inhibition system, auditory sensory gating, and pave the way for a sensory gating model of AVH. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Single electron transistor with P-type sidewall spacer gates.

    Science.gov (United States)

    Lee, Jung Han; Li, Dong Hua; Lee, Joung-Eob; Kang, Kwon-Chil; Kim, Kyungwan; Park, Byung-Gook

    2011-07-01

    A single-electron transistor (SET) is one of the promising solutions to overcome the scaling limit of the Metal-Oxide-Semiconductor Field Effect Transistor (MOSFET). Up to now, various kinds of SETs are being proposed and SETs with a dual gate (DG) structure using an electrical potential barrier have been demonstrated for room temperature operation. To operate DG-SETs, however, extra bias of side gates is necessary. It causes new problems that the electrode for side gates and the extra bias for electrical barrier increase the complexity in circuit design and operation power consumption, respectively. For the reason, a new mechanism using work function (WF) difference is applied to operate a SET at room temperature by three electrodes. Its structure consists of an undoped active region, a control gate, n-doped source/drain electrodes, and metal/silicide or p-type silicon side gates, and a SET with metal/silicide gates or p-type silicon gates forms tunnel barriers induced by work function between an undoped channel and grounded side gates. Via simulation, the effectiveness of the new mechanism is confirmed through various silicide materials that have different WF values. Furthermore, by considering the realistic conditions of the fabrication process, SET with p-type sidewall spacer gates was designed, and its brief fabrication process was introduced. The characteristics of its electrical barrier and the controllability of its control gate were also confirmed via simulation. Finally, a single-hole transistor with n-type sidewall spacer gates was designed.

  9. Error-Transparent Quantum Gates for Small Logical Qubit Architectures

    Science.gov (United States)

    Kapit, Eliot

    2018-02-01

    One of the largest obstacles to building a quantum computer is gate error, where the physical evolution of the state of a qubit or group of qubits during a gate operation does not match the intended unitary transformation. Gate error stems from a combination of control errors and random single qubit errors from interaction with the environment. While great strides have been made in mitigating control errors, intrinsic qubit error remains a serious problem that limits gate fidelity in modern qubit architectures. Simultaneously, recent developments of small error-corrected logical qubit devices promise significant increases in logical state lifetime, but translating those improvements into increases in gate fidelity is a complex challenge. In this Letter, we construct protocols for gates on and between small logical qubit devices which inherit the parent device's tolerance to single qubit errors which occur at any time before or during the gate. We consider two such devices, a passive implementation of the three-qubit bit flip code, and the author's own [E. Kapit, Phys. Rev. Lett. 116, 150501 (2016), 10.1103/PhysRevLett.116.150501] very small logical qubit (VSLQ) design, and propose error-tolerant gate sets for both. The effective logical gate error rate in these models displays superlinear error reduction with linear increases in single qubit lifetime, proving that passive error correction is capable of increasing gate fidelity. Using a standard phenomenological noise model for superconducting qubits, we demonstrate a realistic, universal one- and two-qubit gate set for the VSLQ, with error rates an order of magnitude lower than those for same-duration operations on single qubits or pairs of qubits. These developments further suggest that incorporating small logical qubits into a measurement based code could substantially improve code performance.

  10. Gate-first integration of tunable work function metal gates of different thicknesses into high-k metal gates CMOS FinFETs for multi- VTh engineering

    KAUST Repository

    Hussain, Muhammad Mustafa

    2010-03-01

    Gate-first integration of tunable work function metal gates of different thicknesses (320 nm) into high-k/metal gates CMOS FinFETs was demonstrated to achieve multiple threshold voltages (VTh) for 32-nm technology and beyond logic, memory, input/output, and system-on-a-chip applications. The fabricated devices showed excellent short-channel effect immunity (drain-induced barrier lowering ∼ 40 mV/V), nearly symmetric VTh, low T inv(∼ 1.4 nm), and high Ion(∼780μAμm) for N/PMOS without any intentional strain enhancement. © 2006 IEEE.

  11. DNA probes

    International Nuclear Information System (INIS)

    Castelino, J.

    1992-01-01

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  12. Nrf1 CNC-bZIP protein promotes cell survival and nucleotide excision repair through maintaining glutathione homeostasis.

    Science.gov (United States)

    Han, Weinong; Ming, Mei; Zhao, Rui; Pi, Jingbo; Wu, Chunli; He, Yu-Ying

    2012-05-25

    Skin cancer is the most common cancer in the United States. Its major environmental risk factor is UVB radiation in sunlight. In response to UVB damage, epidermal keratinocytes activate a specific repair pathway, i.e. nucleotide excision repair, to remove UVB-induced DNA lesions. However, the regulation of UVB response is not fully understood. Here we show that the long isoform of the nuclear factor erythroid 2-related factor 1 (Nrf1, also called NFE2L1), a cytoprotective transcription factor critical for the expression of multiple antioxidant response element-dependent genes, plays an important role in the response of keratinocytes to UVB. Nrf1 loss sensitized keratinocytes to UVB-induced apoptosis by up-regulating the expression of the proapoptotic Bcl-2 family member Bik through reducing glutathione levels. Knocking down Bik reduced UVB-induced apoptosis in Nrf1-inhibited cells. In UVB-irradiated surviving cells, however, disruption of Nrf1 impaired nucleotide excision repair through suppressing the transcription of xeroderma pigmentosum C (XPC), a factor essential for initiating the global genome nucleotide excision repair by recognizing the DNA lesion and recruiting downstream factors. Nrf1 enhanced XPC expression by increasing glutathione availability but was independent of the transcription repressor of XPC. Adding XPC or glutathione restored the DNA repair capacity in Nrf1-inhibited cells. Finally, we demonstrate that Nrf1 levels are significantly reduced by UVB radiation in mouse skin and are lower in human skin tumors than in normal skin. These results indicate a novel role of Nrf1 in UVB-induced DNA damage repair and suggest Nrf1 as a tumor suppressor in the skin.

  13. Universal quantum gates for Single Cooper Pair Box based quantum computing

    Science.gov (United States)

    Echternach, P.; Williams, C. P.; Dultz, S. C.; Braunstein, S.; Dowling, J. P.

    2000-01-01

    We describe a method for achieving arbitrary 1-qubit gates and controlled-NOT gates within the context of the Single Cooper Pair Box (SCB) approach to quantum computing. Such gates are sufficient to support universal quantum computation.

  14. The SlZRT1 Gene Encodes a Plasma Membrane-Located ZIP (Zrt-, Irt-Like Protein Transporter in the Ectomycorrhizal Fungus Suillus luteus

    Directory of Open Access Journals (Sweden)

    Laura Coninx

    2017-11-01

    Full Text Available Zinc (Zn is an essential micronutrient but may become toxic when present in excess. In Zn-contaminated environments, trees can be protected from Zn toxicity by their root-associated micro-organisms, in particular ectomycorrhizal fungi. The mechanisms of cellular Zn homeostasis in ectomycorrhizal fungi and their contribution to the host tree’s Zn status are however not yet fully understood. The aim of this study was to identify and characterize transporters involved in Zn uptake in the ectomycorrhizal fungus Suillus luteus, a cosmopolitan pine mycobiont. Zn uptake in fungi is known to be predominantly governed by members of the ZIP (Zrt/IrtT-like protein family of Zn transporters. Four ZIP transporter encoding genes were identified in the S. luteus genome. By in silico and phylogenetic analysis, one of these proteins, SlZRT1, was predicted to be a plasma membrane located Zn importer. Heterologous expression in yeast confirmed the predicted function and localization of the protein. A gene expression analysis via RT-qPCR was performed in S. luteus to establish whether SlZRT1 expression is affected by external Zn concentrations. SlZRT1 transcripts accumulated almost immediately, though transiently upon growth in the absence of Zn. Exposure to elevated concentrations of Zn resulted in a significant reduction of SlZRT1 transcripts within the first hour after initiation of the exposure. Altogether, the data support a role as cellular Zn importer for SlZRT1 and indicate a key role in cellular Zn uptake of S. luteus. Further research is needed to understand the eventual contribution of SlZRT1 to the Zn status of the host plant.

  15. Cross-sectional association between ZIP code-level gentrification and homelessness among a large community-based sample of people who inject drugs in 19 US cities.

    Science.gov (United States)

    Linton, Sabriya L; Cooper, Hannah Lf; Kelley, Mary E; Karnes, Conny C; Ross, Zev; Wolfe, Mary E; Friedman, Samuel R; Jarlais, Don Des; Semaan, Salaam; Tempalski, Barbara; Sionean, Catlainn; DiNenno, Elizabeth; Wejnert, Cyprian; Paz-Bailey, Gabriela

    2017-06-20

    Housing instability has been associated with poor health outcomes among people who inject drugs (PWID). This study investigates the associations of local-level housing and economic conditions with homelessness among a large sample of PWID, which is an underexplored topic to date. PWID in this cross-sectional study were recruited from 19 large cities in the USA as part of National HIV Behavioral Surveillance. PWID provided self-reported information on demographics, behaviours and life events. Homelessness was defined as residing on the street, in a shelter, in a single room occupancy hotel, or in a car or temporarily residing with friends or relatives any time in the past year. Data on county-level rental housing unaffordability and demand for assisted housing units, and ZIP code-level gentrification (eg, index of percent increases in non-Hispanic white residents, household income, gross rent from 1990 to 2009) and economic deprivation were collected from the US Census Bureau and Department of Housing and Urban Development. Multilevel models evaluated the associations of local economic and housing characteristics with homelessness. Sixty percent (5394/8992) of the participants reported homelessness in the past year. The multivariable model demonstrated that PWID living in ZIP codes with higher levels of gentrification had higher odds of homelessness in the past year (gentrification: adjusted OR=1.11, 95% CI=1.04 to 1.17). Additional research is needed to determine the mechanisms through which gentrification increases homelessness among PWID to develop appropriate community-level interventions. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  16. Implementation of a funnel-and-gate trademark remediation system

    International Nuclear Information System (INIS)

    O'Brien, K.; Keyes, G.; Sherman, N.

    1997-01-01

    Funnel-and-gate trademark systems are gaining attention, not necessarily because they speed up the remediation process, but because their use recognizes the limitations of groundwater cleanup programs and factors these limitations into minimizing the lifetime costs of implementing remedial actions. The term funnel-and-gate refers to the installation of low-permeability barriers downgradient of impacted groundwater which are arranged so as to direct the flow of the groundwater through treatment gates. The flow through the treatment gates is driven by natural groundwater gradients, eliminating extraction pumps and above-ground treatment systems. The treatment gates are designed specifically to treat the contamination in the groundwater that will flow through the gates. Funnel-and-gate trademark systems attempt to eliminate or at least minimize mechanical systems, thereby reducing the long-term operation and maintenance costs that so often drive up the lifetime costs of remedial projects. Long-term operation and maintenance costs are reduced because the site does not need a continuous input of energy or manpower. In addition, groundwater monitoring and system compliance issues can be streamlined for even greater cost savings. Since it is a developing technology, there are few commercial applications where funnel-and-gate trademark systems have been proven. Concurrent with groundwater investigations, a number of remedial actions had been undertaken at a property in California. Underground storage tanks which contain diesel fuels were excavated and removed. A former dry well suspected of being the source of chlorinated-solvent impacts was also excavated

  17. Subframe burst gating for Raman spectroscopy in combustion.

    Science.gov (United States)

    Kojima, Jun; Fischer, David; Nguyen, Quang-Viet

    2010-05-01

    We describe an architecture for spontaneous Raman scattering utilizing a frame-transfer CCD sensor operating in a subframe burst-gating mode to realize time-resolved combustion diagnostics. The technique permits all-electronic optical gating with microsecond shutter speeds (noise.

  18. Oracle GoldenGate 12c implementer's guide

    CERN Document Server

    Jeffries, John P

    2015-01-01

    The book is aimed at Oracle database administrators, project managers, and solution architects who wish to extend their knowledge of GoldenGate. The reader is assumed to be familiar with Oracle databases. No knowledge of GoldenGate is required.

  19. Implementation of a funnel-and-gate remediation system

    International Nuclear Information System (INIS)

    O'Brien, K.; Keyes, G.; Sherman, N.

    1997-01-01

    A funnel-and-gate trademark system incorporating activated carbon was deemed the most attractive remediation method for an active lumber mill in the western United States. Petroleum hydrocarbons, chlorinated solvents, pentachlorophenol, and tetrachlorophenol were detected in on-site groundwater samples. The shallow aquifer consists of a heterogeneous mixture of marine deposits and artificial fill, underlain by low-permeability siltstones and mudstone. In the funnel-and-gate trademark system, a low-permeability cutoff wall was installed to funnel groundwater flow to a smaller area (a open-quotes gateclose quotes) where a passive below-grade treatment system treats the plume as it flows through the gate. Groundwater flow modeling focused on the inhomogeneities of the aquifer and the spatial relationship between gate(s) and barrier walls. The gate design incorporates several factors, including contaminant concentration, flow rate, and time between carbon changeouts. To minimize back pressure and maximize residence time, each gate was designed using 1.25-meter (4-foot) diameter corrugated metal pipe filled with a 1.25-meter (4-foot) thick bed of activated carbon. The configuration will allow water to flow through the treatment gates without pumps. The installed system is 190 meters (625 feet) long and treats approximately 76 L/min (20 gpm) during the winter months

  20. Gate controlled high efficiency ballistic energy conversion system

    NARCIS (Netherlands)

    Xie, Yanbo; Bos, Diederik; de Boer, Hans L.; van den Berg, Albert; Eijkel, Jan C.T.; Zengerle, R.

    2013-01-01

    Last year we demonstrated the microjet ballistic energy conversion system[1]. Here we show that the efficiency of such a system can be further improved by gate control. With gate control the electrical current generation is enhanced a hundred times with respect to the current generated from the zeta

  1. Development of insulated gate bipolar transistor-based power ...

    Indian Academy of Sciences (India)

    [5] S V Nakhe et al, National Laser Symposium, 81–82 (2001). [6] E G Cook et al, 8th IEEE Pulsed Power Conference, June 1991. [7] L Druckmann et al, IEEE Power Modulator Symposium, 213–216 (1992). [8] Hybrid gate drivers and gate drive power supplies, M57962L datasheet from Mitsubishi. Electric Corpn. Pramana ...

  2. Tunnel field-effect transistor with two gated intrinsic regions

    Directory of Open Access Journals (Sweden)

    Y. Zhang

    2014-07-01

    Full Text Available In this paper, we propose and validate (using simulations a novel design of silicon tunnel field-effect transistor (TFET, based on a reverse-biased p+-p-n-n+ structure. 2D device simulation results show that our devices have significant improvements of switching performance compared with more conventional devices based on p-i-n structure. With independent gate voltages applied to two gated intrinsic regions, band-to-band tunneling (BTBT could take place at the p-n junction, and no abrupt degenerate doping profile is required. We developed single-side-gate (SSG structure and double-side-gate (DSG structure. SSG devices with HfO2 gate dielectric have a point subthreshold swing of 9.58 mV/decade, while DSG devices with polysilicon gate electrode material and HfO2 gate dielectric have a point subthreshold swing of 16.39 mV/decade. These DSG devices have ON-current of 0.255 μA/μm, while that is lower for SSG devices. Having two nano-scale independent gates will be quite challenging to realize with good uniformity across the wafer and the improved behavior of our TFET makes it a promising steep-slope switch candidate for further investigations.

  3. Gated developments: International experiences and the South African context

    CSIR Research Space (South Africa)

    Spocter, M

    2012-03-01

    Full Text Available developments in the form of secure estates or fortified townhouse complexes. A review of international research on gated developments reveals four broad themes into which such research can be placed. South African gated development research is discussed within...

  4. A self-aligned gate definition process with submicron gaps

    NARCIS (Netherlands)

    Warmerdam, L.F.P.; Aarnink, Antonius A.I.; Holleman, J.; Wallinga, Hans

    1989-01-01

    A self-aligned gate definition process is proposed. Spacings between adjacent gates of 0.5 µm and smaller are fabricated. The spacing is realized by an edge-etch technique, combined with anisotropic plasma etching of the single poly-silicon layer. Straight gaps with minor width variation are

  5. Quantum computer gate simulations | Dada | Journal of the Nigerian ...

    African Journals Online (AJOL)

    A new interactive simulator for Quantum Computation has been developed for simulation of the universal set of quantum gates and for construction of new gates of up to 3 qubits. The simulator also automatically generates an equivalent quantum circuit for any arbitrary unitary transformation on a qubit. Available quantum ...

  6. DNA data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  7. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  8. DNA nanotechnology

    Science.gov (United States)

    Seeman, Nadrian C.; Sleiman, Hanadi F.

    2018-01-01

    DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.

  9. Cleaning Challenges of High-κ/Metal Gate Structures

    KAUST Repository

    Hussain, Muhammad Mustafa

    2010-12-20

    High-κ/metal gates are used as transistors for advanced logic applications to improve speed and eliminate electrical issues associated with polySi and SiO2 gates. Various integration schemes are possible and will be discussed, such as dual gate, gate-first, and gate-last, both of which require specialized cleaning and etching steps. Specific areas of discussion will include cleaning and conditioning of the silicon surface, forming a high-quality chemical oxide, removal of the high-κ dielectric with selectivity to the SiO2 layer, cleaning and residue removal after etching, and prevention of galvanic corrosion during cleaning. © 2011 Scrivener Publishing LLC. All rights reserved.

  10. Flexible Proton-Gated Oxide Synaptic Transistors on Si Membrane.

    Science.gov (United States)

    Zhu, Li Qiang; Wan, Chang Jin; Gao, Ping Qi; Liu, Yang Hui; Xiao, Hui; Ye, Ji Chun; Wan, Qing

    2016-08-24

    Ion-conducting materials have received considerable attention for their applications in fuel cells, electrochemical devices, and sensors. Here, flexible indium zinc oxide (InZnO) synaptic transistors with multiple presynaptic inputs gated by proton-conducting phosphorosilicate glass-based electrolyte films are fabricated on ultrathin Si membranes. Transient characteristics of the proton gated InZnO synaptic transistors are investigated, indicating stable proton-gating behaviors. Short-term synaptic plasticities are mimicked on the proposed proton-gated synaptic transistors. Furthermore, synaptic integration regulations are mimicked on the proposed synaptic transistor networks. Spiking logic modulations are realized based on the transition between superlinear and sublinear synaptic integration. The multigates coupled flexible proton-gated oxide synaptic transistors may be interesting for neuroinspired platforms with sophisticated spatiotemporal information processing.

  11. A System For High Flexibility Entangling Gates With Trapped Ions

    Science.gov (United States)

    Milne, Alistair; Edmunds, Claire; Mavadia, Sandeep; Green, Todd; Biercuk, Michael

    Trapped ion qubits may be entangled via coupling to shared modes of motion using spin-dependent forces generated by optical fields. Residual qubit-motional coupling at the conclusion of the entangling operation is the dominant source of infidelity in this type of gate. For synchronously entangling increasing numbers of ions, longer gate times are required to minimise this residual coupling. We present a scheme that enables the state of each qubit to be simultaneously decoupled from all motional modes in an arbitrarily chosen gate time, increasing the gate fidelity and scalability. This is achieved by implementing discrete phase shifts in the optical field moderating the entangling operation. We describe an experimental system based on trapped ytterbium ions and demonstrate this scheme for two-qubit entangling gates on ytterbium ion pairs.

  12. Robust quantum gates between trapped ions using shaped pulses

    Energy Technology Data Exchange (ETDEWEB)

    Zou, Ping, E-mail: zouping@m.scnu.edu.cn; Zhang, Zhi-Ming, E-mail: zmzhang@scnu.edu.cn

    2015-12-18

    We improve two existing entangling gate schemes between trapped ion qubits immersed in a large linear crystal. Based on the existing two-qubit gate schemes by applying segmented forces on the individually addressed qubits, we present a systematic method to optimize the shapes of the forces to suppress the dominant source of infidelity. The spin-dependent forces in the scheme can be from periodic photon kicks or from continuous optical pulses. The entangling gates are fast, robust, and have high fidelity. They can be used to implement scalable quantum computation and quantum simulation. - Highlights: • We present a systematic method to optimize the shape of the pulses to decouple qubits from intermediary motional modes. • Our optimized scheme can be applied to both the ultrafast gate and fast gate. • Our optimized scheme can suppress the dominant source of infidelity to arbitrary order. • When the number of trapped ions increase, the number of needed segments increases slowly.

  13. Possibilities Of Opening Up the Stage-Gate Model

    Directory of Open Access Journals (Sweden)

    Biljana Stošić

    2014-12-01

    Full Text Available The paper presents basic elements of the Stage-Gate and Open innovation models, and possible connection of these two, resulting in what is frequently called an “Open Stage-Gate” model. This connection is based on opening up the new product development process and integration of the open innovation principles with the Stage-Gate concept, facilitating the import and export of information and technologies. Having in mind that the Stage Gate has originally been classified as the third generation model of innovation, the paper is dealing with the capabilities for applying the sixth generation Open innovation principles in today’s improved and much more flexible phases and gates of the Stage Gate. Lots of innovative companies are actually using both models in their NPD practice, looking for the most appropriate means of opening up the well-known closed innovation, especially in the domain of ideation through co-creation.

  14. Single-atom gating and magnetic interactions in quantum corrals

    Energy Technology Data Exchange (ETDEWEB)

    Ngo, Anh T.; Kim, Eugene H.; Ulloa, Sergio E.

    2017-04-01

    Single-atom gating, achieved by manipulation of adatoms on a surface, has been shown in experiments to allow precise control over superposition of electronic states in quantum corrals. Using a Green's function approach, we demonstrate theoretically that such atom gating can also be used to control the coupling between magnetic degrees of freedom in these systems. Atomic gating enables control not only on the direct interaction between magnetic adatoms, but also over superpositions of many-body states which can then control long distance interactions. We illustrate this effect by considering the competition between direct exchange between magnetic impurities and the Kondo screening mediated by the host electrons, and how this is affected by gating. These results suggest that both magnetic and nonmagnetic single-atom gating may be used to investigate magnetic impurity systems with tailored interactions, and may allow the control of entanglement of different spin states.

  15. Modal gating of muscle nicotinic acetylcholine receptors

    Science.gov (United States)

    Vij, Ridhima

    Many ion channels exhibit multiple patterns of kinetic activity in single-channel currents. This behavior is rare in WT mouse muscle nicotinic acetylcholine receptors (AChRs), where A2C↔A2O gating events are well-described by single exponentials. Also, single-channel open probability (PO) is essentially homogeneous at a given agonist concentration in the WT receptors. Here I report that perturbations of almost all the residues in loop C (alpha188-alpha199, at the agonist binding site) generate heterogeneity in PO ('modes'). Such unsettled activity was apparent with an alanine substitution at all positions in loop C (except alphaY190 and alphaY198) and with different side chain substitutions at alphaP197 for both adult- and fetal-type AChRs. I used single channel electrophysiology along with site-directed mutagenesis to study modal gating in AChRs consequent to mutations/deletions in loop C. The multiple patterns of kinetic activity arose from the difference in agonist affinity rather than in intrinsic AChR gating. Out of the four different agonists used to study the modal behavior, acetylcholine (ACh) showed a higher degree of kinetic heterogeneity compared to others. The time constant for switching between modes was long (~mins), suggesting that they arise from alternative, stable protein conformations. By studying AChRs having only 1 functional binding site, I attempted to find the source of the affinity difference, which was traced mainly to the alphadelta agonist site. Affinity at the neurotransmitter binding site is mainly determined by a core of five aromatic residues (alphaY93, alphaW149, alphaY190, alphaY198 and deltaW57). Phenylalanine substitutions at all aromatic residues except alphaY93 resulted in elimination of modes. Modes were also eliminated by alanine mutation at deltaW57 on the complementary side but not at other aromatics. Also, by substituting four gamma subunit residues into the delta subunit on the complementary beta sheet, I found that

  16. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  17. Integration of biomolecular logic gates with field-effect transducers

    International Nuclear Information System (INIS)

    Poghossian, A.; Malzahn, K.; Abouzar, M.H.; Mehndiratta, P.; Katz, E.; Schoening, M.J.

    2011-01-01

    Highlights: → Enzyme-based AND/OR logic gates are integrated with a capacitive field-effect sensor. → The AND/OR logic gates compose of multi-enzyme system immobilised on sensor surface. → Logic gates were activated by different combinations of chemical inputs (analytes). → The logic output (pH change) produced by the enzymes was read out by the sensor. - Abstract: The integration of biomolecular logic gates with field-effect devices - the basic element of conventional electronic logic gates and computing - is one of the most attractive and promising approaches for the transformation of biomolecular logic principles into macroscopically useable electrical output signals. In this work, capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensors based on a p-Si-SiO 2 -Ta 2 O 5 structure modified with a multi-enzyme membrane have been used for electronic transduction of biochemical signals processed by enzyme-based OR and AND logic gates. The realised OR logic gate composes of two enzymes (glucose oxidase and esterase) and was activated by ethyl butyrate or/and glucose. The AND logic gate composes of three enzymes (invertase, mutarotase and glucose oxidase) and was activated by two chemical input signals: sucrose and dissolved oxygen. The developed integrated enzyme logic gates produce local pH changes at the EIS sensor surface as a result of biochemical reactions activated by different combinations of chemical input signals, while the pH value of the bulk solution remains unchanged. The pH-induced charge changes at the gate-insulator (Ta 2 O 5 ) surface of the EIS transducer result in an electronic signal corresponding to the logic output produced by the immobilised enzymes. The logic output signals have been read out by means of a constant-capacitance method.

  18. Integration of biomolecular logic gates with field-effect transducers

    Energy Technology Data Exchange (ETDEWEB)

    Poghossian, A., E-mail: a.poghossian@fz-juelich.de [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany); Malzahn, K. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Abouzar, M.H. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany); Mehndiratta, P. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Katz, E. [Department of Chemistry and Biomolecular Science, NanoBio Laboratory (NABLAB), Clarkson University, Potsdam, NY 13699-5810 (United States); Schoening, M.J. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany)

    2011-11-01

    Highlights: > Enzyme-based AND/OR logic gates are integrated with a capacitive field-effect sensor. > The AND/OR logic gates compose of multi-enzyme system immobilised on sensor surface. > Logic gates were activated by different combinations of chemical inputs (analytes). > The logic output (pH change) produced by the enzymes was read out by the sensor. - Abstract: The integration of biomolecular logic gates with field-effect devices - the basic element of conventional electronic logic gates and computing - is one of the most attractive and promising approaches for the transformation of biomolecular logic principles into macroscopically useable electrical output signals. In this work, capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensors based on a p-Si-SiO{sub 2}-Ta{sub 2}O{sub 5} structure modified with a multi-enzyme membrane have been used for electronic transduction of biochemical signals processed by enzyme-based OR and AND logic gates. The realised OR logic gate composes of two enzymes (glucose oxidase and esterase) and was activated by ethyl butyrate or/and glucose. The AND logic gate composes of three enzymes (invertase, mutarotase and glucose oxidase) and was activated by two chemical input signals: sucrose and dissolved oxygen. The developed integrated enzyme logic gates produce local pH changes at the EIS sensor surface as a result of biochemical reactions activated by different combinations of chemical input signals, while the pH value of the bulk solution remains unchanged. The pH-induced charge changes at the gate-insulator (Ta{sub 2}O{sub 5}) surface of the EIS transducer result in an electronic signal corresponding to the logic output produced by the immobilised enzymes. The logic output signals have been read out by means of a constant-capacitance method.

  19. Opening of the New Gate E - Final Closure of Gate C - New azur «B» type cern access card

    CERN Multimedia

    Relations with the Host States Service

    2004-01-01

    Gate E ("Charles de Gaulle Gate") to the Meyrin Site will be open, for those entitled to use it, from 1 November 2004. The opening of this Gate should contribute to relieving congestion not only on the Prévessin - RN84 and Meyrin Route border crossings but also at Gates A and B. As a result, Gate C will be closed indefinitely from 1 November 2004. Providing a direct link between the Meyrin Site and the French territory beyond the fenced part of the CERN site, Gate E is the subject of international agreements between CERN, Switzerland and France, on the basis of which the Director-General has issued the "Rules for the Use of Gate E", (document CERN/DSU-RH/12222 of 27 October 2004; see also the latest news in "publications" at http://www.cern.ch/relations/). The main provisions of these Rules are as follows: Gate E is open from Monday to Friday, except on official CERN holidays, from 7.30 a.m. to 9.30 a.m. for access into the site, and from 4.30 p.m. to 6.30 p.m. for passage out of the site. Persons are aut...

  20. Analyses of Short Channel Effects of Single-Gate and Double-Gate Graphene Nanoribbon Field Effect Transistors

    Directory of Open Access Journals (Sweden)

    Hojjatollah Sarvari

    2016-01-01

    Full Text Available Short channel effects of single-gate and double-gate graphene nanoribbon field effect transistors (GNRFETs are studied based on the atomistic pz orbital model for the Hamiltonian of graphene nanoribbon using the nonequilibrium Green’s function formalism. A tight-binding Hamiltonian with an atomistic pz orbital basis set is used to describe the atomistic details in the channel of the GNRFETs. We have investigated the vital short channel effect parameters such as Ion and Ioff, the threshold voltage, the subthreshold swing, and the drain induced barrier lowering versus the channel length and oxide thickness of the GNRFETs in detail. The gate capacitance and the transconductance of both devices are also computed in order to calculate the intrinsic cut-off frequency and switching delay of GNRFETs. Furthermore, the effects of doping of the channel on the threshold voltage and the frequency response of the double-gate GNRFET are discussed. We have shown that the single-gate GNRFET suffers more from short channel effects if compared with those of the double-gate structure; however, both devices have nearly the same cut-off frequency in the range of terahertz. This work provides a collection of data comparing different features of short channel effects of the single gate with those of the double gate GNRFETs. The results give a very good insight into the devices and are very useful for their digital applications.