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.

Artificial modulation of the gating behavior of a K+ channel in a KvAP-DNA chimera.

Directory of Open Access Journals (Sweden)

Andrew Wang

Full Text Available We present experiments where the gating behavior of a voltage-gated ion channel is modulated by artificial ligand binding. We construct a channel-DNA chimera with the KvAP potassium channel reconstituted in an artificial membrane. The channel is functional and the single channel ion conductivity unperturbed by the presence of the DNA. However, the channel opening probability vs. bias voltage, i.e., the gating, can be shifted considerably by the electrostatic force between the charges on the DNA and the voltage sensing domain of the protein. Different hybridization states of the chimera DNA thus lead to different response curves of the channel.

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.

Geographic data: Zip Codes (Shape File)

Data.gov (United States)

Montgomery County of Maryland — This dataset contains all zip codes in Montgomery County. Zip codes are the postal delivery areas defined by USPS. Zip codes with mailboxes only are not included. As...

A ZIP6-ZIP10 heteromer controls NCAM1 phosphorylation and integration into focal adhesion complexes during epithelial-to-mesenchymal transition.

Science.gov (United States)

Brethour, Dylan; Mehrabian, Mohadeseh; Williams, Declan; Wang, Xinzhu; Ghodrati, Farinaz; Ehsani, Sepehr; Rubie, Elizabeth A; Woodgett, James R; Sevalle, Jean; Xi, Zhengrui; Rogaeva, Ekaterina; Schmitt-Ulms, Gerold

2017-01-18

The prion protein (PrP) evolved from the subbranch of ZIP metal ion transporters comprising ZIPs 5, 6 and 10, raising the prospect that the study of these ZIPs may reveal insights relevant for understanding the function of PrP. Building on data which suggested PrP and ZIP6 are critical during epithelial-to-mesenchymal transition (EMT), we investigated ZIP6 in an EMT paradigm using ZIP6 knockout cells, mass spectrometry and bioinformatic methods. Reminiscent of PrP, ZIP6 levels are five-fold upregulated during EMT and the protein forms a complex with NCAM1. ZIP6 also interacts with ZIP10 and the two ZIP transporters exhibit interdependency during their expression. ZIP6 contributes to the integration of NCAM1 in focal adhesion complexes but, unlike cells lacking PrP, ZIP6 deficiency does not abolish polysialylation of NCAM1. Instead, ZIP6 mediates phosphorylation of NCAM1 on a cluster of cytosolic acceptor sites. Substrate consensus motif features and in vitro phosphorylation data point toward GSK3 as the kinase responsible, and interface mapping experiments identified histidine-rich cytoplasmic loops within the ZIP6/ZIP10 heteromer as a novel scaffold for GSK3 binding. Our data suggests that PrP and ZIP6 inherited the ability to interact with NCAM1 from their common ZIP ancestors but have since diverged to control distinct posttranslational modifications of NCAM1.

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

African Journals Online (AJOL)

AJL

2012-06-19

Jun 19, 2012 ... In this study, a novel bZIP-like gene was isolated from Chinese wild Vitis ... Results reveal that it was in lower lever in flower than in leaf, stem, tendril and fruit. .... First-strand cDNA was synthesized from 1 µg of DNase treated.

Biophysical properties of regions flanking the bHLH-Zip motif in the p22 Max protein

International Nuclear Information System (INIS)

Pursglove, Sharon E.; Fladvad, Malin; Bellanda, Massimo; Moshref, Ahmad; Henriksson, Marie; Carey, Jannette; Sunnerhagen, Maria

2004-01-01

The Max protein is the central dimerization partner in the Myc-Max-Mad network of transcriptional regulators, and a founding structural member of the family of basic-helix-loop-helix (bHLH)-leucine zipper (Zip) proteins. Biologically important regions flanking its bHLH-Zip motif have been disordered or absent in crystal structures. The present study shows that these regions are resistant to proteolysis in both the presence and absence of DNA, and that Max dimers containing both flanking regions have significantly higher helix content as measured by circular dichroism than that predicted from the crystal structures. Nuclear magnetic resonance measurements in the absence of DNA also support the inferred structural order. Deletion of both flanking regions is required to achieve maximal DNA affinity as measured by EMSA. Thus, the previously observed functionalities of these Max regions in DNA binding, phosphorylation, and apoptosis are suggested to be linked to structural properties

The role of ZIP transporters and group F bZIP transcription factors in the Zn-deficiency response of wheat (Triticum aestivum).

Science.gov (United States)

Evens, Nicholas P; Buchner, Peter; Williams, Lorraine E; Hawkesford, Malcolm J

2017-10-01

Understanding the molecular basis of zinc (Zn) uptake and transport in staple cereal crops is critical for improving both Zn content and tolerance to low-Zn soils. This study demonstrates the importance of group F bZIP transcription factors and ZIP transporters in responses to Zn deficiency in wheat (Triticum aestivum). Seven group F TabZIP genes and 14 ZIPs with homeologs were identified in hexaploid wheat. Promoter analysis revealed the presence of Zn-deficiency-response elements (ZDREs) in a number of the ZIPs. Functional complementation of the zrt1/zrt2 yeast mutant by TaZIP3, -6, -7, -9 and -13 supported an ability to transport Zn. Group F TabZIPs contain the group-defining cysteine-histidine-rich motifs, which are the predicted binding site of Zn 2+ in the Zn-deficiency response. Conservation of these motifs varied between the TabZIPs suggesting that individual TabZIPs may have specific roles in the wheat Zn-homeostatic network. Increased expression in response to low Zn levels was observed for several of the wheat ZIPs and bZIPs; this varied temporally and spatially suggesting specific functions in the response mechanism. The ability of the group F TabZIPs to bind to specific ZDREs in the promoters of TaZIPs indicates a conserved mechanism in monocots and dicots in responding to Zn deficiency. In support of this, TabZIPF1-7DL and TabZIPF4-7AL afforded a strong level of rescue to the Arabidopsis hypersensitive bzip19 bzip23 double mutant under Zn deficiency. These results provide a greater understanding of Zn-homeostatic mechanisms in wheat, demonstrating an expanded repertoire of group F bZIP transcription factors, adding to the complexity of Zn homeostasis. © 2017 The Authors The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

Divergence of the bZIP Gene Family in Strawberry, Peach, and Apple Suggests Multiple Modes of Gene Evolution after Duplication

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Xiao-Long Wang

2015-01-01

Full Text Available The basic leucine zipper (bZIP transcription factors are the most diverse members of dimerizing transcription factors. In the present study, 50, 116, and 47 bZIP genes were identified in Malus domestica (apple, Prunus persica (peach, and Fragaria vesca (strawberry, respectively. Species-specific duplication was the main contributor to the large number of bZIPs observed in apple. After WGD in apple genome, orthologous bZIP genes corresponding to strawberry on duplicated regions in apple genome were retained. However, in peach ancestor, these syntenic regions were quickly lost or deleted. Maybe the positive selection contributed to the expansion of clade S to adapt to the development and environment stresses. In addition, purifying selection was mainly responsible for bZIP sequence-specific DNA binding. The analysis of orthologous pairs between chromosomes indicates that these orthologs derived from one gene duplication located on one of the nine ancient chromosomes in the Rosaceae. The comparative analysis of bZIP genes in three species provides information on the evolutionary fate of bZIP genes in apple and peach after they diverged from strawberry.

A Reversible DNA Logic Gate Platform Operated by One- and Two-Photon Excitations.

Science.gov (United States)

Tam, Dick Yan; Dai, Ziwen; Chan, Miu Shan; Liu, Ling Sum; Cheung, Man Ching; Bolze, Frederic; Tin, Chung; Lo, Pik Kwan

2016-01-04

We demonstrate the use of two different wavelength ranges of excitation light as inputs to remotely trigger the responses of the self-assembled DNA devices (D-OR). As an important feature of this device, the dependence of the readout fluorescent signals on the two external inputs, UV excitation for 1 min and/or near infrared irradiation (NIR) at 800 nm fs laser pulses, can mimic function of signal communication in OR logic gates. Their operations could be reset easily to its initial state. Furthermore, these DNA devices exhibit efficient cellular uptake, low cytotoxicity, and high bio-stability in different cell lines. They are considered as the first example of a photo-responsive DNA logic gate system, as well as a biocompatible, multi-wavelength excited system in response to UV and NIR. This is an important step to explore the concept of photo-responsive DNA-based systems as versatile tools in DNA computing, display devices, optical communication, and biology. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genome-wide systematic characterization of the bZIP transcriptional factor family in tomato (Solanum lycopersicum L.).

Science.gov (United States)

Li, Dayong; Fu, Fuyou; Zhang, Huijuan; Song, Fengming

2015-10-12

Transcription factors of the basic leucine zipper (bZIP) family represent exclusively in eukaryotes and have been shown to regulate diverse biological processes in plant growth and development as well as in abiotic and biotic stress responses. However, little is known about the bZIP family in tomato (Solanum lycopersicum L.). The SlbZIP genes were identified using local BLAST and hidden Markov model profile searches. The phylogenetic trees, conserved motifs and gene structures were generated by MEGA6.06, MEME tool and gene Structure Display Server, respectively. The syntenic block diagrams were generated by the Circos software. The transcriptional gene expression profiles were obtained using Genevestigator tool and quantitative RT-PCR. In the present study, we carried out a genome-wide identification and systematic analyses of 69 SlbZIP genes that distributes unevenly on the tomato chromosomes. This family can be divided into 9 groups according to the phylogenetic relationship among the SlbZIP proteins. Six kinds of intron patterns (a-f) within the basic and hinge regions are defined. The additional conserved motifs and their presence of the group specificity were also identified. Further, we predicted the DNA-binding patterns and the dimerization property on the basis of the characteristic features in the basic and hinge regions and the leucine zipper, respectively, which supports our classification greatly and helps to classify 24 distinct subfamilies. Within the SlbZIP family, a total of 40 SlbZIP genes are located in the segmental duplicate regions in the tomato genome, suggesting that the segment chromosomal duplications contribute greatly to the expansion of the tomato SlbZIP family. Expression profiling analyses of 59 SlbZIP genes using quantitative RT-PCR and publicly available microarray data indicate that the tomato SlbZIP genes have distinct and diverse expression patterns in different tissues and developmental stages and many of the tomato bZIP genes

A Novel Wheat C-bZIP Gene, TabZIP14-B, Participates in Salt and Freezing Tolerance in Transgenic Plants

Directory of Open Access Journals (Sweden)

Lina Zhang

2017-05-01

Full Text Available The group C-bZIP transcription factors (TFs are involved in diverse biological processes, such as the regulation of seed storage protein (SSP production and the responses to pathogen challenge and abiotic stress. However, our knowledge of the abiotic functions of group C-bZIP genes in wheat remains limited. Here, we present the function of a novel TabZIP14-B gene in wheat. This gene belongs to the group C-bZIP TFs and contains six exons and five introns; three haplotypes were identified among accessions of tetraploid and hexaploid wheat. A subcellular localization analysis indicated that TabZIP14-B was targeted to the nucleus of tobacco epidermal cells. A transactivation assay demonstrated that TabZIP14-B showed transcriptional activation ability and was capable of binding the abscisic acid (ABA responsive element (ABRE in yeast. RT-qPCR revealed that TabZIP14-B was expressed in the roots, stems, leaves, and young spikes and was up-regulated by exogenous ABA, salt, low-temperature, and polyethylene glycol (PEG stress treatments. Furthermore, Arabidopsis plants overexpressing TabZIP14-B exhibited enhanced tolerance to salt, freezing stresses and ABA sensitivity. Overexpression of TabZIP14-B resulted in increased expression of the AtRD29A, AtCOR47, AtRD20, AtGSTF6, and AtRAB18 genes and changes in several physiological characteristics. These results suggest that TabZIP14-B could function as a positive regulator in mediating the abiotic stress response.

Automatic Sequences and Zip-Specifications

NARCIS (Netherlands)

Grabmayer, C.A.; Endrullis, J.; Hendriks, D.; Klop, J.W.; Moss, L.S.

2012-01-01

We consider infinite sequences of symbols, also known as streams, and the decidability question for equality of streams defined in a restricted format. This restricted format consists of prefixing a symbol at the head of a stream, of the stream function `zip', and recursion variables. Here `zip'

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

Soybean extracts increase cell surface ZIP4 abundance and cellular zinc levels: a potential novel strategy to enhance zinc absorption by ZIP4 targeting.

Science.gov (United States)

Hashimoto, Ayako; Ohkura, Katsuma; Takahashi, Masakazu; Kizu, Kumiko; Narita, Hiroshi; Enomoto, Shuichi; Miyamae, Yusaku; Masuda, Seiji; Nagao, Masaya; Irie, Kazuhiro; Ohigashi, Hajime; Andrews, Glen K; Kambe, Taiho

2015-12-01

Dietary zinc deficiency puts human health at risk, so we explored strategies for enhancing zinc absorption. In the small intestine, the zinc transporter ZIP4 functions as an essential component of zinc absorption. Overexpression of ZIP4 protein increases zinc uptake and thereby cellular zinc levels, suggesting that food components with the ability to increase ZIP4 could potentially enhance zinc absorption via the intestine. In the present study, we used mouse Hepa cells, which regulate mouse Zip4 (mZip4) in a manner indistinguishable from that in intestinal enterocytes, to screen for suitable food components that can increase the abundance of ZIP4. Using this ZIP4-targeting strategy, two such soybean extracts were identified that were specifically able to decrease mZip4 endocytosis in response to zinc. These soybean extracts also effectively increased the abundance of apically localized mZip4 in transfected polarized Caco2 and Madin-Darby canine kidney cells and, moreover, two apically localized mZip4 acrodermatitis enteropathica mutants. Soybean components were purified from one extract and soyasaponin Bb was identified as an active component that increased both mZip4 protein abundance and zinc levels in Hepa cells. Finally, we confirmed that soyasaponin Bb is capable of enhancing cell surface endogenous human ZIP4 in human cells. Our results suggest that ZIP4 targeting may represent a new strategy to improve zinc absorption in humans. © 2015 Authors; published by Portland Press Limited.

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.

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.

Multiple advanced logic gates made of DNA-Ag nanocluster and the application for intelligent detection of pathogenic bacterial genes.

Science.gov (United States)

Lin, Xiaodong; Liu, Yaqing; Deng, Jiankang; Lyu, Yanlong; Qian, Pengcheng; Li, Yunfei; Wang, Shuo

2018-02-21

The integration of multiple DNA logic gates on a universal platform to implement advance logic functions is a critical challenge for DNA computing. Herein, a straightforward and powerful strategy in which a guanine-rich DNA sequence lighting up a silver nanocluster and fluorophore was developed to construct a library of logic gates on a simple DNA-templated silver nanoclusters (DNA-AgNCs) platform. This library included basic logic gates, YES, AND, OR, INHIBIT, and XOR, which were further integrated into complex logic circuits to implement diverse advanced arithmetic/non-arithmetic functions including half-adder, half-subtractor, multiplexer, and demultiplexer. Under UV irradiation, all the logic functions could be instantly visualized, confirming an excellent repeatability. The logic operations were entirely based on DNA hybridization in an enzyme-free and label-free condition, avoiding waste accumulation and reducing cost consumption. Interestingly, a DNA-AgNCs-based multiplexer was, for the first time, used as an intelligent biosensor to identify pathogenic genes, E. coli and S. aureus genes, with a high sensitivity. The investigation provides a prototype for the wireless integration of multiple devices on even the simplest single-strand DNA platform to perform diverse complex functions in a straightforward and cost-effective way.

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.

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.

Download - KAIKOcDNA | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available rch and download 1 README README_e.html - 2 EST Table kaiko_cdna_main.zip (157 MB...) Simple search and download 3 Cluster Table kaiko_cdna_cluster.zip (453 KB) Simple search and download 4 ORF Table kaiko_cdna..._orf.zip (11 MB) Simple search and download 5 InterProScan Result kaiko_cdna_interpro.zip ...(3.1 MB) Simple search and download 6 cDNA library Table kaiko_cdna_library.zip (

Bioinformatic Analyses of Subgroup-A Members of the Wheat bZIP Transcription Factor Family and Functional Identification of TabZIP174 Involved in Drought Stress Response

Directory of Open Access Journals (Sweden)

Xueyin Li

2016-11-01

Full Text Available Extensive studies in Arabidopsis and rice have demonstrated that Subgroup-A members of the bZIP transcription factor family play important roles in plant responses to multiple abiotic stresses. Although common wheat (Triticum aestivum is one of the most widely cultivated and consumed food crops in the world, there are limited investigations into Subgroup A of the bZIP family in wheat. In this study, we performed bioinformatic analyses of the 41 Subgroup-A members of the wheat bZIP family. Phylogenetic and conserved motif analyses showed that most of the Subgroup-A bZIP proteins involved in abiotic stress responses of wheat, Arabidopsis and rice clustered in Clade A1 of the phylogenetic tree, and shared a majority of conserved motifs, suggesting the potential importance of Clade-A1 members in abiotic stress responses. Gene structure analysis showed that TabZIP genes with close phylogenetic relationships tended to possess similar exon-intron compositions, and the positions of introns in the hinge regions of the bZIP domains were highly conserved, whereas introns in the leucine zipper regions were at variable positions. Additionally, eleven groups of homologs and two groups of tandem paralogs were also identified in Subgroup A of the wheat bZIP family. Expression profiling analysis indicated that most Subgroup-A TabZIP genes were responsive to abscisic acid and various abiotic stress treatments. TabZIP27, TabZIP74, TabZIP138 and TabZIP174 proteins were localized in the nucleus of wheat protoplasts, whereas TabZIP9-GFP fusion protein was simultaneously present in the nucleus, cytoplasm and cell membrane. Transgenic Arabidopsis overexpressing TabZIP174 displayed increased seed germination rates and primary root lengths under drought treatments. Overexpression of TabZIP174 in transgenic Arabidopsis conferred enhanced drought tolerance, and transgenic plants exhibited lower water loss rates, higher survival rates, higher proline, soluble sugar and leaf

Bioinformatic Analyses of Subgroup-A Members of the Wheat bZIP Transcription Factor Family and Functional Identification of TabZIP174 Involved in Drought Stress Response

Science.gov (United States)

Li, Xueyin; Feng, Biane; Zhang, Fengjie; Tang, Yimiao; Zhang, Liping; Ma, Lingjian; Zhao, Changping; Gao, Shiqing

2016-01-01

Extensive studies in Arabidopsis and rice have demonstrated that Subgroup-A members of the bZIP transcription factor family play important roles in plant responses to multiple abiotic stresses. Although common wheat (Triticum aestivum) is one of the most widely cultivated and consumed food crops in the world, there are limited investigations into Subgroup A of the bZIP family in wheat. In this study, we performed bioinformatic analyses of the 41 Subgroup-A members of the wheat bZIP family. Phylogenetic and conserved motif analyses showed that most of the Subgroup-A bZIP proteins involved in abiotic stress responses of wheat, Arabidopsis, and rice clustered in Clade A1 of the phylogenetic tree, and shared a majority of conserved motifs, suggesting the potential importance of Clade-A1 members in abiotic stress responses. Gene structure analysis showed that TabZIP genes with close phylogenetic relationships tended to possess similar exon–intron compositions, and the positions of introns in the hinge regions of the bZIP domains were highly conserved, whereas introns in the leucine zipper regions were at variable positions. Additionally, eleven groups of homologs and two groups of tandem paralogs were also identified in Subgroup A of the wheat bZIP family. Expression profiling analysis indicated that most Subgroup-A TabZIP genes were responsive to abscisic acid and various abiotic stress treatments. TabZIP27, TabZIP74, TabZIP138, and TabZIP174 proteins were localized in the nucleus of wheat protoplasts, whereas TabZIP9-GFP fusion protein was simultaneously present in the nucleus, cytoplasm, and cell membrane. Transgenic Arabidopsis overexpressing TabZIP174 displayed increased seed germination rates and primary root lengths under drought treatments. Overexpression of TabZIP174 in transgenic Arabidopsis conferred enhanced drought tolerance, and transgenic plants exhibited lower water loss rates, higher survival rates, higher proline, soluble sugar, and leaf chlorophyll

cDNA library Table - KAIKOcDNA | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available c00951-005 Description of data contents List of Bombyx mori cDNA libraries. Data file File name: kaiko_cdna_...library.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kaiko-cdna/LATEST/kaiko_cdna_library.zip File size:... 4.8 KB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/kaiko_cdna_l

Development of a sensor to study the DNA conformation using molecular logic gates

Science.gov (United States)

Roy, Arpan Datta; Dey, Dibyendu; Saha, Jaba; Chakraborty, Santanu; Bhattacharjee, D.; Hussain, Syed Arshad

2015-02-01

This communication reports our investigations on the Fluorescence Resonance Energy Transfer (FRET) between two laser dyes Acriflavine and Rhodamine B in absence and presence of DNA at different pH. It has been observed that energy transfer efficiency is largely affected by the presence of DNA as well as the pH of the system. It is well known that with increase in pH, DNA conformation changes from double stranded to single stranded (denaturation) and finally form random coil. Based on our experimental results two different types of molecular logic gates namely, XOR and OR logic have been demonstrated which can be used to have an idea about DNA conformation in solution.

Control of electrochemical signals from quantum dots conjugated to organic materials by using DNA structure in an analog logic gate.

Science.gov (United States)

Chen, Qi; Yoo, Si-Youl; Chung, Yong-Ho; Lee, Ji-Young; Min, Junhong; Choi, Jeong-Woo

2016-10-01

Various bio-logic gates have been studied intensively to overcome the rigidity of single-function silicon-based logic devices arising from combinations of various gates. Here, a simple control tool using electrochemical signals from quantum dots (QDs) was constructed using DNA and organic materials for multiple logic functions. The electrochemical redox current generated from QDs was controlled by the DNA structure. DNA structure, in turn, was dependent on the components (organic materials) and the input signal (pH). Independent electrochemical signals from two different logic units containing QDs were merged into a single analog-type logic gate, which was controlled by two inputs. We applied this electrochemical biodevice to a simple logic system and achieved various logic functions from the controlled pH input sets. This could be further improved by choosing QDs, ionic conditions, or DNA sequences. This research provides a feasible method for fabricating an artificial intelligence system. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

Development of a sensor to study the DNA conformation using molecular logic gates.

Science.gov (United States)

Roy, Arpan Datta; Dey, Dibyendu; Saha, Jaba; Chakraborty, Santanu; Bhattacharjee, D; Hussain, Syed Arshad

2015-02-05

This communication reports our investigations on the Fluorescence Resonance Energy Transfer (FRET) between two laser dyes Acriflavine and Rhodamine B in absence and presence of DNA at different pH. It has been observed that energy transfer efficiency is largely affected by the presence of DNA as well as the pH of the system. It is well known that with increase in pH, DNA conformation changes from double stranded to single stranded (denaturation) and finally form random coil. Based on our experimental results two different types of molecular logic gates namely, XOR and OR logic have been demonstrated which can be used to have an idea about DNA conformation in solution. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

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.

Exploring the bZIP transcription factor regulatory network in Neurospora crassa.

Science.gov (United States)

Tian, Chaoguang; Li, Jingyi; Glass, N Louise

2011-03-01

Transcription factors (TFs) are key nodes of regulatory networks in eukaryotic organisms, including filamentous fungi such as Neurospora crassa. The 178 predicted DNA-binding TFs in N. crassa are distributed primarily among six gene families, which represent an ancient expansion in filamentous ascomycete genomes; 98 TF genes show detectable expression levels during vegetative growth of N. crassa, including 35 that show a significant difference in expression level between hyphae at the periphery versus hyphae in the interior of a colony. Regulatory networks within a species genome include paralogous TFs and their respective target genes (TF regulon). To investigate TF network evolution in N. crassa, we focused on the basic leucine zipper (bZIP) TF family, which contains nine members. We performed baseline transcriptional profiling during vegetative growth of the wild-type and seven isogenic, viable bZIP deletion mutants. We further characterized the regulatory network of one member of the bZIP family, NCU03905. NCU03905 encodes an Ap1-like protein (NcAp-1), which is involved in resistance to multiple stress responses, including oxidative and heavy metal stress. Relocalization of NcAp-1 from the cytoplasm to the nucleus was associated with exposure to stress. A comparison of the NcAp-1 regulon with Ap1-like regulons in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Aspergillus fumigatus showed both conservation and divergence. These data indicate how N. crassa responds to stress and provide information on pathway evolution.

Overexpression of a wheat (Triticum aestivum L.) bZIP transcription factor gene, TabZIP6, decreased the freezing tolerance of transgenic Arabidopsis seedlings by down-regulating the expression of CBFs.

Science.gov (United States)

Cai, Wangting; Yang, Yaling; Wang, Weiwei; Guo, Guangyan; Liu, Wei; Bi, Caili

2018-03-01

The basic leucine zipper (bZIP) proteins play important roles against abiotic stress in plants, including cold stress. However, most bZIPs involved in plant freezing tolerance are positive regulators. Only a few bZIPs function negatively in cold stress response. In this study, TabZIP6, a Group C bZIP transcription factor gene from common wheat (Triticum aestivum L.), was cloned and characterized. The transcript of TabZIP6 was strongly induced by cold treatment (4 °C). TabZIP6 is a nuclear-localized protein with transcriptional activation activity. Arabidopsis plants overexpressing TabZIP6 showed decreased tolerance to freezing stress. Microarray as well as quantitative real-time PCR (qRT-PCR) analysis showed that CBFs and some key COR genes, including COR47 and COR15B, were down-regulated by cold treatment in TabZIP6-overexpressing Arabidopsis lines. TabZIP6 was capable of binding to the G-box motif and the CBF1 and CBF3 promoters in yeast cells. A yeast two-hybrid assay revealed that TabZIP6, as well as the other two Group S bZIP proteins involved in cold stress tolerance in wheat, Wlip19 and TaOBF1, can form homodimers by themselves and heterodimers with each other. These results suggest that TabZIP6 may function negatively in the cold stress response by binding to the promoters of CBFs, and thereby decreasing the expression of downstream COR genes in TabZIP6-overexpressing Arabidopsis seedlings. Copyright © 2018. Published by Elsevier Masson SAS.

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)

A DNAzyme-mediated logic gate for programming molecular capture and release on DNA origami.

Science.gov (United States)

Li, Feiran; Chen, Haorong; Pan, Jing; Cha, Tae-Gon; Medintz, Igor L; Choi, Jong Hyun

2016-06-28

Here we design a DNA origami-based site-specific molecular capture and release platform operated by a DNAzyme-mediated logic gate process. We show the programmability and versatility of this platform with small molecules, proteins, and nanoparticles, which may also be controlled by external light signals.

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...

Amplifying genetic logic gates.

Science.gov (United States)

Bonnet, Jerome; Yin, Peter; Ortiz, Monica E; Subsoontorn, Pakpoom; Endy, Drew

2013-05-03

Organisms must process information encoded via developmental and environmental signals to survive and reproduce. Researchers have also engineered synthetic genetic logic to realize simpler, independent control of biological processes. We developed a three-terminal device architecture, termed the transcriptor, that uses bacteriophage serine integrases to control the flow of RNA polymerase along DNA. Integrase-mediated inversion or deletion of DNA encoding transcription terminators or a promoter modulates transcription rates. We realized permanent amplifying AND, NAND, OR, XOR, NOR, and XNOR gates actuated across common control signal ranges and sequential logic supporting autonomous cell-cell communication of DNA encoding distinct logic-gate states. The single-layer digital logic architecture developed here enables engineering of amplifying logic gates to control transcription rates within and across diverse organisms.

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...

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

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.

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.

Novel mechanism of aberrant ZIP4 expression with zinc supplementation in oral tumorigenesis

International Nuclear Information System (INIS)

Ishida, Sho; Kasamatsu, Atsushi; Endo-Sakamoto, Yosuke; Nakashima, Dai; Koide, Nao; Takahara, Toshikazu; Shimizu, Toshihiro; Iyoda, Manabu; Shiiba, Masashi; Tanzawa, Hideki; Uzawa, Katsuhiro

2017-01-01

Zrt-Irt-like protein 4 (ZIP4) is critical molecule for proper mammalian development and releasing zinc from vesicular compartments. Recent studies suggested that ZIP4 plays an important role of tumor progression in pancreatic, prostate, and hepatocellular cancers, however, little is known about the detail mechanism of ZIP4 in their cancers. In the present study, we examined the possibility of ZIP4 as a new molecular target for oral squamous cell carcinoma (OSCC). We evaluated ZIP4 expression in OSCC-derived cell lines and primary OSCC samples by quantitative RT-PCR, immunoblotting, and immunohistochemistry (IHC). We also analyzed the clinical correlation between ZIP4 status and clinical behaviors in patients with OSCC. In addition, ZIP4 knockdown cells (shZIP4 cells) and ZnCl 2 treatment were used for functional experiments, including cellular proliferation assay, zinc uptake assay, and cell-cycle analysis. ZIP4 mRNA and protein were up-regulated significantly in OSCCs compared with normal counterparts in vitro and in vivo. IHC showed that ZIP4 expression in the primary OSCC was positively correlated with primary tumoral size. The shZIP4 cells showed decrease accumulation of intercellular zinc and decreased cellular growth by cell-cycle arrest at the G1 phase, resulting from up-regulation of cyclin-dependent kinase inhibitors and down-regulation of cyclins and cyclin-dependent kinases. Since cellular growth of OSCC cells after treatment with zinc was significantly greater than control cells, we speculated that intercellular ZnCl 2 accumulation is an important factor for cellular growth. Consistent with our hypothesis, not only decreased zinc uptake by ZIP4 knockdown but also chelating agent, N,N,N′,N′-tetrakis(2-pyridylmethyl) ethylenediamine (TPEN), showed inhibitory effects of cellular proliferation. Therefore, our data provide evidence for an essential role of ZIP4 and intracellular zinc for tumoral growth in OSCC, suggesting that zinc uptake might be a

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.

Towards a DNA Nanoprocessor: Reusable Tile-Integrated DNA Circuits.

Science.gov (United States)

Gerasimova, Yulia V; Kolpashchikov, Dmitry M

2016-08-22

Modern electronic microprocessors use semiconductor logic gates organized on a silicon chip to enable efficient inter-gate communication. Here, arrays of communicating DNA logic gates integrated on a single DNA tile were designed and used to process nucleic acid inputs in a reusable format. Our results lay the foundation for the development of a DNA nanoprocessor, a small and biocompatible device capable of performing complex analyses of DNA and RNA inputs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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)

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.

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

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...

Multiple advanced logic gates made of DNA-Ag nanocluster and the application for intelligent detection of pathogenic bacterial genes† †Electronic supplementary information (ESI) available: Chemicals, materials and DNA sequences used in the investigation, the construction of YES, AND, OR, XOR and INH logic gates, CD and PAGE experimental results. See DOI: 10.1039/c7sc05246d

Science.gov (United States)

Lin, Xiaodong; Deng, Jiankang; Lyu, Yanlong; Qian, Pengcheng; Li, Yunfei

2018-01-01

The integration of multiple DNA logic gates on a universal platform to implement advance logic functions is a critical challenge for DNA computing. Herein, a straightforward and powerful strategy in which a guanine-rich DNA sequence lighting up a silver nanocluster and fluorophore was developed to construct a library of logic gates on a simple DNA-templated silver nanoclusters (DNA-AgNCs) platform. This library included basic logic gates, YES, AND, OR, INHIBIT, and XOR, which were further integrated into complex logic circuits to implement diverse advanced arithmetic/non-arithmetic functions including half-adder, half-subtractor, multiplexer, and demultiplexer. Under UV irradiation, all the logic functions could be instantly visualized, confirming an excellent repeatability. The logic operations were entirely based on DNA hybridization in an enzyme-free and label-free condition, avoiding waste accumulation and reducing cost consumption. Interestingly, a DNA-AgNCs-based multiplexer was, for the first time, used as an intelligent biosensor to identify pathogenic genes, E. coli and S. aureus genes, with a high sensitivity. The investigation provides a prototype for the wireless integration of multiple devices on even the simplest single-strand DNA platform to perform diverse complex functions in a straightforward and cost-effective way. PMID:29675221

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

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.

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.

Separable Crossover-Promoting and Crossover-Constraining Aspects of Zip1 Activity during Budding Yeast Meiosis.

Directory of Open Access Journals (Sweden)

Karen Voelkel-Meiman

2015-06-01

Full Text Available Accurate chromosome segregation during meiosis relies on the presence of crossover events distributed among all chromosomes. MutSγ and MutLγ homologs (Msh4/5 and Mlh1/3 facilitate the formation of a prominent group of meiotic crossovers that mature within the context of an elaborate chromosomal structure called the synaptonemal complex (SC. SC proteins are required for intermediate steps in the formation of MutSγ-MutLγ crossovers, but whether the assembled SC structure per se is required for MutSγ-MutLγ-dependent crossover recombination events is unknown. Here we describe an interspecies complementation experiment that reveals that the mature SC is dispensable for the formation of Mlh3-dependent crossovers in budding yeast. Zip1 forms a major structural component of the budding yeast SC, and is also required for MutSγ and MutLγ-dependent crossover formation. Kluyveromyces lactis ZIP1 expressed in place of Saccharomyces cerevisiae ZIP1 in S. cerevisiae cells fails to support SC assembly (synapsis but promotes wild-type crossover levels in those nuclei that progress to form spores. While stable, full-length SC does not assemble in S. cerevisiae cells expressing K. lactis ZIP1, aggregates of K. lactis Zip1 displayed by S. cerevisiae meiotic nuclei are decorated with SC-associated proteins, and K. lactis Zip1 promotes the SUMOylation of the SC central element protein Ecm11, suggesting that K. lactis Zip1 functionally interfaces with components of the S. cerevisiae synapsis machinery. Moreover, K. lactis Zip1-mediated crossovers rely on S. cerevisiae synapsis initiation proteins Zip3, Zip4, Spo16, as well as the Mlh3 protein, as do the crossovers mediated by S. cerevisiae Zip1. Surprisingly, however, K. lactis Zip1-mediated crossovers are largely Msh4/Msh5 (MutSγ-independent. This separation-of-function version of Zip1 thus reveals that neither assembled SC nor MutSγ is required for Mlh3-dependent crossover formation per se in budding yeast

cDNA - ASTRA | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available ontents List of cDNA in locus Data file File name: astra_cdna.zip File URL: ftp://ftp.biosciencedbc.jp/archive/astra/LATEST/astra_cdn...a.zip File size: 3.3 MB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/astra_cdna...n, Department of Molecular Genetics, National Institute of Agrobiological Sciences (Kikuchi et al., 2003; ftp://cdna

Cluster Table - KAIKOcDNA | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available Description of data contents List of number of identical cDNA sequences that make up cluster. Data file File name: kaiko_cdna..._cluster.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kaiko-cdna/LATEST/kaiko_cdna_clu...ster.zip File size: 453 KB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/kaiko_cdna

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

Lifescience Database Archive (English)

Full Text Available of data contents Results of homology search to cDNA clones in the KOME. Data file File name: rpd_cdna.zip F...ile URL: ftp://ftp.biosciencedbc.jp/archive/rpd/LATEST/rpd_cdna.zip File size: 15 KB Simple search URL http:...//togodb.biosciencedbc.jp/togodb/view/rpd_cdna#en Data acquisition method - Data

Hepatic ZIP14-mediated zinc transport is required for adaptation to endoplasmic reticulum stress.

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Kim, Min-Hyun; Aydemir, Tolunay B; Kim, Jinhee; Cousins, Robert J

2017-07-18

Extensive endoplasmic reticulum (ER) stress damages the liver, causing apoptosis and steatosis despite the activation of the unfolded protein response (UPR). Restriction of zinc from cells can induce ER stress, indicating that zinc is essential to maintain normal ER function. However, a role for zinc during hepatic ER stress is largely unknown despite important roles in metabolic disorders, including obesity and nonalcoholic liver disease. We have explored a role for the metal transporter ZIP14 during pharmacologically and high-fat diet-induced ER stress using Zip14 -/- (KO) mice, which exhibit impaired hepatic zinc uptake. Here, we report that ZIP14-mediated hepatic zinc uptake is critical for adaptation to ER stress, preventing sustained apoptosis and steatosis. Impaired hepatic zinc uptake in Zip14 KO mice during ER stress coincides with greater expression of proapoptotic proteins. ER stress-induced Zip14 KO mice show greater levels of hepatic steatosis due to higher expression of genes involved in de novo fatty acid synthesis, which are suppressed in ER stress-induced WT mice. During ER stress, the UPR-activated transcription factors ATF4 and ATF6α transcriptionally up-regulate Zip14 expression. We propose ZIP14 mediates zinc transport into hepatocytes to inhibit protein-tyrosine phosphatase 1B (PTP1B) activity, which acts to suppress apoptosis and steatosis associated with hepatic ER stress. Zip14 KO mice showed greater hepatic PTP1B activity during ER stress. These results show the importance of zinc trafficking and functional ZIP14 transporter activity for adaptation to ER stress associated with chronic metabolic disorders.

Genome-wide analysis of the homeodomain-leucine zipper (HD-ZIP) gene family in peach (Prunus persica).

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Zhang, C H; Ma, R J; Shen, Z J; Sun, X; Korir, N K; Yu, M L

2014-04-08

In this study, 33 homeodomain-leucine zipper (HD-ZIP) genes were identified in peach using the HD-ZIP amino acid sequences of Arabidopsis thaliana as a probe. Based on the phylogenetic analysis and the individual gene or protein characteristics, the HD-ZIP gene family in peach can be classified into 4 subfamilies, HD-ZIP I, II, III, and IV, containing 14, 7, 4, and 8 members, respectively. The most closely related peach HD-ZIP members within the same subfamilies shared very similar gene structure in terms of either intron/exon numbers or lengths. Almost all members of the same subfamily shared common motif compositions, thereby implying that the HD-ZIP proteins within the same subfamily may have functional similarity. The 33 peach HD-ZIP genes were distributed across scaffolds 1 to 7. Although the primary structure varied among HD-ZIP family proteins, their tertiary structures were similar. The results from this study will be useful in selecting candidate genes from specific subfamilies for functional analysis.

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

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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 .

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

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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.

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

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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.

Zinc transporter ZIP14 functions in hepatic zinc, iron and glucose homeostasis during the innate immune response (endotoxemia.

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Tolunay Beker Aydemir

Full Text Available ZIP14 (slc39A14 is a zinc transporter induced in response to pro-inflammatory stimuli. ZIP14 induction accompanies the reduction in serum zinc (hypozincemia of acute inflammation. ZIP14 can transport Zn(2+ and non-transferrin-bound Fe(2+ in vitro. Using a Zip14(-/- mouse model we demonstrated that ZIP14 was essential for control of phosphatase PTP1B activity and phosphorylation of c-Met during liver regeneration. In the current studies, a global screening of ZIP transporter gene expression in response to LPS-induced endotoxemia was conducted. Following LPS, Zip14 was the most highly up-regulated Zip transcript in liver, but also in white adipose tissue and muscle. Using ZIP14(-/- mice we show that ZIP14 contributes to zinc absorption from the gastrointestinal tract directly or indirectly as zinc absorption was decreased in the KOs. In contrast, Zip14(-/- mice absorbed more iron. The Zip14 KO mice did not exhibit hypozincemia following LPS, but do have hypoferremia. Livers of Zip14-/- mice had increased transcript abundance for hepcidin, divalent metal transporter-1, ferritin and transferrin receptor-1 and greater accumulation of iron. The Zip14(-/- phenotype included greater body fat, hypoglycemia and higher insulin levels, as well as increased liver glucose and greater phosphorylation of the insulin receptor and increased GLUT2, SREBP-1c and FASN expression. The Zip14 KO mice exhibited decreased circulating IL-6 with increased hepatic SOCS-3 following LPS, suggesting SOCS-3 inhibited insulin signaling which produced the hypoglycemia in this genotype. The results are consistent with ZIP14 ablation yielding abnormal labile zinc pools which lead to increased SOCS-3 production through G-coupled receptor activation and increased cAMP production as well as signaled by increased pSTAT3 via the IL-6 receptor, which inhibits IRS 1/2 phosphorylation. Our data show the role of ZIP14 in the hepatocyte is multi-functional since zinc and iron trafficking are

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

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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.

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

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...... 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...... 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...

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.

A model of competing species that exhibits zip bifurcation

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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.

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

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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.

Influence of DNA-methylation on zinc homeostasis in myeloid cells: Regulation of zinc transporters and zinc binding proteins.

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Kessels, Jana Elena; Wessels, Inga; Haase, Hajo; Rink, Lothar; Uciechowski, Peter

2016-09-01

The distribution of intracellular zinc, predominantly regulated through zinc transporters and zinc binding proteins, is required to support an efficient immune response. Epigenetic mechanisms such as DNA methylation are involved in the expression of these genes. In demethylation experiments using 5-Aza-2'-deoxycytidine (AZA) increased intracellular (after 24 and 48h) and total cellular zinc levels (after 48h) were observed in the myeloid cell line HL-60. To uncover the mechanisms that cause the disturbed zinc homeostasis after DNA demethylation, the expression of human zinc transporters and zinc binding proteins were investigated. Real time PCR analyses of 14 ZIP (solute-linked carrier (SLC) SLC39A; Zrt/IRT-like protein), and 9 ZnT (SLC30A) zinc transporters revealed significantly enhanced mRNA expression of the zinc importer ZIP1 after AZA treatment. Because ZIP1 protein was also enhanced after AZA treatment, ZIP1 up-regulation might be the mediator of enhanced intracellular zinc levels. The mRNA expression of ZIP14 was decreased, whereas zinc exporter ZnT3 mRNA was also significantly increased; which might be a cellular reaction to compensate elevated zinc levels. An enhanced but not significant chromatin accessibility of ZIP1 promoter region I was detected by chromatin accessibility by real-time PCR (CHART) assays after demethylation. Additionally, DNA demethylation resulted in increased mRNA accumulation of zinc binding proteins metallothionein (MT) and S100A8/S100A9 after 48h. MT mRNA was significantly enhanced after 24h of AZA treatment also suggesting a reaction of the cell to restore zinc homeostasis. These data indicate that DNA methylation is an important epigenetic mechanism affecting zinc binding proteins and transporters, and, therefore, regulating zinc homeostasis in myeloid cells. Copyright © 2016 Elsevier GmbH. All rights reserved.

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

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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

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

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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.

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

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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

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

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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

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.

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

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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.

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

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

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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.

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

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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.

Isolation and expression analysis of EcbZIP17 from different finger millet genotypes shows conserved nature of the gene.

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Chopperla, Ramakrishna; Singh, Sonam; Mohanty, Sasmita; Reddy, Nanja; Padaria, Jasdeep C; Solanke, Amolkumar U

2017-10-01

Basic leucine zipper (bZIP) transcription factors comprise one of the largest gene families in plants. They play a key role in almost every aspect of plant growth and development and also in biotic and abiotic stress tolerance. In this study, we report isolation and characterization of EcbZIP17 , a group B bZIP transcription factor from a climate smart cereal, finger millet ( Eleusine coracana L.). The genomic sequence of EcbZIP17 is 2662 bp long encompassing two exons and one intron with ORF of 1722 bp and peptide length of 573 aa. This gene is homologous to AtbZIP17 ( Arabidopsis ), ZmbZIP17 (maize) and OsbZIP60 (rice) which play a key role in endoplasmic reticulum (ER) stress pathway. In silico analysis confirmed the presence of basic leucine zipper (bZIP) and transmembrane (TM) domains in the EcbZIP17 protein. Allele mining of this gene in 16 different genotypes by Sanger sequencing revealed no variation in nucleotide sequence, including the 618 bp long intron. Expression analysis of EcbZIP17 under heat stress exhibited similar pattern of expression in all the genotypes across time intervals with highest upregulation after 4 h. The present study established the conserved nature of EcbZIP17 at nucleotide and expression level.

Zinc Transporter SLC39A7/ZIP7 Promotes Intestinal Epithelial Self-Renewal by Resolving ER Stress

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Ohashi, Wakana; Kimura, Shunsuke; Iwanaga, Toshihiko; Furusawa, Yukihiro; Irié, Tarou; Izumi, Hironori; Watanabe, Takashi; Hara, Takafumi; Ohara, Osamu; Koseki, Haruhiko; Sato, Toshiro; Robine, Sylvie; Mori, Hisashi; Hattori, Yuichi; Mishima, Kenji; Ohno, Hiroshi; Hase, Koji; Fukada, Toshiyuki

2016-01-01

Zinc transporters play a critical role in spatiotemporal regulation of zinc homeostasis. Although disruption of zinc homeostasis has been implicated in disorders such as intestinal inflammation and aberrant epithelial morphology, it is largely unknown which zinc transporters are responsible for the intestinal epithelial homeostasis. Here, we show that Zrt-Irt-like protein (ZIP) transporter ZIP7, which is highly expressed in the intestinal crypt, is essential for intestinal epithelial proliferation. Mice lacking Zip7 in intestinal epithelium triggered endoplasmic reticulum (ER) stress in proliferative progenitor cells, leading to significant cell death of progenitor cells. Zip7 deficiency led to the loss of Olfm4+ intestinal stem cells and the degeneration of post-mitotic Paneth cells, indicating a fundamental requirement for Zip7 in homeostatic intestinal regeneration. Taken together, these findings provide evidence for the importance of ZIP7 in maintenance of intestinal epithelial homeostasis through the regulation of ER function in proliferative progenitor cells and maintenance of intestinal stem cells. Therapeutic targeting of ZIP7 could lead to effective treatment of gastrointestinal disorders. PMID:27736879

Zinc Transporter SLC39A7/ZIP7 Promotes Intestinal Epithelial Self-Renewal by Resolving ER Stress.

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Wakana Ohashi

2016-10-01

Full Text Available Zinc transporters play a critical role in spatiotemporal regulation of zinc homeostasis. Although disruption of zinc homeostasis has been implicated in disorders such as intestinal inflammation and aberrant epithelial morphology, it is largely unknown which zinc transporters are responsible for the intestinal epithelial homeostasis. Here, we show that Zrt-Irt-like protein (ZIP transporter ZIP7, which is highly expressed in the intestinal crypt, is essential for intestinal epithelial proliferation. Mice lacking Zip7 in intestinal epithelium triggered endoplasmic reticulum (ER stress in proliferative progenitor cells, leading to significant cell death of progenitor cells. Zip7 deficiency led to the loss of Olfm4+ intestinal stem cells and the degeneration of post-mitotic Paneth cells, indicating a fundamental requirement for Zip7 in homeostatic intestinal regeneration. Taken together, these findings provide evidence for the importance of ZIP7 in maintenance of intestinal epithelial homeostasis through the regulation of ER function in proliferative progenitor cells and maintenance of intestinal stem cells. Therapeutic targeting of ZIP7 could lead to effective treatment of gastrointestinal disorders.

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

Science.gov (United States)

Page, Kedar Mohan

SuperCDMS is a leading direct dark matter search experiment which uses solid state detectors (Ge crystals) at milliKelvin temperatures to look for nuclear recoils caused by dark matter interactions in the detector. 'Weakly Interacting Massive Particles' (WIMPs) are the most favoured dark matter candidate particles. SuperCDMS, like many other direct dark matter search experiments, primarily looks for WIMPs. The measurement of both the ionization and the lattice vibration (phonon) signals from an interaction in the detector allow it to discriminate against electron recoils which are the main source of background for WIMP detection. SuperCDMS currently operates about 9 kgs worth of germanium detectors at the Soudan underground lab in northern Minnesota. In its next phase, SuperCDMS SNOLAB, it plans to use 100-200 kg of target mass (Ge) which would allow it to probe more of the interesting and unexplored parameter space for WIMPs predicted by theoretical models. The SuperCDMS Queen's Test Facility is a detector testing facility which is intended to serve detector testing and detector research and development purposes for the SuperCDMS experiment. A modified detector called the 'HiZIP' (Half-iZIP), which is reduced in complexity in comparison to the currently used iZIP (interleaved Z-sensitive Ionization and Phonon mediated) detectors, is studied in this thesis. The HiZIP detector design also serves to discriminate against background from multiple scatter events occurring close to the surfaces in a single detector. Studies carried out to compare the surface event leakage in the HiZIP detector using limited information from iZIP data taken at SuperCDMS test facility at UC Berkley produce a highly conservative upper limit of 5 out of 10,000 events at 90% confidence level. This upper limit is the best among many different HiZIP configurations that were investigated and is comparable to the upper limit calculated for an iZIP detector in the same way using the same data. A

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

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.

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

Summary: High expression of zinc (Zn)-regulated, iron-regulated transporter-like protein (ZIP) genes increases root Zn uptake in dicots, leading to high accumulation of Zn in shoots. However, none of the ZIP genes tested previously in monocots could enhance shoot Zn accumulation. In this report...... were also generated to further understand the functions of HvZIP7 in metal transport. HvZIP7 is strongly induced by Zn deficiency, primarily in vascular tissues of roots and leaves, and its protein was localized in the plasma membrane. These properties are similar to its closely related homologs...... 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...

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.

Isolation and functional characterisation of two new bZIP maize regulators of the ABA responsive gene rab28.

Science.gov (United States)

Nieva, Claudia; Busk, Peter K; Domínguez-Puigjaner, Eva; Lumbreras, Victoria; Testillano, Pilar S; Risueño, Maria-Carmen; Pagès, Montserrat

2005-08-01

The plant hormone abscisic acid regulates gene expression in response to growth stimuli and abiotic stress. Previous studies have implicated members of the bZIP family of transcription factors as mediators of abscisic acid dependent gene expression through the ABRE cis-element. Here, we identify two new maize bZIP transcription factors, EmBP-2 and ZmBZ-1 related to EmBP-1 and OsBZ-8 families. They are differentially expressed during embryo development; EmBP-2 is constitutive, whereas ZmBZ-1 is abscisic acid-inducible and accumulates during late embryogenesis. Both factors are nuclear proteins that bind to ABREs and activate transcription of the abscisic acid-inducible gene rab28 from maize. EmBP-2 and ZmBZ-1 are phosphorylated by protein kinase CK2 and phosphorylation alters their DNA binding properties. Our data suggest that EmBP-2 and ZmBZ-1 are involved in the expression of abscisic acid inducible genes such as rab28 and their activity is modulated by ABA and by phosphorylation.

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 ...

Genome Wide Identification of Orthologous ZIP Genes Associated with Zinc and Iron Translocation in Setaria italica.

Science.gov (United States)

Alagarasan, Ganesh; Dubey, Mahima; Aswathy, Kumar S; Chandel, Girish

2017-01-01

Genes in the ZIP family encode transcripts to store and transport bivalent metal micronutrient, particularly iron (Fe) and or zinc (Zn). These transcripts are important for a variety of functions involved in the developmental and physiological processes in many plant species, including most, if not all, Poaceae plant species and the model species Arabidopsis. Here, we present the report of a genome wide investigation of orthologous ZIP genes in Setaria italica and the identification of 7 single copy genes. RT-PCR shows 4 of them could be used to increase the bio-availability of zinc and iron content in grains. Of 36 ZIP members, 25 genes have traces of signal peptide based sub-cellular localization, as compared to those of plant species studied previously, yet translocation of ions remains unclear. In silico analysis of gene structure and protein nature suggests that these two were preeminent in shaping the functional diversity of the ZIP gene family in S. italica . NAC, bZIP and bHLH are the predominant Fe and Zn responsive transcription factors present in SiZIP genes. Together, our results provide new insights into the signal peptide based/independent iron and zinc translocation in the plant system and allowed identification of ZIP genes that may be involved in the zinc and iron absorption from the soil, and thus transporting it to the cereal grain underlying high micronutrient accumulation.

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...

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

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 ...

Compound list: doxorubicin [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available doxorubicin DOX 00149 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/...in_vitro/doxorubicin.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_...vitro/doxorubicin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/...Liver/Single/doxorubicin.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/...archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/doxorubicin.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.bios

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_v...itro/ethanol.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/et...hanol.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 ...

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_vi...tro/adapin.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/adap...in.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/ad...apin.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 ...

Compound list: danazol [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available danazol DNZ 00127 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_v...itro/danazol.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/da...nazol.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single.../danazol.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/danazol.Rat.in_vivo.Liver.Repeat.zip ...

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/allopurinol.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_...vitro/allopurinol.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/...Liver/Single/allopurinol.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/...archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/allopurinol.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.bios

Compound list: ciprofloxacin [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available ciprofloxacin CPX 00050 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Huma...n/in_vitro/ciprofloxacin.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat.../in_vitro/ciprofloxacin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in..._vivo/Liver/Single/ciprofloxacin.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscienc...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/ciprofloxacin.Rat.in_vivo.Liver.Repeat.zip ftp:

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_v...itro/tacrine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/ta...crine.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 ...

Compound list: monocrotaline [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available monocrotaline MCT 00058 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Huma...n/in_vitro/monocrotaline.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat.../in_vitro/monocrotaline.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in..._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:

Stage-specific regulation of four HD-ZIP III transcription factors during polar pattern formation in Larix leptolepis somatic embryos.

Science.gov (United States)

Li, Shui-gen; Li, Wan-feng; Han, Su-ying; Yang, Wen-hua; Qi, Li-wang

2013-06-15

Polar auxin transport provides a developmental signal for cell fate specification during somatic embryogenesis. Some members of the HD-ZIP III transcription factors participate in regulation of auxin transport, but little is known about this regulation in somatic embryogenesis. Here, four HD-ZIP III homologues from Larix leptolepis were identified and designated LaHDZ31, 32, 33 and 34. The occurrence of a miR165/166 target sequence in all four cDNA sequences indicated that they might be targets of miR165/166. Identification of the cleavage products of LaHDZ31 and LaHDZ32 in vivo confirmed that they were regulated by miRNA. Their mRNA accumulation patterns during somatic embryogenesis and the effects of 1-N-naphthylphthalamic acid (NPA) on their transcript levels and somatic embryo maturation were investigated. The results showed that the four genes had higher transcript levels at mature stages than at the proliferation stage, and that NPA treatment down-regulated the mRNA abundance of LaHDZ31, 32 and 33 at cotyledonary embryo stages, but had no effect on the mRNA abundance of LaHDZ34. We concluded that these four members of Larix HD-ZIP III family might participate in polar auxin transport and the development of somatic embryos, providing new insights into the regulatory mechanisms of somatic embryogenesis. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

The zinc transporter ZIP12 regulates the pulmonary vascular response to chronic hypoxia.

Science.gov (United States)

Zhao, Lan; Oliver, Eduardo; Maratou, Klio; Atanur, Santosh S; Dubois, Olivier D; Cotroneo, Emanuele; Chen, Chien-Nien; Wang, Lei; Arce, Cristina; Chabosseau, Pauline L; Ponsa-Cobas, Joan; Frid, Maria G; Moyon, Benjamin; Webster, Zoe; Aldashev, Almaz; Ferrer, Jorge; Rutter, Guy A; Stenmark, Kurt R; Aitman, Timothy J; Wilkins, Martin R

2015-08-20

The typical response of the adult mammalian pulmonary circulation to a low oxygen environment is vasoconstriction and structural remodelling of pulmonary arterioles, leading to chronic elevation of pulmonary artery pressure (pulmonary hypertension) and right ventricular hypertrophy. Some mammals, however, exhibit genetic resistance to hypoxia-induced pulmonary hypertension. We used a congenic breeding program and comparative genomics to exploit this variation in the rat and identified the gene Slc39a12 as a major regulator of hypoxia-induced pulmonary vascular remodelling. Slc39a12 encodes the zinc transporter ZIP12. Here we report that ZIP12 expression is increased in many cell types, including endothelial, smooth muscle and interstitial cells, in the remodelled pulmonary arterioles of rats, cows and humans susceptible to hypoxia-induced pulmonary hypertension. We show that ZIP12 expression in pulmonary vascular smooth muscle cells is hypoxia dependent and that targeted inhibition of ZIP12 inhibits the rise in intracellular labile zinc in hypoxia-exposed pulmonary vascular smooth muscle cells and their proliferation in culture. We demonstrate that genetic disruption of ZIP12 expression attenuates the development of pulmonary hypertension in rats housed in a hypoxic atmosphere. This new and unexpected insight into the fundamental role of a zinc transporter in mammalian pulmonary vascular homeostasis suggests a new drug target for the pharmacological management of pulmonary hypertension.

OsbZIP58, a basic leucine zipper transcription factor, regulates starch biosynthesis in rice endosperm.

Science.gov (United States)

Wang, Jie-Chen; Xu, Heng; Zhu, Ying; Liu, Qiao-Quan; Cai, Xiu-Ling

2013-08-01

Starch composition and the amount in endosperm, both of which contribute dramatically to seed yield, cooking quality, and taste in cereals, are determined by a series of complex biochemical reactions. However, the mechanism regulating starch biosynthesis in cereal seeds is not well understood. This study showed that OsbZIP58, a bZIP transcription factor, is a key transcriptional regulator controlling starch synthesis in rice endosperm. OsbZIP58 was expressed mainly in endosperm during active starch synthesis. osbzip58 null mutants displayed abnormal seed morphology with altered starch accumulation in the white belly region and decreased amounts of total starch and amylose. Moreover, osbzip58 had a higher proportion of short chains and a lower proportion of intermediate chains of amylopectin. Furthermore, OsbZIP58 was shown to bind directly to the promoters of six starch-synthesizing genes, OsAGPL3, Wx, OsSSIIa, SBE1, OsBEIIb, and ISA2, and to regulate their expression. These findings indicate that OsbZIP58 functions as a key regulator of starch synthesis in rice seeds and provide new insights into seed quality control.

Compound list: phenacetin [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available phenacetin PCT 00138 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/i...n_vitro/phenacetin.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/phenacetin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/phenacetin.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/phenacetin.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.bioscienc

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/i...n_vitro/imipramine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/imipramine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/imipramine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/imipramine.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.bioscienc

Compound list: ethinylestradiol [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available ethinylestradiol EE 00055 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Hu...man/in_vitro/ethinylestradiol.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATES...T/Rat/in_vitro/ethinylestradiol.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATES...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.Repeat.zip ftp:

Compound list: carboplatin [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available carboplatin CBP 00133 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in..._vitro/carboplatin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo.../Liver/Single/carboplatin.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATES...T/Rat/in_vivo/Liver/Repeat/carboplatin.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.bio...sciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/carboplatin.Rat.in_vivo.Kidney.Single.zip ftp:

Compound list: cephalothin [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available cephalothin CLT 00141 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in..._vitro/cephalothin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo.../Liver/Single/cephalothin.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATES...T/Rat/in_vivo/Liver/Repeat/cephalothin.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.bio...sciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/cephalothin.Rat.in_vivo.Kidney.Single.zip ftp:

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/i...n_vitro/omeprazole.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/omeprazole.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/omeprazole.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/omeprazole.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.bioscienc

Compound list: triamterene [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available triamterene TRI 00101 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in..._vitro/triamterene.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo.../Liver/Single/triamterene.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATES...T/Rat/in_vivo/Liver/Repeat/triamterene.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.bio...sciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/triamterene.Rat.in_vivo.Kidney.Single.zip ftp:

Compound list: nitrofurantoin [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available nitrofurantoin NFT 00020 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Hum...an/in_vitro/nitrofurantoin.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/R...at/in_vitro/nitrofurantoin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat.../in_vivo/Liver/Single/nitrofurantoin.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosc...iencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/nitrofurantoin.Rat.in_vivo.Liver.Repeat.zip ftp:

The prion-ZIP connection: From cousins to partners in iron uptake

Science.gov (United States)

Singh, Neena; Asthana, Abhishek; Baksi, Shounak; Desai, Vilok; Haldar, Swati; Hari, Sahi; Tripathi, Ajai K

2015-01-01

ABSTRACT Converging observations from disparate lines of inquiry are beginning to clarify the cause of brain iron dyshomeostasis in sporadic Creutzfeldt-Jakob disease (sCJD), a neurodegenerative condition associated with the conversion of prion protein (PrPC), a plasma membrane glycoprotein, from α-helical to a β-sheet rich PrP-scrapie (PrPSc) isoform. Biochemical evidence indicates that PrPC facilitates cellular iron uptake by functioning as a membrane-bound ferrireductase (FR), an activity necessary for the transport of iron across biological membranes through metal transporters. An entirely different experimental approach reveals an evolutionary link between PrPC and the Zrt, Irt-like protein (ZIP) family, a group of proteins involved in the transport of zinc, iron, and manganese across the plasma membrane. Close physical proximity of PrPC with certain members of the ZIP family on the plasma membrane and increased uptake of extracellular iron by cells that co-express PrPC and ZIP14 suggest that PrPC functions as a FR partner for certain members of this family. The connection between PrPC and ZIP proteins therefore extends beyond common ancestry to that of functional cooperation. Here, we summarize evidence supporting the facilitative role of PrPC in cellular iron uptake, and implications of this activity on iron metabolism in sCJD brains. PMID:26689487

Memory Retrieval Has a Dynamic Influence on the Maintenance Mechanisms That Are Sensitive to ζ-Inhibitory Peptide (ZIP).

Science.gov (United States)

Levitan, David; Fortis-Santiago, Yaihara; Figueroa, Joshua A; Reid, Emily E; Yoshida, Takashi; Barry, Nicholas C; Russo, Abigail; Katz, Donald B

2016-10-12

In neuroscientists' attempts to understand the long-term storage of memory, topics of particular importance and interest are the cellular and system mechanisms of maintenance (e.g., those sensitive to ζ-inhibitory peptide, ZIP) and those induced by memory retrieval (i.e., reconsolidation). Much is known about each of these processes in isolation, but less is known concerning how they interact. It is known that ZIP sensitivity and memory retrieval share at least some molecular targets (e.g., recycling α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid, AMPA, receptors to the plasma membrane); conversely, the fact that sensitivity to ZIP emerges only after consolidation ends suggests that consolidation (and by extension reconsolidation) and maintenance might be mutually exclusive processes, the onset of one canceling the other. Here, we use conditioned taste aversion (CTA) in rats, a cortically dependent learning paradigm, to test this hypothesis. First, we demonstrate that ZIP infusions into gustatory cortex begin interfering with CTA memory 43-45 h after memory acquisition-after consolidation ends. Next, we show that a retrieval trial administered after this time point interrupts the ability of ZIP to induce amnesia and that ZIP's ability to induce amnesia is reengaged only 45 h after retrieval. This pattern of results suggests that memory retrieval and ZIP-sensitive maintenance mechanisms are mutually exclusive and that the progression from one to the other are similar after acquisition and retrieval. They also reveal concrete differences between ZIP-sensitive mechanisms induced by acquisition and retrieval: the latency with which ZIP-sensitive mechanisms are expressed differ for the two processes. Memory retrieval and the molecular mechanisms that are sensitive to ζ-inhibitory peptide (ZIP) are the few manipulations that have been shown to effect memory maintenance. Although much is known about their effect on maintenance separately, it is unknown how they

Genome Wide Identification of Orthologous ZIP Genes Associated with Zinc and Iron Translocation in Setaria italica

Directory of Open Access Journals (Sweden)

Ganesh Alagarasan

2017-05-01

Full Text Available Genes in the ZIP family encode transcripts to store and transport bivalent metal micronutrient, particularly iron (Fe and or zinc (Zn. These transcripts are important for a variety of functions involved in the developmental and physiological processes in many plant species, including most, if not all, Poaceae plant species and the model species Arabidopsis. Here, we present the report of a genome wide investigation of orthologous ZIP genes in Setaria italica and the identification of 7 single copy genes. RT-PCR shows 4 of them could be used to increase the bio-availability of zinc and iron content in grains. Of 36 ZIP members, 25 genes have traces of signal peptide based sub-cellular localization, as compared to those of plant species studied previously, yet translocation of ions remains unclear. In silico analysis of gene structure and protein nature suggests that these two were preeminent in shaping the functional diversity of the ZIP gene family in S. italica. NAC, bZIP and bHLH are the predominant Fe and Zn responsive transcription factors present in SiZIP genes. Together, our results provide new insights into the signal peptide based/independent iron and zinc translocation in the plant system and allowed identification of ZIP genes that may be involved in the zinc and iron absorption from the soil, and thus transporting it to the cereal grain underlying high micronutrient accumulation.

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

Compound list: gentamicin [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available gentamicin GMC 00147 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/gentam...icin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/gentam...at/in_vivo/Liver/Repeat/gentamicin.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.bioscie...ncedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/gentamicin.Rat.in_vivo.Kidney.Single.zip ftp...://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Repeat/gentamicin.Rat.in_vivo.Kidney.Repeat.zip ...

Compound list: bucetin [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available bucetin BCT 00139 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_v...itro/bucetin.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/bu...cetin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single.../bucetin.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-tgg...ates/LATEST/Rat/in_vivo/Liver/Repeat/bucetin.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.biosciencedbc.jp/archive

Compound list: cisplatin [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available cisplatin CSP 00132 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_v...itro/cisplatin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/cisplatin.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/...in_vivo/Liver/Repeat/cisplatin.Rat.in_vivo.Liver.Repeat.zip ftp://ftp.bioscienced...bc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/cisplatin.Rat.in_vivo.Kidney.Single.zip ftp://ft

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

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

Phosphorylation of the Synaptonemal Complex Protein Zip1 Regulates the Crossover/Noncrossover Decision during Yeast Meiosis.

Directory of Open Access Journals (Sweden)

Xiangyu Chen

2015-12-01

Full Text Available Interhomolog crossovers promote proper chromosome segregation during meiosis and are formed by the regulated repair of programmed double-strand breaks. This regulation requires components of the synaptonemal complex (SC, a proteinaceous structure formed between homologous chromosomes. In yeast, SC formation requires the "ZMM" genes, which encode a functionally diverse set of proteins, including the transverse filament protein, Zip1. In wild-type meiosis, Zmm proteins promote the biased resolution of recombination intermediates into crossovers that are distributed throughout the genome by interference. In contrast, noncrossovers are formed primarily through synthesis-dependent strand annealing mediated by the Sgs1 helicase. This work identifies a conserved region on the C terminus of Zip1 (called Zip1 4S, whose phosphorylation is required for the ZMM pathway of crossover formation. Zip1 4S phosphorylation is promoted both by double-strand breaks (DSBs and the meiosis-specific kinase, MEK1/MRE4, demonstrating a role for MEK1 in the regulation of interhomolog crossover formation, as well as interhomolog bias. Failure to phosphorylate Zip1 4S results in meiotic prophase arrest, specifically in the absence of SGS1. This gain of function meiotic arrest phenotype is suppressed by spo11Δ, suggesting that it is due to unrepaired breaks triggering the meiotic recombination checkpoint. Epistasis experiments combining deletions of individual ZMM genes with sgs1-md zip1-4A indicate that Zip1 4S phosphorylation functions prior to the other ZMMs. These results suggest that phosphorylation of Zip1 at DSBs commits those breaks to repair via the ZMM pathway and provides a mechanism by which the crossover/noncrossover decision can be dynamically regulated during yeast meiosis.

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_vitr...o/TNFa.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 ...

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 ...

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/phenobarbital.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/...in_vitro/phenobarbital.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_...vivo/Liver/Single/phenobarbital.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscience

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.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_...vivo/Liver/Single/sulfasalazine.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscience

Compound list: methapyrilene [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available methapyrilene MP 00025 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human.../in_vitro/methapyrilene.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/...in_vitro/methapyrilene.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_...vivo/Liver/Single/methapyrilene.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscience

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 ...

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

Hybrids of the bHLH and bZIP protein motifs display different DNA-binding activities in vivo vs. in vitro.

Directory of Open Access Journals (Sweden)

Hiu-Kwan Chow

Full Text Available Minimalist hybrids comprising the DNA-binding domain of bHLH/PAS (basic-helix-loop-helix/Per-Arnt-Sim protein Arnt fused to the leucine zipper (LZ dimerization domain from bZIP (basic region-leucine zipper protein C/EBP were designed to bind the E-box DNA site, CACGTG, targeted by bHLHZ (basic-helix-loop-helix-zipper proteins Myc and Max, as well as the Arnt homodimer. The bHLHZ-like structure of ArntbHLH-C/EBP comprises the Arnt bHLH domain fused to the C/EBP LZ: i.e. swap of the 330 aa PAS domain for the 29 aa LZ. In the yeast one-hybrid assay (Y1H, transcriptional activation from the E-box was strong by ArntbHLH-C/EBP, and undetectable for the truncated ArntbHLH (PAS removed, as detected via readout from the HIS3 and lacZ reporters. In contrast, fluorescence anisotropy titrations showed affinities for the E-box with ArntbHLH-C/EBP and ArntbHLH comparable to other transcription factors (K(d 148.9 nM and 40.2 nM, respectively, but only under select conditions that maintained folded protein. Although in vivo yeast results and in vitro spectroscopic studies for ArntbHLH-C/EBP targeting the E-box correlate well, the same does not hold for ArntbHLH. As circular dichroism confirms that ArntbHLH-C/EBP is a much more strongly alpha-helical structure than ArntbHLH, we conclude that the nonfunctional ArntbHLH in the Y1H must be due to misfolding, leading to the false negative that this protein is incapable of targeting the E-box. Many experiments, including protein design and selections from large libraries, depend on protein domains remaining well-behaved in the nonnative experimental environment, especially small motifs like the bHLH (60-70 aa. Interestingly, a short helical LZ can serve as a folding- and/or solubility-enhancing tag, an important device given the focus of current research on exploration of vast networks of biomolecular interactions.

Compound list: chlorpheniramine [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available chlorpheniramine CHL 00090 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/chlorpheni...ramine.Human.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 ...

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/chlorampheni...col.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST...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 ...

Compound list: meloxicam [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available meloxicam MLX 00124 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in..._vitro/meloxicam.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitr...o/meloxicam.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/...Single/meloxicam.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/

Compound list: disopyramide [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available disopyramide DIS 00102 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human.../in_vitro/disopyramide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/i...n_vitro/disopyramide.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...vo/Liver/Single/disopyramide.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc

Compound list: ethionamide [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available ethionamide ETH 00135 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/...in_vitro/ethionamide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_...vitro/ethionamide.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/...Liver/Single/ethionamide.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/

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.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.

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_v...itro/diclofenac.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Li...ver/Single/diclofenac.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arc

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/i...n_vitro/theophylline.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...vo/Liver/Single/theophylline.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc

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/Sin...gle/pemoline.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open

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/griseofulvin.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in..._vitro/griseofulvin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_viv...o/Liver/Single/griseofulvin.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.

Compound list: propylthiouracil [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available propylthiouracil PTU 00029 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/H...uman/in_vitro/propylthiouracil.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATE...ST/Rat/in_vitro/propylthiouracil.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATE...ST/Rat/in_vivo/Liver/Single/propylthiouracil.Rat.in_vivo.Liver.Single.zip ftp://f

Compound list: carbamazepine [Open TG-GATEs

Lifescience Database Archive (English)

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

Compound list: benziodarone [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available benziodarone BZD 00130 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human.../in_vitro/benziodarone.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/i...n_vitro/benziodarone.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...vo/Liver/Single/benziodarone.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc

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_vitr...o/quinidine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/...Single/quinidine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/

Compound list: naproxen [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available naproxen NPX 00073 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_...vitro/naproxen.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/...naproxen.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Sin...gle/naproxen.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open

Compound list: nitrofurazone [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available nitrofurazone NFZ 00065 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Huma...n/in_vitro/nitrofurazone.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat.../in_vitro/nitrofurazone.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in..._vivo/Liver/Single/nitrofurazone.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscienc

Compound list: trimethadione [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available trimethadione TMD 00122 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Huma...n/in_vitro/trimethadione.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat.../in_vitro/trimethadione.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in..._vivo/Liver/Single/trimethadione.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscienc

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.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/

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.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/

Compound list: ibuprofen [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available ibuprofen IBU 00072 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in..._vitro/ibuprofen.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitr...o/ibuprofen.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/...Single/ibuprofen.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/

Compound list: chlormezanone [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available chlormezanone CMN 00052 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Huma...n/in_vitro/chlormezanone.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat.../in_vitro/chlormezanone.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in..._vivo/Liver/Single/chlormezanone.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscienc

Compound list: chlorpropamide [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available chlorpropamide CPP 00080 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Hum...an/in_vitro/chlorpropamide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/R...at/in_vitro/chlorpropamide.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat.../in_vivo/Liver/Single/chlorpropamide.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosc

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/i...n_vitro/azathioprine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...vo/Liver/Single/azathioprine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc

Compound list: simvastatin [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available simvastatin SST 00117 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/...in_vitro/simvastatin.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_...vitro/simvastatin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/...Liver/Single/simvastatin.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/

Compound list: phenytoin [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available phenytoin PHE 00026 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in..._vitro/phenytoin.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitr...o/phenytoin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/...Single/phenytoin.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/

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/sulindac.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/...sulindac.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Sin...gle/sulindac.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open

Compound list: metformin [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available metformin MFM 00053 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in..._vitro/metformin.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitr...o/metformin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/...Single/metformin.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/

Compound list: methimazole [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available methimazole MTZ 00057 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/...in_vitro/methimazole.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_...vitro/methimazole.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/...Liver/Single/methimazole.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/

Compound list: bendazac [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available bendazac BDZ 00129 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_...vitro/bendazac.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/...bendazac.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Sin...gle/bendazac.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open

Compound list: sulpiride [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available sulpiride SLP 00115 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in..._vitro/sulpiride.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitr...o/sulpiride.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/...Single/sulpiride.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/

Compound list: fenofibrate [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available fenofibrate FFB 00079 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/...in_vitro/fenofibrate.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_...vitro/fenofibrate.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/...Liver/Single/fenofibrate.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/

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/i...n_vitro/thioridazine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...vo/Liver/Single/thioridazine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc

Compound list: acarbose [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available acarbose ACA 00116 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_...vitro/acarbose.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/...acarbose.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Sin...gle/acarbose.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open

Compound list: isoniazid [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available isoniazid INAH 00002 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/i...n_vitro/isoniazid.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vit...ro/isoniazid.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver.../Single/isoniazid.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive

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/labetalol.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitr...o/labetalol.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/...Single/labetalol.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/

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 ...

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 ...

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 ...

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 ...

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/glibenclam...ide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/glibenclam..._vivo/Liver/Single/glibenclamide.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscienc...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/glibenclamide.Rat.in_vivo.Liver.Repeat.zip ...

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.

Compound list: naphthyl isothiocyanate [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available naphthyl isothiocyanate ANIT 00009 ftp://ftp.biosciencedbc.jp/archive/open-tggates/...LATEST/Human/in_vitro/naphthyl_isothiocyanate.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/op...en-tggates/LATEST/Rat/in_vitro/naphthyl_isothiocyanate.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/arc...hive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/naphthyl_isothiocyanate.Rat.in_...vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/naphthyl_isothiocyanate.Rat.in_vivo.Liver.Repeat.zip ...

Compound list: carbon tetrachloride [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available carbon tetrachloride CCL4 00003 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LAT...EST/Human/in_vitro/carbon_tetrachloride.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tgg...ates/LATEST/Rat/in_vitro/carbon_tetrachloride.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open...-tggates/LATEST/Rat/in_vivo/Liver/Single/carbon_tetrachloride.Rat.in_vivo.Liver.S...ingle.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/carbon_tetrachloride.Rat.in_vivo.Liver.Repeat.zip ...

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/Hum...an/in_vitro/amphotericin_B.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/R...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.zip ftp:...//ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/amphotericin_B.Rat.in_vivo.Kidney.Single.zip ftp:

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

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 ...

Compound list: diltiazem [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available diltiazem DIL 00092 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/diltia...zem.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/diltia...zem.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/diltia...open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/diltiazem.Rat.in_vivo.Liver.Repeat.zip ...

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/flutam...ide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/flutam...ide.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/flutam...pen-tggates/LATEST/Rat/in_vivo/Liver/Repeat/flutamide.Rat.in_vivo.Liver.Repeat.zip ...

Compound list: tamoxifen [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available tamoxifen TMX 00054 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/tam...oxifen.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/tam...oxifen.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/tam...open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/tamoxifen.Rat.in_vivo.Liver.Repeat.zip ...

Compound list: acetamidofluorene [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available acetamidofluorene AAF 00144 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/acetam...idofluorene.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/acetam...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 ...

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/papaverine.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 ...

Compound list: gemfibrozil [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available gemfibrozil GFZ 00031 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/gemfibrozil....Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/gemfibrozil....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/gemfibrozil...archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/gemfibrozil.Rat.in_vivo.Liver.Repeat.zip ...

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/diaz...epam.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/diaz...epam.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/diaz...-tggates/LATEST/Rat/in_vivo/Liver/Repeat/diazepam.Rat.in_vivo.Liver.Repeat.zip ...

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/i...n_vitro/famotidine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/famotidine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/famotidine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch

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/i...n_vitro/nifedipine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/nifedipine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/nifedipine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch

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/i...n_vitro/perhexiline.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_v...itro/perhexiline.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/L...iver/Single/perhexiline.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/a

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/i...n_vitro/colchicine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/colchicine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/colchicine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch

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/i...n_vitro/ranitidine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/ranitidine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/ranitidine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch

Compound list: nimesulide [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available nimesulide NIM 00136 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/i...n_vitro/nimesulide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/nimesulide.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/nimesulide.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch

Compound list: dantrolene [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available dantrolene DTL 00119 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/i...n_vitro/dantrolene.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/dantrolene.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/dantrolene.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch

Compound list: moxisylyte [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available moxisylyte MXS 00061 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/i...n_vitro/moxisylyte.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/moxisylyte.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/moxisylyte.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch

Compound list: iproniazid [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available iproniazid IPA 00062 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/i...n_vitro/iproniazid.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/iproniazid.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/iproniazid.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch

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/i...n_vitro/methyldopa.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/methyldopa.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/methyldopa.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch

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/i...n_vitro/mexiletine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/mexiletine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/mexiletine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch

Compound list: lornoxicam [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available lornoxicam LNX 00125 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/i...n_vitro/lornoxicam.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/lornoxicam.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/lornoxicam.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch

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/i...n_vitro/phalloidin.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/phalloidin.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/phalloidin.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch

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/i...n_vitro/cimetidine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vi...tro/cimetidine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liv...er/Single/cimetidine.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/arch

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 ...

Compound list: coumarin [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available coumarin CMA 00027 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/coumari...n.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/coumari...n.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/coumari...-tggates/LATEST/Rat/in_vivo/Liver/Repeat/coumarin.Rat.in_vivo.Liver.Repeat.zip ...

Compound list: triazolam [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available triazolam TZM 00120 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/triazolam.Human.in_vitro.Liver.zip ftp://ftp.bi...osciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/triazolam....Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/triazolam...open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/triazolam.Rat.in_vivo.Liver.Repeat.zip ...

Deregulation of sucrose-controlled translation of a bZIP-type transcription factor results in sucrose accumulation in leaves.

Directory of Open Access Journals (Sweden)

Sunil Kumar Thalor

Full Text Available Sucrose is known to repress the translation of Arabidopsis thaliana AtbZIP11 transcript which encodes a protein belonging to the group of S (S--stands for small basic region-leucine zipper (bZIP-type transcription factor. This repression is called sucrose-induced repression of translation (SIRT. It is mediated through the sucrose-controlled upstream open reading frame (SC-uORF found in the AtbZIP11 transcript. The SIRT is reported for 4 other genes belonging to the group of S bZIP in Arabidopsis. Tobacco tbz17 is phylogenetically closely related to AtbZIP11 and carries a putative SC-uORF in its 5'-leader region. Here we demonstrate that tbz17 exhibits SIRT mediated by its SC-uORF in a manner similar to genes belonging to the S bZIP group of the Arabidopsis genus. Furthermore, constitutive transgenic expression of tbz17 lacking its 5'-leader region containing the SC-uORF leads to production of tobacco plants with thicker leaves composed of enlarged cells with 3-4 times higher sucrose content compared to wild type plants. Our finding provides a novel strategy to generate plants with high sucrose content.

Deregulation of sucrose-controlled translation of a bZIP-type transcription factor results in sucrose accumulation in leaves.

Science.gov (United States)

Thalor, Sunil Kumar; Berberich, Thomas; Lee, Sung Shin; Yang, Seung Hwan; Zhu, Xujun; Imai, Ryozo; Takahashi, Yoshihiro; Kusano, Tomonobu

2012-01-01

Sucrose is known to repress the translation of Arabidopsis thaliana AtbZIP11 transcript which encodes a protein belonging to the group of S (S--stands for small) basic region-leucine zipper (bZIP)-type transcription factor. This repression is called sucrose-induced repression of translation (SIRT). It is mediated through the sucrose-controlled upstream open reading frame (SC-uORF) found in the AtbZIP11 transcript. The SIRT is reported for 4 other genes belonging to the group of S bZIP in Arabidopsis. Tobacco tbz17 is phylogenetically closely related to AtbZIP11 and carries a putative SC-uORF in its 5'-leader region. Here we demonstrate that tbz17 exhibits SIRT mediated by its SC-uORF in a manner similar to genes belonging to the S bZIP group of the Arabidopsis genus. Furthermore, constitutive transgenic expression of tbz17 lacking its 5'-leader region containing the SC-uORF leads to production of tobacco plants with thicker leaves composed of enlarged cells with 3-4 times higher sucrose content compared to wild type plants. Our finding provides a novel strategy to generate plants with high sucrose content.

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/flu...phenazine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/flu...phenazine.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/flu...jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/fluphenazine.Rat.in_vivo.Liver.Repeat.zip ...

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/amit...riptyline.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/amit...riptyline.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/amit...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/amitriptyline.Rat.in_vivo.Liver.Repeat.zip ...

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/furose...mide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/furose...mide.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/furose...ive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/furosemide.Rat.in_vivo.Liver.Repeat.zip ...

Compound list: benzbromarone [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available benzbromarone BBr 00021 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/benz...bromarone.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/benz...bromarone.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/benz...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/benzbromarone.Rat.in_vivo.Liver.Repeat.zip ...

Compound list: tolbutamide [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available tolbutamide TLB 00114 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/tolbutam...ide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/tolbutam...ide.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/tolbutam...archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/tolbutamide.Rat.in_vivo.Liver.Repeat.zip ...

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 ...

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

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...uman/in_vitro/cyclophosphamide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATE...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.

Compound list: bromoethylamine [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available bromoethylamine BEA 00134 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/bromoethylam...ine.Human.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...t.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/bromoethylamine.Rat.i

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/diethyl_male.../Rat/in_vitro/diethyl_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 ... ...ate.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST

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 ...

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

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/thioacetamide.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

Compound list: acetazolamide [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available acetazolamide ACZ 00108 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/acetazolam...ide.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/acetazolam..._vivo/Liver/Single/acetazolamide.Rat.in_vivo.Liver.Single.zip ftp://ftp.bioscienc...edbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/acetazolamide.Rat.in_vivo.Liver.Repeat.zip ftp:...//ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Kidney/Single/acetazolamide.Rat.in_vivo.Kidne

Compound list: methylene dianiline [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available methylene dianiline DAPM 00155 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/methyle...es/LATEST/Rat/in_vivo/Liver/Single/methylene_dianiline.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc....jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/methylene_dianiline.Rat.in_vivo.Liver.Repeat.zip ... ...ne_dianiline.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggat

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 ...

Compound list: fluoxetine hydrochloride [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available fluoxetine hydrochloride FLX 00158 ftp://ftp.biosciencedbc.jp/archive/open-tggates/...LATEST/Human/in_vitro/fluoxetine_hydrochloride.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/o...pen-tggates/LATEST/Rat/in_vivo/Liver/Single/fluoxetine_hydrochloride.Rat.in_vivo.Liver.Single.zip ftp://ftp....biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/fluoxetine_hydrochloride.Rat.in_vivo.Liver.Repeat.zip ...

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.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/

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/Hum...an/in_vitro/mefenamic_acid.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/R...at/in_vitro/mefenamic_acid.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat.../in_vivo/Liver/Single/mefenamic_acid.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosc

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/Hum...an/in_vitro/nicotinic_acid.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/R...at/in_vitro/nicotinic_acid.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat.../in_vivo/Liver/Single/nicotinic_acid.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosc

Expression analysis of OsbZIP transcription factors in resistance ...

African Journals Online (AJOL)

zino

2013-08-21

Aug 21, 2013 ... Plant basic leucine zipper (bZIP) proteins play an essential role in the genes expression and regulation in higher plants. They have been shown to regulate diverse plant specific phenomena, including germination, floral induction and development, seed maturation, photomorphogenesis, biotic and.

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.

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/i...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

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/ketoco...nazole.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/ketoco...nazole.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/ketoco...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

Compound list: vitamin A [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available vitamin A VA 00059 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_vitro/vitam...in_A.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/vitam...in_A.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/vitam...pen-tggates/LATEST/Rat/in_vivo/Liver/Repeat/vitamin_A.Rat.in_vivo.Liver.Repeat.zip ...

Compound list: WY-14643 [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available WY-14643 WY 00030 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in_v...itro/WY-14643.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/W...Y-14643.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Sing...le/WY-14643.Rat.in_vivo.Liver.Single.zip ftp://ftp.biosciencedbc.jp/archive/open-

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_v...itro/alpidem.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/alpidem.Rat.in_vitro.Liver.zip ...

Compound list: buspirone [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available buspirone BPR 00173 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Human/in..._vitro/buspirone.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/buspirone.Rat.in_vitro.Liver.zip ...

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 ...

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 ...

Decryption-decompression of AES protected ZIP files on GPUs

Science.gov (United States)

Duong, Tan Nhat; Pham, Phong Hong; Nguyen, Duc Huu; Nguyen, Thuy Thanh; Le, Hung Duc

2011-10-01

AES is a strong encryption system, so decryption-decompression of AES encrypted ZIP files requires very large computing power and techniques of reducing the password space. This makes implementations of techniques on common computing system not practical. In [1], we reduced the original very large password search space to a much smaller one which surely containing the correct password. Based on reduced set of passwords, in this paper, we parallel decryption, decompression and plain text recognition for encrypted ZIP files by using CUDA computing technology on graphics cards GeForce GTX295 of NVIDIA, to find out the correct password. The experimental results have shown that the speed of decrypting, decompressing, recognizing plain text and finding out the original password increases about from 45 to 180 times (depends on the number of GPUs) compared to sequential execution on the Intel Core 2 Quad Q8400 2.66 GHz. These results have demonstrated the potential applicability of GPUs in this cryptanalysis field.

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

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.

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 ...

ZIP4H (TEX11 deficiency in the mouse impairs meiotic double strand break repair and the regulation of crossing over.

Directory of Open Access Journals (Sweden)

Carrie A Adelman

2008-03-01

Full Text Available We have recently shown that hypomorphic Mre11 complex mouse mutants exhibit defects in the repair of meiotic double strand breaks (DSBs. This is associated with perturbation of synaptonemal complex morphogenesis, repair and regulation of crossover formation. To further assess the Mre11 complex's role in meiotic progression, we identified testis-specific NBS1-interacting proteins via two-hybrid screening in yeast. In this screen, Zip4h (Tex11, a male germ cell specific X-linked gene was isolated. Based on sequence and predicted structural similarity to the S. cerevisiae and A. thaliana Zip4 orthologs, ZIP4H appears to be the mammalian ortholog. In S. cerevisiae and A. thaliana, Zip4 is a meiosis-specific protein that regulates the level of meiotic crossovers, thus influencing homologous chromosome segregation in these organisms. As is true for hypomorphic Nbs1 (Nbs1(DeltaB/DeltaB mice, Zip4h(-/Y mutant mice were fertile. Analysis of spermatocytes revealed a delay in meiotic double strand break repair and decreased crossover formation as inferred from DMC1 and MLH1 staining patterns, respectively. Achiasmate chromosomes at the first meiotic division were also observed in Zip4h(-/Y mutants, consistent with the observed reduction in MLH1 focus formation. These results indicate that meiotic functions of Zip4 family members are conserved and support the view that the Mre11 complex and ZIP4H interact functionally during the execution of the meiotic program in mammals.

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

KAUST Repository

Elshurafa, Amro M.; El-Masry, Ezz I.

2010-01-01

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

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.

A model for the mechanism of strand passage by DNA gyrase

DEFF Research Database (Denmark)

Kampranis, S C; Bates, A D; Maxwell, A

1999-01-01

this mechanism by probing the topology of the bound DNA segment at distinct steps of the catalytic cycle. We propose a model in which gyrase captures a contiguous DNA segment with high probability, irrespective of the superhelical density of the DNA substrate, setting up an equilibrium of the transported segment......The mechanism of type II DNA topoisomerases involves the formation of an enzyme-operated gate in one double-stranded DNA segment and the passage of another segment through this gate. DNA gyrase is the only type II topoisomerase able to introduce negative supercoils into DNA, a feature that requires...... the enzyme to dictate the directionality of strand passage. Although it is known that this is a consequence of the characteristic wrapping of DNA by gyrase, the detailed mechanism by which the transported DNA segment is captured and directed through the DNA gate is largely unknown. We have addressed...

Mounting a Curricular Revolution: An Interview with Henry Louis Gates, Jr.

Science.gov (United States)

von Zastrow, Claus

2009-01-01

This article presents an interview with Henry Louis Gates, Jr., Harvard professor and cultural critic who has captured 25 million viewers with his PBS documentary series, African American Lives (WNET). Using genealogical research and DNA science, Gates traces the family history of 19 famous African Americans. What results is a rich and moving…

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

Water-gel for gating graphene transistors.

Science.gov (United States)

Kim, Beom Joon; Um, Soong Ho; Song, Woo Chul; Kim, Yong Ho; Kang, Moon Sung; Cho, Jeong Ho

2014-05-14

Water, the primary electrolyte in biology, attracts significant interest as an electrolyte-type dielectric material for transistors compatible with biological systems. Unfortunately, the fluidic nature and low ionic conductivity of water prevents its practical usage in such applications. Here, we describe the development of a solid state, megahertz-operating, water-based gate dielectric system for operating graphene transistors. The new electrolyte systems were prepared by dissolving metal-substituted DNA polyelectrolytes into water. The addition of these biocompatible polyelectrolytes induced hydrogelation to provide solid-state integrity to the system. They also enhanced the ionic conductivities of the electrolytes, which in turn led to the quick formation of an electric double layer at the graphene/electrolyte interface that is beneficial for modulating currents in graphene transistors at high frequencies. At the optimized conditions, the Na-DNA water-gel-gated flexible transistors and inverters were operated at frequencies above 1 MHz and 100 kHz, respectively.

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.

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.

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/valpr...oic_acid.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vitro/valpr...oic_acid.Rat.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/Rat/in_vivo/Liver/Single/valpr...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

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.

Expression Patterns and Correlations with Metabolic Markers of Zinc Transporters ZIP14 and ZNT1 in Obesity and Polycystic Ovary Syndrome

Science.gov (United States)

Maxel, Trine; Svendsen, Pernille Fog; Smidt, Kamille; Lauridsen, Jesper Krogh; Brock, Birgitte; Pedersen, Steen Bønlykke; Rungby, Jørgen; Larsen, Agnete

2017-01-01

Polycystic ovary syndrome (PCOS) is associated with infertility, increased androgen levels, and insulin resistance. In adipose tissue, zinc facilitates insulin signaling. Circulating zinc levels are altered in obesity, diabetes, and PCOS; and zinc supplementation can ameliorate metabolic disturbances in PCOS. In adipose tissue, expression of zinc influx transporter ZIP14 varies with body mass index (BMI), clinical markers of metabolic syndrome, and peroxisome proliferator-activated receptor gamma (PPARG). In this study, we investigated expression levels of ZIP14 and PPARG in subcutaneous adipose tissue of 36 PCOS women (17 lean and 19 obese women) compared with 23 healthy controls (7 lean and 16 obese women). Further, expression levels of zinc transporter ZIP9, a recently identified androgen receptor, and zinc efflux transporter ZNT1 were investigated, alongside lipid profile and markers of glucose metabolism [insulin degrading enzyme, retinol-binding protein 4 (RBP4), and glucose transporter 4 (GLUT4)]. We find that ZIP14 expression is reduced in obesity and positively correlates with PPARG expression, which is downregulated with increasing BMI. ZNT1 is upregulated in obesity, and both ZIP14 and ZNT1 expression significantly correlates with clinical markers of altered glucose metabolism. In addition, RBP4 and GLUT4 associate with obesity, but an association with PCOS as such was present only for PPARG and RBP4. ZIP14 and ZNT1 does not relate to clinical androgen status and ZIP9 is unaffected by all parameters investigated. In conclusion, our findings support the existence of a zinc dyshomeostasis in adipose tissue in metabolic disturbances including PCOS-related obesity. PMID:28303117

Isolation and expression analysis of four HD-ZIP III family genes targeted by microRNA166 in peach.

Science.gov (United States)

Zhang, C H; Zhang, B B; Ma, R J; Yu, M L; Guo, S L; Guo, L

2015-10-30

MicroRNA166 (miR166) is known to have highly conserved targets that encode proteins of the class III homeodomain-leucine zipper (HD-ZIP III) family, in a broad range of plant species. To further understand the relationship between HD-ZIP III genes and miR166, four HD-ZIP III family genes (PpHB14, PpHB15, PpHB8, and PpREV) were isolated from peach (Prunus persica) tissue and characterized. Spatio-temporal expression profiles of the genes were analyzed. Genes of the peach HD-ZIP III family were predicted to encode five conserved domains. Deduced amino acid sequences and tertiary structures of the four peach HD-ZIP III genes were highly conserved, with corresponding genes in Arabidopsis thaliana. The expression level of four targets displayed the opposite trend to that of miR166 throughout fruit development, with the exception of PpHB14 from 35 to 55 days after full bloom (DAFB). This finding indicates that miR166 may negatively regulate its four targets throughout fruit development. As for leaf and phloem, the same trend in expression level was observed between four targets and miR166 from 75 to 105 DAFB. However, the opposite trend was observed for the transcript level between four targets and miR166 from 35 to 55 DAFB. miRNA166 may negatively regulate four targets in some but not all developmental stages for a given tissue. The four genes studied were observed to have, exactly or generally, the same change tendency as individual tissue development, a finding that suggests genes of the HD-ZIP III family in peach may have complementary or cooperative functions in various tissues.

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-nitroflu...orene.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 ...

Compound list: N-nitrosomorpholine [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available N-nitrosomorpholine NMOR 00163 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATE...es/LATEST/Rat/in_vivo/Liver/Single/N-nitrosomorpholine.Rat.in_vivo.Liver.Single.zip ... ...ST/Human/in_vitro/N-nitrosomorpholine.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-tggat

A genome-wide survey of homeodomain-leucine zipper genes and analysis of cold-responsive HD-Zip I members' expression in tomato.

Science.gov (United States)

Zhang, Zhenzhu; Chen, Xiuling; Guan, Xin; Liu, Yang; Chen, Hongyu; Wang, Tingting; Mouekouba, Liana Dalcantara Ongouya; Li, Jingfu; Wang, Aoxue

2014-01-01

Homeodomain-leucine zipper (HD-Zip) proteins are a kind of transcriptional factors that play a vital role in plant growth and development. However, no detailed information of HD-Zip family in tomato has been reported till now. In this study, 51 HD-Zip genes (SlHZ01-51) in this family were identified and categorized into 4 classes by exon-intron and protein structure in tomato (Solanum lycopersicum) genome. The synthetical phylogenetic tree of tomato, Arabidopsis and rice HD-Zip genes were established for an insight into their evolutionary relationships and putative functions. The results showed that the contribution of segmental duplication was larger than that of tandem duplication for expansion and evolution of genes in this family of tomato. The expression profile results under abiotic stress suggested that all SlHZ I genes were responsive to cold stress. This study will provide a clue for the further investigation of functional identification and the role of tomato HD-Zip I subfamily in plant cold stress responses and developmental events.

A DNA Logic Gate Automaton for Detection of Rabies and Other Lyssaviruses.

Science.gov (United States)

Vijayakumar, Pavithra; Macdonald, Joanne

2017-07-05

Immediate activation of biosensors is not always desirable, particularly if activation is due to non-specific interactions. Here we demonstrate the use of deoxyribozyme-based logic gate networks arranged into visual displays to precisely control activation of biosensors, and demonstrate a prototype molecular automaton able to discriminate between seven different genotypes of Lyssaviruses, including Rabies virus. The device uses novel mixed-base logic gates to enable detection of the large diversity of Lyssavirus sequence populations, while an ANDNOT logic gate prevents non-specific activation across genotypes. The resultant device provides a user-friendly digital-like, but molecule-powered, dot-matrix text output for unequivocal results read-out that is highly relevant for point of care applications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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

Amplification of the Kaposi's sarcoma-associated herpesvirus/human herpesvirus 8 lytic origin of DNA replication is dependent upon a cis-acting AT-rich region and an ORF50 response element and the trans-acting factors ORF50 (K-Rta) and K8 (K-bZIP)

International Nuclear Information System (INIS)

AuCoin, David P.; Colletti, Kelly S.; Cei, Sylvia A.; Papouskova, Iva; Tarrant, Margaret; Pari, Gregory S.

2004-01-01

Kaposi's sarcoma-associated herpesvirus (KSHV), also known as human herpesvirus 8 (HHV8), has significant sequence homology to Epstein-Barr virus (EBV). In cell culture, HHV8 is primarily latent, and viral genes associated with lytic replication are not expressed. Two lytic origins of DNA replication (oriLyt) are present within the HHV8 genome and are composed of an AT-rich region adjacent to GC-rich DNA sequences. We have now identified essential cis- and trans-acting elements required for oriLyt-dependent DNA replication. The transient replication assay was used to show that two AT-rich elements, three consensus AP1 transcription factor-binding sites, an ORF50 response element (RE), and a consensus TATA box motif are essential for efficient origin-dependent DNA replication. Transient transfection of luciferase reporter constructs indicated that the downstream region of the HHV8 oriLyt responds to ORF50 and suggests that part of the oriLyt may be an enhancer/promoter. In addition, a transient cotransfection-replication assay elucidated the set of trans-acting factors required for lytic DNA replication. These factors consist of homologues to the core replication proteins: ORF6 (ssDNA binding protein), ORF9 (DNA polymerase), ORF40-41 (primase-associated factor), ORF44 (helicase), ORF56 (primase), and ORF59 (polymerase processivity factor) common to all herpesviruses along with ORF50 (K-Rta) and K8 (K-bZIP)

PpHB22, a member of HD-Zip proteins, activates PpDAM1 to regulate bud dormancy transition in 'Suli' pear (Pyrus pyrifolia White Pear Group).

Science.gov (United States)

Yang, Qinsong; Niu, Qingfeng; Li, Jianzhao; Zheng, Xiaoyan; Ma, Yunjing; Bai, Songling; Teng, Yuanwen

2018-06-01

Homeodomain-leucine zipper (HD-Zip) proteins, which form one of the largest and most diverse families, regulate many biological processes in plants, including differentiation, flowering, vascular development, and stress signaling. Abscisic acid (ABA) has been proved to be one of the key regulators of bud dormancy and to influence several HD-Zip genes expression. However, the role of HD-Zip genes in regulating bud dormancy remains unclear. We identified 47 pear (P. pyrifolia White Pear Group) HD-Zip genes, which were classified into four subfamilies (HD-Zip I-IV). We further revealed that gene expression levels of some HD-Zip members were closely related to ABA concentrations in flower buds during dormancy transition. Exogenous ABA treatment confirmed that PpHB22 and several other HD-Zip genes responded to ABA. Yeast one-hybrid and dual luciferase assay results combining subcellular localization showed that PpHB22 was present in nucleus and directly induced PpDAM1 (dormancy associated MADS-box 1) expression. Thus, PpHB22 is a negative regulator of plant growth associated with the ABA response pathway and functions upstream of PpDAM1. These findings enrich our understanding of the function of HD-Zip genes related to the bud dormancy transition. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

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.

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.

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.

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.

Computing travel time when the exact address is unknown: a comparison of point and polygon ZIP code approximation methods.

Science.gov (United States)

Berke, Ethan M; Shi, Xun

2009-04-29

Travel time is an important metric of geographic access to health care. We compared strategies of estimating travel times when only subject ZIP code data were available. Using simulated data from New Hampshire and Arizona, we estimated travel times to nearest cancer centers by using: 1) geometric centroid of ZIP code polygons as origins, 2) population centroids as origin, 3) service area rings around each cancer center, assigning subjects to rings by assuming they are evenly distributed within their ZIP code, 4) service area rings around each center, assuming the subjects follow the population distribution within the ZIP code. We used travel times based on street addresses as true values to validate estimates. Population-based methods have smaller errors than geometry-based methods. Within categories (geometry or population), centroid and service area methods have similar errors. Errors are smaller in urban areas than in rural areas. Population-based methods are superior to the geometry-based methods, with the population centroid method appearing to be the best choice for estimating travel time. Estimates in rural areas are less reliable.

DNA Assembly in 3D Printed Fluidics (Open Access, Publisher’s Version)

Science.gov (United States)

2015-12-30

millifluidics to mix linear double stranded DNA with enzymes to assemble plasmids via Golden Gate biochemistry . The assembly reac- tions occurred at...used, a constitutively expressed yellow fluorescent protein (YFP) reporter, and a plasmid backbone containing an ampicillin selection marker ( AMP ) and...proof-of- principle that 3D printed devices can adequately mix the Golden Gate enzymes and DNA and that the Golden Gate biochemistry proceeds

Avatar DNA Nanohybrid System in Chip-on-a-Phone

Science.gov (United States)

Park, Dae-Hwan; Han, Chang Jo; Shul, Yong-Gun; Choy, Jin-Ho

2014-05-01

Long admired for informational role and recognition function in multidisciplinary science, DNA nanohybrids have been emerging as ideal materials for molecular nanotechnology and genetic information code. Here, we designed an optical machine-readable DNA icon on microarray, Avatar DNA, for automatic identification and data capture such as Quick Response and ColorZip codes. Avatar icon is made of telepathic DNA-DNA hybrids inscribed on chips, which can be identified by camera of smartphone with application software. Information encoded in base-sequences can be accessed by connecting an off-line icon to an on-line web-server network to provide message, index, or URL from database library. Avatar DNA is then converged with nano-bio-info-cogno science: each building block stands for inorganic nanosheets, nucleotides, digits, and pixels. This convergence could address item-level identification that strengthens supply-chain security for drug counterfeits. It can, therefore, provide molecular-level vision through mobile network to coordinate and integrate data management channels for visual detection and recording.

Side-gated ultrathin-channel nanopore FET sensors

International Nuclear Information System (INIS)

Yanagi, Itaru; Haga, Takanobu; Ando, Masahiko; Yamamoto, Jiro; Mine, Toshiyuki; Ishida, Takeshi; Hatano, Toshiyuki; Akahori, Rena; Yokoi, Takahide; Anazawa, Takashi; Oura, Takeshi

2016-01-01

A side-gated, ultrathin-channel nanopore FET (SGNAFET) is proposed for fast and label-free DNA sequencing. The concept of the SGNAFET comprises the detection of changes in the channel current during DNA translocation through a nanopore and identifying the four types of nucleotides as a result of these changes. To achieve this goal, both p- and n-type SGNAFETs with a channel thicknesses of 2 or 4 nm were fabricated, and the stable transistor operation of both SGNAFETs in air, water, and a KCl buffer solution were confirmed. In addition, synchronized current changes were observed between the ionic current through the nanopore and the SGNAFET’s drain current during DNA translocation through the nanopore. (paper)

Bio Organic-Semiconductor Field-Effect Transistor (BioFET) Based on Deoxyribonucleic Acid (DNA) Gate Dielectric

Science.gov (United States)

2010-03-31

floating gate devices and metal-insulator-oxide-semiconductor (MIOS) devices. First attempts to use polarizable gate insulators in combination with...bulk of the semiconductor (ii) Due to the polarizable gate dielectric (iii) dipole polarization and (iv)electret effect due to mobile ions in the...characterization was carried out under an argon environment inside the glove box. An Agilent model E5273A with a two source-measurement unit instrument was

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), ...

Near-Infrared Ag2S Quantum Dots-Based DNA Logic Gate Platform for miRNA Diagnostics.

Science.gov (United States)

Miao, Peng; Tang, Yuguo; Wang, Bidou; Meng, Fanyu

2016-08-02

Dysregulation of miRNA expression is correlated with the development and progression of many diseases. These miRNAs are regarded as promising biomarkers. However, it is challenging to measure these low abundant molecules without employing time-consuming radioactive labeling or complex amplification strategies. Here, we present a DNA logic gate platform for miRNA diagnostics with fluorescence outputs from near-infrared (NIR) Ag2S quantum dots (QDs). Carefully designed toehold exchange-mediated strand displacements with different miRNA inputs occur on a solid-state interface, which control QDs release from solid-state interface to solution, responding to multiplex information on initial miRNAs. Excellent fluorescence emission properties of NIR Ag2S QDs certify the great prospect for amplification-free and sensitive miRNA assay. We demonstrate the potential of this platform by achieving femtomolar level miRNA analysis and the versatility of a series of logic circuits computation.

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...

Probing Conformational Changes in Human DNA Topoisomerase IIα by Pulsed Alkylation Mass Spectrometry*

Science.gov (United States)

Chen, Yu-tsung; Collins, Tammy R. L.; Guan, Ziqiang; Chen, Vincent B.; Hsieh, Tao-Shih

2012-01-01

Type II topoisomerases are essential enzymes for solving DNA topological problems by passing one segment of DNA duplex through a transient double-strand break in a second segment. The reaction requires the enzyme to precisely control DNA cleavage and gate opening coupled with ATP hydrolysis. Using pulsed alkylation mass spectrometry, we were able to monitor the solvent accessibilities around 13 cysteines distributed throughout human topoisomerase IIα by measuring the thiol reactivities with monobromobimane. Most of the measured reactivities are in accordance with the predicted ones based on a homology structural model generated from available crystal structures. However, these results reveal new information for both the residues not covered in the structural model and potential differences between the modeled and solution holoenzyme structures. Furthermore, on the basis of the reactivity changes of several cysteines located at the N-gate and DNA gate, we could monitor the movement of topoisomerase II in the presence of cofactors and detect differences in the DNA gate between two closed clamp enzyme conformations locked by either 5′-adenylyl β,γ-imidodiphosphate or the anticancer drug ICRF-193. PMID:22679013

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

Compound list: N-methyl-N-nitrosourea [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available N-methyl-N-nitrosourea MNU 00164 ftp://ftp.biosciencedbc.jp/archive/open-tggates/LA...TEST/Human/in_vitro/N-methyl-N-nitrosourea.Human.in_vitro.Liver.zip ftp://ftp.biosciencedbc.jp/archive/open-...tggates/LATEST/Rat/in_vivo/Liver/Single/N-methyl-N-nitrosourea.Rat.in_vivo.Liver.Single.zip ...

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.

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

Identification and characterization of bZIP-type transcription factors involved in carrot (Daucus carota L.) somatic embryogenesis.

Science.gov (United States)

Guan, Yucheng; Ren, Haibo; Xie, He; Ma, Zeyang; Chen, Fan

2009-10-01

Seed dormancy is an important adaptive trait that enables seeds of many species to remain quiescent until conditions become favorable for germination. Abscisic acid (ABA) plays an important role in these developmental processes. Like dormancy and germination, the elongation of carrot somatic embryo radicles is retarded by sucrose concentrations at or above 6%, and normal growth resumes at sucrose concentrations below 3%. Using a yeast one-hybrid screening system, we isolated two bZIP-type transcription factors, CAREB1 and CAREB2, from a cDNA library prepared from carrot somatic embryos cultured in a high-sucrose medium. Both CAREB1 and CAREB2 were localized to the nucleus, and specifically bound to the ABA response element (ABRE) in the Dc3 promoter. Expression of CAREB2 was induced in seedlings by drought and exogenous ABA application; whereas expression of CAREB1 increased during late embryogenesis, and reduced dramatically when somatic embryos were treated with fluridone, an inhibitor of ABA synthesis. Overexpression of CAREB1 caused somatic embryos to develop slowly when cultured in low-sucrose medium, and retarded the elongation of the radicles. These results indicate that CAREB1 and CAREB2 have similar DNA-binding activities, but play different roles during carrot development. Our results indicate that CAREB1 functions as an important trans-acting factor in the ABA signal transduction pathway during carrot somatic embryogenesis.

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.

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

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.

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.

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

Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella.

Science.gov (United States)

Papenfort, Kai; Espinosa, Elena; Casadesús, Josep; Vogel, Jörg

2015-08-25

Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution but constitutes a complex process that requires synchronization with the physiological state of the host bacteria. Although several host transcription factors are known to regulate plasmid-borne transfer genes, RNA-based regulatory circuits for host-plasmid communication remain unknown. We describe a posttranscriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two separate seed-pairing domains to activate the mRNAs of both the sigma-factor σ(S) and the RicI protein, a previously uncharacterized membrane protein here shown to inhibit conjugation. Transcription of ricI requires σ(S) and, together, RprA and σ(S) orchestrate a coherent feedforward loop with AND-gate logic to tightly control the activation of RicI synthesis. RicI interacts with the conjugation apparatus protein TraV and limits plasmid transfer under membrane-damaging conditions. To our knowledge, this study reports the first small RNA-controlled feedforward loop relying on posttranscriptional activation of two independent targets and an unexpected role of the conserved RprA small RNA in controlling extrachromosomal DNA transfer.

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

A high performance gate drive for large gate turn off thyristors

Energy Technology Data Exchange (ETDEWEB)

Szilagyi, C.P.

1993-01-01

Past approaches to gate turn-off (GTO) gating are application oriented, inefficient and dissipate power even when inactive. They allow the gate to avalanch, and do not reduce GTO turn-on and turn-off losses. A new approach is proposed which will allow modular construction and adaptability to large GTOs in the 50 amp to 2000 amp range. The proposed gate driver can be used in large voltage source and current source inverters and other power converters. The approach consists of a power metal-oxide-silicon field effect transistor (MOSFET) technology gating unit, with associated logic and supervisory circuits and an isolated flyback converter as the dc power source for the gating unit. The gate driver formed by the gating unit and the flyback converter is designed for 4000 V isolation. Control and supervisory signals are exchanged between the gate driver and the remote control system via fiber optics. The gating unit has programmable front-porch current amplitude and pulse-width, programmable closed-loop controlled back-porch current, and a turn-off switch capable of supplying negative gate current at demand as a function of peak controllable forward anode current. The GTO turn-on, turn-off and gate avalanch losses are reduced to a minimum. The gate driver itself has minimum operating losses. Analysis, design and practical realization are reported. 19 refs., 54 figs., 1 tab.

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.

A novel optical gating method for laser gated imaging

Science.gov (United States)

Ginat, Ran; Schneider, Ron; Zohar, Eyal; Nesher, Ofer

2013-06-01

For the past 15 years, Elbit Systems is developing time-resolved active laser-gated imaging (LGI) systems for various applications. Traditional LGI systems are based on high sensitive gated sensors, synchronized to pulsed laser sources. Elbit propriety multi-pulse per frame method, which is being implemented in LGI systems, improves significantly the imaging quality. A significant characteristic of the LGI is its ability to penetrate a disturbing media, such as rain, haze and some fog types. Current LGI systems are based on image intensifier (II) sensors, limiting the system in spectral response, image quality, reliability and cost. A novel propriety optical gating module was developed in Elbit, untying the dependency of LGI system on II. The optical gating module is not bounded to the radiance wavelength and positioned between the system optics and the sensor. This optical gating method supports the use of conventional solid state sensors. By selecting the appropriate solid state sensor, the new LGI systems can operate at any desired wavelength. In this paper we present the new gating method characteristics, performance and its advantages over the II gating method. The use of the gated imaging systems is described in a variety of applications, including results from latest field experiments.

DNA-FET using carbon nanotube electrodes

International Nuclear Information System (INIS)

Sasaki, T K; Ikegami, A; Aoki, N; Ochiai, Y

2006-01-01

We demonstrate DNA field effect transistor (DNA-FET) using multiwalled carbon nanotube (MWNT) as nano-structural source and drain electrodes. The MWNT electrodes have been fabricated by focused ion-beam bombardment (FIBB). A very short channel, approximately 50 nm, was easily formed between the severed MWNT. The current-voltage (I-V) characteristics of DNA molecules between the MWNT electrodes showed hopping transport property. We have also measured the gate-voltage dependence in the I-V characteristics and found that poly DNA molecules exhibits p-type conduction. The transport of DNA-FET can be explained by two hopping lengths which depend on the range of the source-drain bias voltages

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

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.

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.

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

Science.gov (United States)

2016-06-01

Army uses commercial market segmentation data to analyze markets and past accessions to assign recruiters and quotas to maximize production. We use...Army Recruiting Command to rely on proprietary data with 66 market segments per ZIP code for market analysis and predicting recruiting potential...have different densities of potential recruits; the Army uses commercial market segmentation data to analyze markets and past accessions to assign

Isolate extended state in the DNA molecular transistor with surface interaction

Energy Technology Data Exchange (ETDEWEB)

Wang, Le, E-mail: wang_le917@gs.zzu.edu.cn; Qin, Zhi-Jie

2016-02-01

The field effect characteristic of a DNA molecular device is investigated in a tight binding model with binary disorder and side site correlation. Using the transfer-matrix method and Landauer–Büttiker theory, we find that the system has isolated extended state that is irrespective of the DNA sequence and can be modulated by the gate voltage. When the gate voltage reaches some proper value, the isolated extended state appears at the Fermi level of the system and the long range charge transport is greatly enhanced. We attribute this phenomenon to the combination of the external field, the surface interaction, and the intrinsic disorder of DNA. The result is a generic feature of the nanowire with binary disorder and surface interaction.

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......BACKGROUND: The expansion and function of adipose tissue are important during the development of insulin resistance and inflammation in obesity. Zinc dyshomeostasis is common in obese individuals. In the liver, zinc influx transporter ZIP14, affects proliferation and glucose metabolism but the role...

Capsella rubella TGA4, a bZIP transcription factor, causes delayed flowering in Arabidopsis thaliana

Directory of Open Access Journals (Sweden)

Li Maofu

2016-01-01

Full Text Available Flowering time is usually regulated by many environmental factors and endogenous signals. TGA family members are bZIP transcription factors that bind to the octopine synthase element, which has been closely linked to defense/stress responses. Most TGA factors interact with non-expressor of PR1 (NPR1 and plant defense responses are strengthened by this interaction. TGA1and TGA4factors bind to NPR1 only in salicylic acid (SA-induced leaves, suggesting that TGA4 has another function during plant development. Here, we isolated a bZIP transcription factor gene, TGA4, from Capsella rubella. TGA4transcripts were detected in most tissues, with high expression in leaves, low expression in stems and flowering buds, and undetectable in siliques. CruTGA4was over expressed in Arabidopsis thaliana wild typeCol-0 plants. Flowering time and total leaf number in the transgenic plants showed that overexpression of CruTGA4could delay flowering in A. thaliana. Our findings suggest that TGA4 may act as flowering regulator that controls plant flowering.

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)

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

ISAC's Gating-ML 2.0 data exchange standard for gating description.

Science.gov (United States)

Spidlen, Josef; Moore, Wayne; Brinkman, Ryan R

2015-07-01

The lack of software interoperability with respect to gating has traditionally been a bottleneck preventing the use of multiple analytical tools and reproducibility of flow cytometry data analysis by independent parties. To address this issue, ISAC developed Gating-ML, a computer file format to encode and interchange gates. Gating-ML 1.5 was adopted and published as an ISAC Candidate Recommendation in 2008. Feedback during the probationary period from implementors, including major commercial software companies, instrument vendors, and the wider community, has led to a streamlined Gating-ML 2.0. Gating-ML has been significantly simplified and therefore easier to support by software tools. To aid developers, free, open source reference implementations, compliance tests, and detailed examples are provided to stimulate further commercial adoption. ISAC has approved Gating-ML as a standard ready for deployment in the public domain and encourages its support within the community as it is at a mature stage of development having undergone extensive review and testing, under both theoretical and practical conditions. © 2015 International Society for Advancement of Cytometry.

The AT-Hook motif as a versatile minor groove anchor for promoting DNA binding of transcription factor fragments? ?Electronic supplementary information (ESI) available: Peptide synthesis, full experimental procedures and analytical data of the peptides and products obtained. See DOI: 10.1039/c5sc01415h Click here for additional data file.

OpenAIRE

Rodr?guez, J?ssica; Mosquera, Jes?s; Couceiro, Jose R.; V?zquez, M. Eugenio; Mascare?as, Jos? L.

2015-01-01

We report the development of chimeric DNA binding peptides comprising a DNA binding fragment of natural transcription factors (the basic region of a bZIP protein or a monomeric zinc finger module) and an AT-Hook peptide motif. The resulting peptide conjugates display high DNA affinity and excellent sequence selectivity. Furthermore, the AT-Hook motif also favors the cell internalization of the conjugates.

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

The membrane tethered transcription factor EcbZIP17 from finger millet promotes plant growth and enhances tolerance to abiotic stresses.

Science.gov (United States)

Ramakrishna, Chopperla; Singh, Sonam; Raghavendrarao, Sangala; Padaria, Jasdeep C; Mohanty, Sasmita; Sharma, Tilak Raj; Solanke, Amolkumar U

2018-02-01

The occurrence of various stresses, as the outcome of global climate change, results in the yield losses of crop plants. Prospecting of genes in stress tolerant plant species may help to protect and improve their agronomic performance. Finger millet (Eleusine coracana L.) is a valuable source of superior genes and alleles for stress tolerance. In this study, we isolated a novel endoplasmic reticulum (ER) membrane tethered bZIP transcription factor from finger millet, EcbZIP17. Transgenic tobacco plants overexpressing this gene showed better vegetative growth and seed yield compared with wild type (WT) plants under optimal growth conditions and confirmed upregulation of brassinosteroid signalling genes. Under various abiotic stresses, such as 250 mM NaCl, 10% PEG6000, 400 mM mannitol, water withdrawal, and heat stress, the transgenic plants showed higher germination rate, biomass, primary and secondary root formation, and recovery rate, compared with WT plants. The transgenic plants exposed to an ER stress inducer resulted in greater leaf diameter and plant height as well as higher expression of the ER stress-responsive genes BiP, PDIL, and CRT1. Overall, our results indicated that EcbZIP17 improves plant growth at optimal conditions through brassinosteroid signalling and provide tolerance to various environmental stresses via ER signalling pathways.

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

Abscisic acid signaling is controlled by a BRANCHED1/HD-ZIP I cascade in Arabidopsis axillary buds.

Science.gov (United States)

González-Grandío, Eduardo; Pajoro, Alice; Franco-Zorrilla, José M; Tarancón, Carlos; Immink, Richard G H; Cubas, Pilar

2017-01-10

Shoot-branching patterns determine key aspects of plant life and are important targets for crop breeding. However, we are still largely ignorant of the genetic networks controlling locally the most important decision during branch development: whether the axillary bud, or branch primordium, grows out to give a lateral shoot or remains dormant. Here we show that, inside the buds, the TEOSINTE BRANCHED1, CYCLOIDEA, PCF (TCP) transcription factor BRANCHED1 (BRC1) binds to and positively regulates the transcription of three related Homeodomain leucine zipper protein (HD-ZIP)-encoding genes: HOMEOBOX PROTEIN 21 (HB21), HOMEOBOX PROTEIN 40 (HB40), and HOMEOBOX PROTEIN 53 (HB53). These three genes, together with BRC1, enhance 9-CIS-EPOXICAROTENOID DIOXIGENASE 3 (NCED3) expression, lead to abscisic acid accumulation, and trigger hormone response, thus causing suppression of bud development. This TCP/HD-ZIP genetic module seems to be conserved in dicot and monocotyledonous species to prevent branching under light-limiting conditions.

Protection of hematopoietic cells from O(6)-alkylation damage by O(6)-methylguanine DNA methyltransferase gene transfer: studies with different O(6)-alkylating agents and retroviral backbones.

Science.gov (United States)

Jansen, M; Bardenheuer, W; Sorg, U R; Seeber, S; Flasshove, M; Moritz, T

2001-07-01

Overexpression of O(6)-methylguanine DNA methyltransferase (MGMT) can protect hematopoietic cells from O(6)-alkylation damage. To identify possible clinical applications of this technology we compared the effect of MGMT gene transfer on the hematotoxicity induced by different O(6)-alkylating agents in clinical use: the chloroethylnitrosoureas ACNU, BCNU, CCNU and the tetrazine derivative temozolomide. In addition, various retroviral vectors expressing the MGMT-cDNA were investigated to identify optimal viral backbones for hematoprotection by MGMT expression. Protection from ACNU, BCNU, CCNU or temozolomide toxicity was evaluated utilizing a Moloney murine leukemia virus-based retroviral vector (N2/Zip-PGK-MGMT) to transduce primary murine bone marrow cells. Increased resistance in murine colony-forming units (CFU) was demonstrated for all four drugs. In comparison to mock-transduced controls, after transduction with N2/Zip-PGK-MGMT the IC50 for CFU increased on average 4.7-fold for ACNU, 2.5-fold for BCNU, 6.3-fold for CCNU and 1.5-fold for temozolomide. To study the effect of the retroviral backbone on hematoprotection various vectors expressing the human MGMT-cDNA from a murine embryonic sarcoma virus LTR (MSCV-MGMT) or a hybrid spleen focus-forming/murine embryonic sarcoma virus LTR (SF1-MGMT) were compared with the N2/Zip-PGK-MGMT vector. While all vectors increased resistance of transduced human CFU to ACNU, the SF1-MGMT construct was most efficient especially at high ACNU concentrations (8-12 microg/ml). Similar results were obtained for protection of murine high-proliferative-potential colony-forming cells. These data may help to optimize treatment design and retroviral constructs in future clinical studies aiming at hematoprotection by MGMT gene transfer.

Gate current for p+-poly PMOS devices under gate injection conditions

NARCIS (Netherlands)

Hof, A.J.; Holleman, J.; Woerlee, P.H.

2001-01-01

In current CMOS processing both n+-poly and p+-poly gates are used. The I-V –relationship and reliability of n+-poly devices are widely studied and well understood. Gate currents and reliability for p+-poly PMOS devices under gate injection conditions are not well understood. In this paper, the

Multiple Independent Gate FETs: How Many Gates Do We Need?

OpenAIRE

Amarù, Luca; Hills, Gage; Gaillardon, Pierre-Emmanuel; Mitra, Subhasish; De Micheli, Giovanni

2015-01-01

Multiple Independent Gate Field Effect Transistors (MIGFETs) are expected to push FET technology further into the semiconductor roadmap. In a MIGFET, supplementary gates either provide (i) enhanced conduction properties or (ii) more intelligent switching functions. In general, each additional gate also introduces a side implementation cost. To enable more efficient digital systems, MIGFETs must leverage their expressive power to realize complex logic circuits with few physical resources. Rese...

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 < 1 to 203 Ma gaps between the U-Pb and ZFT ages. Magmatic growth zonation and Zr/Hf ratios (0.01-0.02) suggest alkaline magmatic sources, while Ti—in—zircon thermometry suggests that most zircons crystallized within ranges between 550 and 830 °C. Chondrite-normalised multi-element plots show variable enrichment patterns, mostly without marked Eu depletion, indicating little plagioclase fractionation in source melts. Key elements and ratios matched against zircons from magmatic rocks suggest a range of ultramafic to felsic source melts. Zircon O-isotope ratios (δ18O in the range 4 to 11‰) and initial Hf isotope ratios (ɛHf in the range +2 to +14) encompass ranges for both mantle and crustal melts. Calculated Depleted Mantle (TDM 0.03-0.56 Ga) and Crustal Residence (0.20-1.02 Ga) model ages suggest several mantle events, continental break-ups (Rodinia and Gondwana) and convergent margin collisions left imprints in the zircon source melts. East Australian ZIP sites reflect prolonged intraplate magmatism (~85 Ma), often during times of fast-migrating lithosphere. In contrast, East Asian-Russian ZIP sites reflect later basaltic magmatism (<40 Ma), often linked to episodes of back-arc rifting and spreading, slow-migrating lithosphere and slab subduction.

Transparently wrap-gated semiconductor nanowire arrays for studies of gate-controlled photoluminescence

Energy Technology Data Exchange (ETDEWEB)

Nylund, Gustav; Storm, Kristian; Torstensson, Henrik; Wallentin, Jesper; Borgström, Magnus T.; Hessman, Dan; Samuelson, Lars [Solid State Physics, Nanometer Structure Consortium, Lund University, Box 118, S-221 00 Lund (Sweden)

2013-12-04

We present a technique to measure gate-controlled photoluminescence (PL) on arrays of semiconductor nanowire (NW) capacitors using a transparent film of Indium-Tin-Oxide (ITO) wrapping around the nanowires as the gate electrode. By tuning the wrap-gate voltage, it is possible to increase the PL peak intensity of an array of undoped InP NWs by more than an order of magnitude. The fine structure of the PL spectrum reveals three subpeaks whose relative peak intensities change with gate voltage. We interpret this as gate-controlled state-filling of luminescing quantum dot segments formed by zincblende stacking faults in the mainly wurtzite NW crystal structure.

Direct protein detection with a nano-interdigitated array gate MOSFET.

Science.gov (United States)

Tang, Xiaohui; Jonas, Alain M; Nysten, Bernard; Demoustier-Champagne, Sophie; Blondeau, Franoise; Prévot, Pierre-Paul; Pampin, Rémi; Godfroid, Edmond; Iñiguez, Benjamin; Colinge, Jean-Pierre; Raskin, Jean-Pierre; Flandre, Denis; Bayot, Vincent

2009-08-15

A new protein sensor is demonstrated by replacing the gate of a metal oxide semiconductor field effect transistor (MOSFET) with a nano-interdigitated array (nIDA). The sensor is able to detect the binding reaction of a typical antibody Ixodes ricinus immunosuppressor (anti-Iris) protein at a concentration lower than 1 ng/ml. The sensor exhibits a high selectivity and reproducible specific detection. We provide a simple model that describes the behavior of the sensor and explains the origin of its high sensitivity. The simulated and experimental results indicate that the drain current of nIDA-gate MOSFET sensor is significantly increased with the successive binding of the thiol layer, Iris and anti-Iris protein layers. It is found that the sensor detection limit can be improved by well optimizing the geometrical parameters of nIDA-gate MOSFET. This nanobiosensor, with real-time and label-free capabilities, can easily be used for the detection of other proteins, DNA, virus and cancer markers. Moreover, an on-chip associated electronics nearby the sensor can be integrated since its fabrication is compatible with complementary metal oxide semiconductor (CMOS) technology.

Dual-Gate p-GaN Gate High Electron Mobility Transistors for Steep Subthreshold Slope.

Science.gov (United States)

Bae, Jong-Ho; Lee, Jong-Ho

2016-05-01

A steep subthreshold slope characteristic is achieved through p-GaN gate HEMT with dual-gate structure. Obtained subthreshold slope is less than 120 μV/dec. Based on the measured and simulated data obtained from single-gate device, breakdown of parasitic floating-base bipolar transistor and floating gate charged with holes are responsible to increase abruptly in drain current. In the dual-gate device, on-current degrades with high temperature but subthreshold slope is not changed. To observe the switching speed of dual-gate device and transient response of drain current are measured. According to the transient responses of drain current, switching speed of the dual-gate device is about 10(-5) sec.

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...

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.

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.

Analytical drain current formulation for gate dielectric engineered dual material gate-gate all around-tunneling field effect transistor

Science.gov (United States)

Madan, Jaya; Gupta, R. S.; Chaujar, Rishu

2015-09-01

In this work, an analytical drain current model for gate dielectric engineered (hetero dielectric)-dual material gate-gate all around tunnel field effect transistor (HD-DMG-GAA-TFET) has been developed. Parabolic approximation has been used to solve the two-dimensional (2D) Poisson equation with appropriate boundary conditions and continuity equations to evaluate analytical expressions for surface potential, electric field, tunneling barrier width and drain current. Further, the analog performance of the device is studied for three high-k dielectrics (Si3N4, HfO2, and ZrO2), and it has been investigated that the problem of lower ION, can be overcome by using the hetero-gate architecture. Moreover, the impact of scaling the gate oxide thickness and bias variations has also been studied. The HD-DMG-GAA-TFET shows an enhanced ION of the order of 10-4 A. The effectiveness of the proposed model is validated by comparing it with ATLAS device simulations.

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 ...

Respiratory gating in positron emission tomography: A quantitative comparison of different gating schemes

International Nuclear Information System (INIS)

Dawood, Mohammad; Buether, Florian; Lang, Norbert; Schober, Otmar; Schaefers, Klaus P

2007-01-01

Respiratory gating is used for reducing the effects of breathing motion in a wide range of applications from radiotherapy treatment to diagnostical imaging. Different methods are feasible for respiratory gating. In this study seven gating methods were developed and tested on positron emission tomography (PET) listmode data. The results of seven patient studies were compared quantitatively with respect to motion and noise. (1) Equal and (2) variable time-based gating methods use only the time information of the breathing cycle to define respiratory gates. (3) Equal and (4) variable amplitude-based gating approaches utilize the amplitude of the respiratory signal. (5) Cycle-based amplitude gating is a combination of time and amplitude-based techniques. A baseline correction was applied to methods (3) and (4) resulting in two new approaches: Baseline corrected (6) equal and (7) variable amplitude-based gating. Listmode PET data from seven patients were acquired together with a respiratory signal. Images were reconstructed applying the seven gating methods. Two parameters were used to quantify the results: Motion was measured as the displacement of the heart due to respiration and noise was defined as the standard deviation of pixel intensities in a background region. The amplitude-based approaches (3) and (4) were superior to the time-based methods (1) and (2). The improvement in capturing the motion was more than 30% (up to 130%) in all subjects. The variable time (2) and amplitude (4) methods had a more uniform noise distribution among all respiratory gates compared to equal time (1) and amplitude (3) methods. Baseline correction did not improve the results. Out of seven different respiratory gating approaches, the variable amplitude method (4) captures the respiratory motion best while keeping a constant noise level among all respiratory phases

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

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.

Effect of copy number and spacing of the ACGT and GT cis elements ...

Indian Academy of Sciences (India)

Unknown

cognized by transcription factors of the bZIP family. The core ACGT element occurs at different relative positions in one or more copies upstream of the minimal promoter region. Protein-DNA interaction studies have shown that sequences flanking the ACGT core affect bZIP protein binding specificity. The bZIP transcription ...

Function of the HD-Zip I gene Oshox22 in ABA-mediated drought and salt tolerances in rice

NARCIS (Netherlands)

Zhang, S.; Kohlen, W.; Jiang, L.; Bouwmeester, H.J.; Meijer, A.H.; Schluepmann, H.; Liu, C.M.; Ouwerkerk, P.B.F.

2012-01-01

Oshox22 belongs to the homeodomain-leucine zipper (HD-Zip) family I of transcription factors, most of which have unknown functions. Here we show that the expression of Oshox22 is strongly induced by salt stress, abscisic acid (ABA), and polyethylene glycol treatment (PEG), and weakly by cold stress.

A highly sensitive protocol for the determination of Hg(2+) in environmental water using time-gated mode.

Science.gov (United States)

Huang, Dawei; Niu, Chenggang; Zeng, Guangming; Wang, Xiaoyu; Lv, Xiaoxiao

2015-01-01

In this paper, a sensitive time-gated fluorescent sensing strategy for mercury ions (Hg(2+)) monitoring is developed based on Hg(2+)-mediated thymine (T)-Hg(2+)-T structure and the mechanism of fluorescence resonance energy transfer from Mn-doped CdS/ZnS quantum dots to graphene oxide. The authors employ two T-rich single-stranded DNA (ssDNA) as the capture probes for Hg(2+), and one of them is modified with Mn-doped CdS/ZnS quantum dots. The addition of Hg(2+) makes the two T-rich ssDNA hybrids with each other to form stable T-Hg(2+)-T coordination chemistry, which makes Mn-doped CdS/ZnS quantum dots far away from the surface of graphene oxide. As a result, the fluorescence signal is increased obviously compared with that without Hg(2+). The time-gated fluorescence intensities are linear with the concentrations of Hg(2+) in the range from 0.20 to 10 nM with a limit of detection of 0.11 nM. The detection limit is much lower than the U.S. Environmental Protection Agency limit of the concentration of Hg(2+) for drinking water. The time-gated fluorescent sensing strategy is specific for Hg(2+) even with interference by other metal ions based on the results of selectivity experiments. Importantly, the proposed sensing strategy is applied successfully to the determination of Hg(2+) in environmental water samples. Copyright © 2014 Elsevier B.V. All rights reserved.

Ultrafast spectroscopy on DNA-cleavage by endonuclease in molecular crowding.

Science.gov (United States)

Singh, Priya; Choudhury, Susobhan; Dutta, Shreyasi; Adhikari, Aniruddha; Bhattacharya, Siddhartha; Pal, Debasish; Pal, Samir Kumar

2017-10-01

The jam-packed intracellular environments differ the activity of a biological macromolecule from that in laboratory environments (in vitro) through a number of mechanisms called molecular crowding related to structure, function and dynamics of the macromolecule. Here, we have explored the structure, function and dynamics of a model enzyme protein DNase I in molecular crowing of polyethylene glycol (PEG; MW 3350). We have used steady state and picosecond resolved dynamics of a well-known intercalator ethidium bromide (EB) in a 20-mer double-stranded DNA (dsDNA) to monitor the DNA-cleavage by the enzyme in absence and presence PEG. We have also labelled the enzyme by a well-known fluorescent probe 8-anilino-1-naphthalenesulfonic acid ammonium salt (ANS) to study the molecular mechanism of the protein-DNA association through exited state relaxation of the probe in absence (dictated by polarity) and presence of EB in the DNA (dictated by Förster resonance energy transfer (FRET)). The overall and local structures of the protein in presence of PEG have been followed by circular dichroism and time resolved polarization gated spectroscopy respectively. The enhanced dynamical flexibility of protein in presence of PEG as revealed from excited state lifetime and polarization gated anisotropy of ANS has been correlated with the stronger DNA-binding for the higher nuclease activity. We have also used conventional experimental strategy of agarose gel electrophoresis to monitor DNA-cleavage and found consistent results of enhanced nuclease activities both on synthetic 20-mer oligonucleotide and long genomic DNA from calf thymus. Copyright © 2017 Elsevier B.V. All rights reserved.

ZIP MK 2 : A Fortran code for calculating the eigenvalues (poles and zeros and frequency responses of large sets of linear equations representing complex dynamic systems)

International Nuclear Information System (INIS)

Sumner, H.M.

1969-03-01

The KDF9/EGDON program ZIP MK 2 is the third of a series of programs for off-line digital computer analysis of dynamic systems: it has been designed specifically to cater for the needs of the design or control engineer in having an input scheme which is minimally computer-oriented. It uses numerical algorithms which are as near fool-proof as the author could discover or devise, and has comprehensive diagnostic sections to help the user in the event of faulty data or machine execution. ZIP MK 2 accepts mathematical models comprising first order linear differential and linear algebraic equations, and from these computes and factorises the transfer functions between specified pairs of output and input variables; if desired, the frequency response may be computed from the computed transfer function. The model input scheme is fully compatible with the frequency response programs FRP MK 1 and MK 2, except that, for ZIP MK 2, transport, or time-delays must be converted by the user to Pade or Bode approximations prior to input. ZIP provides the pole-zero plot, (or complex plane analysis), while FRP provides the frequency response and FIFI the time domain analyses. The pole-zero method of analysis has been little used in the past for complex models, especially where transport delays occur, and one of its primary purposes is as a research tool to investigate the usefulness of this method, for process plant, whether nuclear, chemical or other continuous processes. (author)

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.

Food consumption - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available c00954-01-011 Description of data contents The list regarding results of food consumption measurement acquir...ed from rats used in the in vivo tests. Data file File name: open_tggates_food_consumption.zip File URL: ftp...://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/open_tggates_food_consumption....zip File size: 108 KB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/open_tggates_food_consum...ption#en Data acquisition method The amount of daily food intake of the first day is calculated as the amount of food

A universal molecular translator for non-nucleic acid targets that enables dynamic DNA assemblies and logic operations.

Science.gov (United States)

Tang, Wei; Hu, Shichao; Wang, Huaming; Zhao, Yan; Li, Na; Liu, Feng

2014-11-28

A universal molecular translator based on the target-triggered DNA strand displacement was developed, which was able to convert various kinds of non-nucleic acid targets into a unique output DNA. This translation strategy was successfully applied in directing dynamic DNA assemblies and in realizing three-input logic gate operations.

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

Cdc45 (cell division cycle protein 45) guards the gate of the Eukaryote Replisome helicase stabilizing leading strand engagement

Science.gov (United States)

Petojevic, Tatjana; Pesavento, James J.; Costa, Alessandro; Liang, Jingdan; Wang, Zhijun; Berger, James M.; Botchan, Michael R.

2015-01-01

DNA replication licensing is now understood to be the pathway that leads to the assembly of double hexamers of minichromosome maintenance (Mcm2–7) at origin sites. Cell division control protein 45 (Cdc45) and GINS proteins activate the latent Mcm2–7 helicase by inducing allosteric changes through binding, forming a Cdc45/Mcm2-7/GINS (CMG) complex that is competent to unwind duplex DNA. The CMG has an active gate between subunits Mcm2 and Mcm5 that opens and closes in response to nucleotide binding. The consequences of inappropriate Mcm2/5 gate actuation and the role of a side channel formed between GINS/Cdc45 and the outer edge of the Mcm2–7 ring for unwinding have remained unexplored. Here we uncover a novel function for Cdc45. Cross-linking studies trace the path of the DNA with the CMG complex at a fork junction between duplex and single strands with the bound CMG in an open or closed gate conformation. In the closed state, the lagging strand does not pass through the side channel, but in the open state, the leading strand surprisingly interacts with Cdc45. Mutations in the recombination protein J fold of Cdc45 that ablate this interaction diminish helicase activity. These data indicate that Cdc45 serves as a shield to guard against occasional slippage of the leading strand from the core channel. PMID:25561522

OsLOL1, a C2C2-type zinc finger protein, interacts with OsbZIP58 to promote seed germination through the modulation of gibberellin biosynthesis in Oryza sativa.

Science.gov (United States)

Wu, Jiahe; Zhu, Chuanfeng; Pang, Jinhuan; Zhang, Xiangrong; Yang, Chunlin; Xia, Guixian; Tian, Yingchuan; He, Chaozu

2014-12-01

Seed germination is a key developmental process in the plant life cycle that is influenced by various environmental cues and phytohormones through gene expression and a series of metabolism pathways. In the present study, we investigated a C2C2-type finger protein, OsLOL1, which promotes gibberellin (GA) biosynthesis and affects seed germination in Oryza sativa (rice). We used OsLOL1 antisense and sense transgenic lines to explore OsLOL1 functions. Seed germination timing in antisense plants was restored to wild type when exogenous GA3 was applied. The reduced expression of the GA biosynthesis gene OsKO2 and the accumulation of ent-kaurene were observed during germination in antisense plants. Based on yeast two-hybrid and firefly luciferase complementation analyses, OsLOL1 interacted with the basic leucine zipper protein OsbZIP58. The results from electrophoretic mobility shift and dual-luciferase reporter assays showed that OsbZIP58 binds the G-box cis-element of the OsKO2 promoter and activates LUC reporter gene expression, and that interaction between OsLOL1 and OsbZIP58 activates OsKO2 gene expression. In addition, OsLOL1 decreased SOD1 gene expression and accelerated programmed cell death (PCD) in the aleurone layer of rice grains. These findings demonstrate that the interaction between OsLOL1 and OsbZIP58 influences GA biosynthesis through the activation of OsKO2 via OsbZIP58, thereby stimulating aleurone PCD and seed germination. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

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

KAUST Repository

Nagashima, Yukihiro; Mishiba, Kei-ichiro; Suzuki, Eiji; Shimada, Yukihisa; Iwata, Yuji; Koizumi, Nozomu

2011-01-01

-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

Electrochemical single-molecule conductivity of duplex and quadruplex DNA

DEFF Research Database (Denmark)

Zhang, Ling; Zhang, Jingdong; Ulstrup, Jens

2017-01-01

Photoinduced and electrochemical charge transport in DNA (oligonucleotides, OGNs) and the notions “hopping”, superexchange, polaron, and vibrationally gated charge transport have been in focus over more than two decades. In recent years mapping of electrochemical charge transport of pure and redo...

PISMA: A Visual Representation of Motif Distribution in DNA Sequences

Directory of Open Access Journals (Sweden)

Rogelio Alcántara-Silva

2017-03-01

Full Text Available Background: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code–like, as a gene-map–like, and as a transcript scheme. Results: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. Availability and Implementation: PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas.unam.mx/wp-content/software/pisma.zip and www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf .

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.

Novel Quantum Dot Gate FETs and Nonvolatile Memories Using Lattice-Matched II-VI Gate Insulators

Science.gov (United States)

Jain, F. C.; Suarez, E.; Gogna, M.; Alamoody, F.; Butkiewicus, D.; Hohner, R.; Liaskas, T.; Karmakar, S.; Chan, P.-Y.; Miller, B.; Chandy, J.; Heller, E.

2009-08-01

This paper presents the successful use of ZnS/ZnMgS and other II-VI layers (lattice-matched or pseudomorphic) as high- k gate dielectrics in the fabrication of quantum dot (QD) gate Si field-effect transistors (FETs) and nonvolatile memory structures. Quantum dot gate FETs and nonvolatile memories have been fabricated in two basic configurations: (1) monodispersed cladded Ge nanocrystals (e.g., GeO x -cladded-Ge quantum dots) site-specifically self-assembled over the lattice-matched ZnMgS gate insulator in the channel region, and (2) ZnTe-ZnMgTe quantum dots formed by self-organization, using metalorganic chemical vapor-phase deposition (MOCVD), on ZnS-ZnMgS gate insulator layers grown epitaxially on Si substrates. Self-assembled GeO x -cladded Ge QD gate FETs, exhibiting three-state behavior, are also described. Preliminary results on InGaAs-on-InP FETs, using ZnMgSeTe/ZnSe gate insulator layers, are presented.

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

Easy design of colorimetric logic gates based on nonnatural base pairing and controlled assembly of gold nanoparticles.

Science.gov (United States)

Zhang, Li; Wang, Zhong-Xia; Liang, Ru-Ping; Qiu, Jian-Ding

2013-07-16

Utilizing the principles of metal-ion-mediated base pairs (C-Ag-C and T-Hg-T), the pH-sensitive conformational transition of C-rich DNA strand, and the ligand-exchange process triggered by DL-dithiothreitol (DTT), a system of colorimetric logic gates (YES, AND, INHIBIT, and XOR) can be rationally constructed based on the aggregation of the DNA-modified Au NPs. The proposed logic operation system is simple, which consists of only T-/C-rich DNA-modified Au NPs, and it is unnecessary to exquisitely design and alter the DNA sequence for different multiple molecular logic operations. The nonnatural base pairing combined with unique optical properties of Au NPs promises great potential in multiplexed ion sensing, molecular-scale computers, and other computational logic devices.

Optical XOR gate

Science.gov (United States)

Vawter, G. Allen

2013-11-12

An optical XOR gate is formed as a photonic integrated circuit (PIC) from two sets of optical waveguide devices on a substrate, with each set of the optical waveguide devices including an electroabsorption modulator electrically connected in series with a waveguide photodetector. The optical XOR gate utilizes two digital optical inputs to generate an XOR function digital optical output. The optical XOR gate can be formed from III-V compound semiconductor layers which are epitaxially deposited on a III-V compound semiconductor substrate, and operates at a wavelength in the range of 0.8-2.0 .mu.m.

Intrinsic respiratory gating in small-animal CT

International Nuclear Information System (INIS)

Bartling, Soenke H.; Dinkel, Julien; Kauczor, Hans-Ulrich; Stiller, Wolfram; Semmler, Wolfhard; Grasruck, Michael; Madisch, Ijad; Gupta, Rajiv; Kiessling, Fabian

2008-01-01

Gating in small-animal CT imaging can compensate artefacts caused by physiological motion during scanning. However, all published gating approaches for small animals rely on additional hardware to derive the gating signals. In contrast, in this study a novel method of intrinsic respiratory gating of rodents was developed and tested for mice (n=5), rats (n=5) and rabbits (n=2) in a flat-panel cone-beam CT system. In a consensus read image quality was compared with that of non-gated and retrospective extrinsically gated scans performed using a pneumatic cushion. In comparison to non-gated images, image quality improved significantly using intrinsic and extrinsic gating. Delineation of diaphragm and lung structure improved in all animals. Image quality of intrinsically gated CT was judged to be equivalent to extrinsically gated ones. Additionally 4D datasets were calculated using both gating methods. Values for expiratory, inspiratory and tidal lung volumes determined with the two gating methods were comparable and correlated well with values known from the literature. We could show that intrinsic respiratory gating in rodents makes additional gating hardware and preparatory efforts superfluous. This method improves image quality and allows derivation of functional data. Therefore it bears the potential to find wide applications in small-animal CT imaging. (orig.)

Signatures of Mechanosensitive Gating.

Science.gov (United States)

Morris, Richard G

2017-01-10

The question of how mechanically gated membrane channels open and close is notoriously difficult to address, especially if the protein structure is not available. This perspective highlights the relevance of micropipette-aspirated single-particle tracking-used to obtain a channel's diffusion coefficient, D, as a function of applied membrane tension, σ-as an indirect assay for determining functional behavior in mechanosensitive channels. While ensuring that the protein remains integral to the membrane, such methods can be used to identify not only the gating mechanism of a protein, but also associated physical moduli, such as torsional and dilational rigidity, which correspond to the protein's effective shape change. As an example, three distinct D-versus-σ "signatures" are calculated, corresponding to gating by dilation, gating by tilt, and gating by a combination of both dilation and tilt. Both advantages and disadvantages of the approach are discussed. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Quantum gate decomposition algorithms.

Energy Technology Data Exchange (ETDEWEB)

Slepoy, Alexander

2006-07-01

Quantum computing algorithms can be conveniently expressed in a format of a quantum logical circuits. Such circuits consist of sequential coupled operations, termed ''quantum gates'', or quantum analogs of bits called qubits. We review a recently proposed method [1] for constructing general ''quantum gates'' operating on an qubits, as composed of a sequence of generic elementary ''gates''.

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.

5'-end sequences of budding yeast full-length cDNA clones and quality scores - Budding yeast cDNA sequencing project | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available east_seq_qual.zip File URL: ftp://ftp.biosciencedbc.jp/archive/yeast_cdna/LATEST/...yeast_seq_qual.zip File size: 59.9MB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/budding_yeast_cdna

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

Compound list: transforming growth factor beta 1 [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available transforming growth factor beta 1 TGFB1 00182 ftp://ftp.biosciencedbc.jp/archive/op...en-tggates/LATEST/Human/in_vitro/transforming_growth_factor_beta_1.Human.in_vitro.Liver.zip ...

Low band-to-band tunnelling and gate tunnelling current in novel nanoscale double-gate architecture: simulations and investigation

International Nuclear Information System (INIS)

Datta, Deepanjan; Ganguly, Samiran; Dasgupta, S

2007-01-01

Large band-to-band tunnelling (BTBT) and gate leakage current can limit scalability of nanoscale devices. In this paper, we have proposed a novel nanoscale parallel connected heteromaterial double gate (PCHEM-DG) architecture with triple metal gate which significantly suppress BTBT leakage, making it efficient for low power design in the sub-10 nm regime. We have also proposed a triple gate device with p + poly-n + poly-p + poly gate which has substantially low gate leakage over symmetric DG MOSFET. Simulations are performed using a 2D Poisson-Schroedinger simulator and verified with a 2D device simulator ATLAS. We conclude that, due to intrinsic body doping, negligible gate leakage, suppressed BTBT over symmetric DG devices, metal gate (MG) PCHEM-DG MOSFET is efficient for low power circuit design in the nanometre regime

Visualization of neonatal coronary arteries on multidetector row CT: ECG-gated versus non-ECG-gated technique

International Nuclear Information System (INIS)

Tsai, I.C.; Lee, Tain; Chen, Min-Chi; Fu, Yun-Ching; Jan, Sheng-Lin; Wang, Chung-Chi; Chang, Yen

2007-01-01

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.)

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.

Low band-to-band tunnelling and gate tunnelling current in novel nanoscale double-gate architecture: simulations and investigation

Energy Technology Data Exchange (ETDEWEB)

Datta, Deepanjan [Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47906 (United States); Ganguly, Samiran [Department of Electronics Engineering, Indian School of Mines, Dhanbad-826004 (India); Dasgupta, S [Department of Electronics and Computer Engineering, Indian Institute of Technology, Roorkee-247667 (India)

2007-05-30

Large band-to-band tunnelling (BTBT) and gate leakage current can limit scalability of nanoscale devices. In this paper, we have proposed a novel nanoscale parallel connected heteromaterial double gate (PCHEM-DG) architecture with triple metal gate which significantly suppress BTBT leakage, making it efficient for low power design in the sub-10 nm regime. We have also proposed a triple gate device with p{sup +} poly-n{sup +} poly-p{sup +} poly gate which has substantially low gate leakage over symmetric DG MOSFET. Simulations are performed using a 2D Poisson-Schroedinger simulator and verified with a 2D device simulator ATLAS. We conclude that, due to intrinsic body doping, negligible gate leakage, suppressed BTBT over symmetric DG devices, metal gate (MG) PCHEM-DG MOSFET is efficient for low power circuit design in the nanometre regime.

Solution-gated graphene transistors for chemical and biological sensors.

Science.gov (United States)

Yan, Feng; Zhang, Meng; Li, Jinhua

2014-03-01

Graphene has attracted much attention in biomedical applications for its fascinating properties. Because of the well-known 2D structure, every atom of graphene is exposed to the environment, so the electronic properties of graphene are very sensitive to charged analytes (ions, DNA, cells, etc.) or an electric field around it, which renders graphene an ideal material for high-performance sensors. Solution-gated graphene transistors (SGGTs) can operate in electrolytes and are thus excellent candidates for chemical and biological sensors, which have been extensively studied in the recent 5 years. Here, the device physics, the sensing mechanisms, and the performance of the recently developed SGGT-based chemical and biological sensors, including pH, ion, cell, bacterial, DNA, protein, glucose sensors, etc., are introduced. Their advantages and shortcomings, in comparison with some conventional techniques, are discussed. Conclusions and challenges for the future development of the field are addressed in the end. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sliding-gate valve for use with abrasive materials

Science.gov (United States)

Ayers, Jr., William J.; Carter, Charles R.; Griffith, Richard A.; Loomis, Richard B.; Notestein, John E.

1985-01-01

The invention is a flow and pressure-sealing valve for use with abrasive solids. The valve embodies special features which provide for long, reliable operating lifetimes in solids-handling service. The valve includes upper and lower transversely slidable gates, contained in separate chambers. The upper gate provides a solids-flow control function, whereas the lower gate provides a pressure-sealing function. The lower gate is supported by means for (a) lifting that gate into sealing engagement with its seat when the gate is in its open and closed positions and (b) lowering the gate out of contact with its seat to permit abrasion-free transit of the gate between its open and closed positions. When closed, the upper gate isolates the lower gate from the solids. Because of this shielding action, the sealing surface of the lower gate is not exposed to solids during transit or when it is being lifted or lowered. The chamber containing the lower gate normally is pressurized slightly, and a sweep gas is directed inwardly across the lower-gate sealing surface during the vertical translation of the gate.

Photon-gated spin transistor

OpenAIRE

Li, Fan; Song, Cheng; Cui, Bin; Peng, Jingjing; Gu, Youdi; Wang, Guangyue; Pan, Feng

2017-01-01

Spin-polarized field-effect transistor (spin-FET), where a dielectric layer is generally employed for the electrical gating as the traditional FET, stands out as a seminal spintronic device under the miniaturization trend of electronics. It would be fundamentally transformative if optical gating was used for spin-FET. We report a new type of spin-polarized field-effect transistor (spin-FET) with optical gating, which is fabricated by partial exposure of the (La,Sr)MnO3 channel to light-emitti...

On photonic controlled phase gates

International Nuclear Information System (INIS)

Kieling, K; Eisert, J; O'Brien, J L

2010-01-01

As primitives for entanglement generation, controlled phase gates have a central role in quantum computing. Especially in ideas realizing instances of quantum computation in linear optical gate arrays, a closer look can be rewarding. In such architectures, all effective nonlinearities are induced by measurements. Hence the probability of success is a crucial parameter of such quantum gates. In this paper, we discuss this question for controlled phase gates that implement an arbitrary phase with one and two control qubits. Within the class of post-selected gates in dual-rail encoding with vacuum ancillas, we identify the optimal success probabilities. We construct networks that allow for implementation using current experimental capabilities in detail. The methods employed here appear specifically useful with the advent of integrated linear optical circuits, providing stable interferometers on monolithic structures.

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

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.

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…

Intra-Amygdala ZIP Injections Impair the Memory of Learned Active Avoidance Responses and Attenuate Conditioned Taste-Aversion Acquisition in Rats

Science.gov (United States)

Gamiz, Fernando; Gallo, Milagros

2011-01-01

We have investigated the effect of protein kinase Mzeta (PKM[zeta]) inhibition in the basolateral amygdala (BLA) upon the retention of a nonspatial learned active avoidance response and conditioned taste-aversion (CTA) acquisition in rats. ZIP (10 nmol/[mu]L) injected into the BLA 24 h after training impaired retention of a learned…

Benchmarking gate-based quantum computers

Science.gov (United States)

Michielsen, Kristel; Nocon, Madita; Willsch, Dennis; Jin, Fengping; Lippert, Thomas; De Raedt, Hans

2017-11-01

With the advent of public access to small gate-based quantum processors, it becomes necessary to develop a benchmarking methodology such that independent researchers can validate the operation of these processors. We explore the usefulness of a number of simple quantum circuits as benchmarks for gate-based quantum computing devices and show that circuits performing identity operations are very simple, scalable and sensitive to gate errors and are therefore very well suited for this task. We illustrate the procedure by presenting benchmark results for the IBM Quantum Experience, a cloud-based platform for gate-based quantum computing.

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..

Effect of top gate potential on bias-stress for dual gate amorphous indium-gallium-zinc-oxide thin film transistor

Energy Technology Data Exchange (ETDEWEB)

Chun, Minkyu; Um, Jae Gwang; Park, Min Sang; Chowdhury, Md Delwar Hossain; Jang, Jin, E-mail: jjang@khu.ac.kr [Advanced Display Research Center and Department of Information Display, Kyung Hee University, Seoul 02447 (Korea, Republic of)

2016-07-15

We report the abnormal behavior of the threshold voltage (V{sub TH}) shift under positive bias Temperature stress (PBTS) and negative bias temperature stress (NBTS) at top/bottom gate in dual gate amorphous indium-gallium-zinc-oxide (a-IGZO) thin-film transistors (TFTs). It is found that the PBTS at top gate shows negative transfer shift and NBTS shows positive transfer shift for both top and bottom gate sweep. The shift of bottom/top gate sweep is dominated by top gate bias (V{sub TG}), while bottom gate bias (V{sub BG}) is less effect than V{sub TG}. The X-ray photoelectron spectroscopy (XPS) depth profile provides the evidence of In metal diffusion to the top SiO{sub 2}/a-IGZO and also the existence of large amount of In{sup +} under positive top gate bias around top interfaces, thus negative transfer shift is observed. On the other hand, the formation of OH{sup −} at top interfaces under the stress of negative top gate bias shows negative transfer shift. The domination of V{sub TG} both on bottom/top gate sweep after PBTS/NBTS is obviously occurred due to thin active layer.

CMOS gate array characterization procedures

Science.gov (United States)

Spratt, James P.

1993-09-01

Present procedures are inadequate for characterizing the radiation hardness of gate array product lines prior to personalization because the selection of circuits to be used, from among all those available in the manufacturer's circuit library, is usually uncontrolled. (Some circuits are fundamentally more radiation resistant than others.) In such cases, differences in hardness can result between different designs of the same logic function. Hardness also varies because many gate arrays feature large custom-designed megacells (e.g., microprocessors and random access memories-MicroP's and RAM's). As a result, different product lines cannot be compared equally. A characterization strategy is needed, along with standardized test vehicle(s), methodology, and conditions, so that users can make informed judgments on which gate arrays are best suited for their needs. The program described developed preferred procedures for the radiation characterization of gate arrays, including a gate array evaluation test vehicle, featuring a canary circuit, designed to define the speed versus hardness envelope of the gate array. A multiplier was chosen for this role, and a baseline multiplier architecture is suggested that could be incorporated into an existing standard evaluation circuit chip.

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

Dual-gated cardiac PET-clinical feasibility study

Energy Technology Data Exchange (ETDEWEB)

Teraes, Mika; Kokki, Tommi; Noponen, Tommi; Hoppela, Erika; Sipilae, Hannu T.; Knuuti, Juhani [Turku PET Centre, PO BOX 52, Turku (Finland); Durand-Schaefer, Nicolas [General Electric Medical Systems, Buc (France); Pietilae, Mikko [Turku University Hospital, Department of Internal Medicine, Turku (Finland); Kiss, Jan [Turku University Hospital, Department of Surgery, Turku (Finland)

2010-03-15

Both respiratory and cardiac motions reduce image quality in myocardial imaging. For accurate imaging of small structures such as vulnerable coronary plaques, simultaneous cardiac and respiratory gating is warranted. This study tests the feasibility of a recently developed robust method for cardiac-respiratory gating. List-mode data with triggers from respiratory and cardiac cycles are rearranged into dual-gated segments and reconstructed with standard algorithms of a commercial PET/CT scanner. Cardiac gates were defined as three fixed phases and one variable diastolic phase. Chest motion was measured with a respiratory gating device and post-processed to determine gates. Preservation of quantification in dual-gated images was tested with an IEC whole-body phantom. Minipig and human studies were performed to evaluate the feasibility of the method. In minipig studies, a coronary catheter with radioactive tip was guided in coronary artery for in vivo and ex vivo acquisitions. Dual gating in humans with suspected cardiac disorders was performed using 18-F-FDG as a tracer. The method was found feasible for in vivo imaging and the radioactive catheter tip was better resolved in gated images. In human studies, the dual gating was found feasible and easy for clinical routine. Maximal movement of myocardial surface in cranio-caudal direction was over 20 mm. The shape of myocardium was clearly different between the gates and papillary muscles become more visible in diastolic images. The first clinical experiences using robust cardiac-respiratory dual gating are encouraging. Further testing in larger clinical populations using tracers designed especially for plaque imaging is warranted. (orig.)

Dual-gated cardiac PET-clinical feasibility study

International Nuclear Information System (INIS)

Teraes, Mika; Kokki, Tommi; Noponen, Tommi; Hoppela, Erika; Sipilae, Hannu T.; Knuuti, Juhani; Durand-Schaefer, Nicolas; Pietilae, Mikko; Kiss, Jan

2010-01-01

Both respiratory and cardiac motions reduce image quality in myocardial imaging. For accurate imaging of small structures such as vulnerable coronary plaques, simultaneous cardiac and respiratory gating is warranted. This study tests the feasibility of a recently developed robust method for cardiac-respiratory gating. List-mode data with triggers from respiratory and cardiac cycles are rearranged into dual-gated segments and reconstructed with standard algorithms of a commercial PET/CT scanner. Cardiac gates were defined as three fixed phases and one variable diastolic phase. Chest motion was measured with a respiratory gating device and post-processed to determine gates. Preservation of quantification in dual-gated images was tested with an IEC whole-body phantom. Minipig and human studies were performed to evaluate the feasibility of the method. In minipig studies, a coronary catheter with radioactive tip was guided in coronary artery for in vivo and ex vivo acquisitions. Dual gating in humans with suspected cardiac disorders was performed using 18-F-FDG as a tracer. The method was found feasible for in vivo imaging and the radioactive catheter tip was better resolved in gated images. In human studies, the dual gating was found feasible and easy for clinical routine. Maximal movement of myocardial surface in cranio-caudal direction was over 20 mm. The shape of myocardium was clearly different between the gates and papillary muscles become more visible in diastolic images. The first clinical experiences using robust cardiac-respiratory dual gating are encouraging. Further testing in larger clinical populations using tracers designed especially for plaque imaging is warranted. (orig.)

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...

Integration of G-quadruplex and DNA-templated Ag NCs for nonarithmetic information processing.

Science.gov (United States)

Gao, Ru-Ru; Yao, Tian-Ming; Lv, Xiao-Yan; Zhu, Yan-Yan; Zhang, Yi-Wei; Shi, Shuo

2017-06-01

To create sophisticated molecular logic circuits from scratch, you may not believe how common the building blocks can be and how diverse and powerful such circuits can be when scaled up. Using the two simple building blocks of G-quadruplex and silver nanoclusters (Ag NCs), we experimentally construct a series of multifunctional, label-free, and multi-output logic circuits to perform nonarithmetic functions: a 1-to-2 decoder, a 4-to-2 encoder, an 8-to-3 encoder, dual transfer gates, a 2 : 1 multiplexer, and a 1 : 2 demultiplexer. Moreover, a parity checker which is capable of identifying odd and even numbers from natural numbers is constructed conceptually. Finally, a multi-valued logic gate (ternary inhibit gate) is readily achieved by taking this DNA/Ag NC system as a universal platform. All of the above logic circuits share the same building blocks, indicating the great prospects of the assembly of nanomaterials and DNA for biochemical logic devices. Considering its biocompatibility, the novel prototypes developed here may have potential applications in the fields of biological computers and medical diagnosis and serve as a promising proof of principle in the not-too-distant future.

Quasiparticle propagation in aluminum fins and tungsten TES dynamics in the CDMS ZIP detector

Energy Technology Data Exchange (ETDEWEB)

Pyle, M. [Department of Physics, Stanford University, Stanford, CA 94305 (United States)]. E-mail: mpyle1@stanford.edu; Brink, P.L. [Department of Physics, Stanford University, Stanford, CA 94305 (United States); Cabrera, B. [Department of Physics, Stanford University, Stanford, CA 94305 (United States); Castle, J.P. [Department of Physics, Stanford University, Stanford, CA 94305 (United States); Colling, P. [Department of Physics, Stanford University, Stanford, CA 94305 (United States); Chang, C.L. [Department of Physics, Stanford University, Stanford, CA 94305 (United States); Cooley, J. [Department of Physics, Stanford University, Stanford, CA 94305 (United States); Lipus, T. [Department of Physics, Stanford University, Stanford, CA 94305 (United States); Ogburn, R.W. [Department of Physics, Stanford University, Stanford, CA 94305 (United States); Young, B.A. [Department of Physics, Santa Clara University, Santa Clara, CA 95053 (United States)

2006-04-15

With the aim of improving the rejection of surface beta contamination on the CDMS ZIP detector, we have studied the effectiveness of our phonon pulse-shape discrimination by matching a Monte Carlo calculation to data from a 350{mu}m long Al fin with W TESs (Transition-Edge Sensors) at both ends. From this fit, we determined the Al film diffusivity to be D{sub Al}=0.010+/-0.001m{sup 2}/s, the quasiparticle trapping length in the Al fin to be l{sub trap}=180+/-10{mu}m, and the Al to W TES transmission to be f{sub Al/W}=0.002+/-0.001.

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.

An evaluation of gating window size, delivery method, and composite field dosimetry of respiratory-gated IMRT

International Nuclear Information System (INIS)

Hugo, Geoffrey D.; Agazaryan, Nzhde; Solberg, Timothy D.

2002-01-01

A respiratory gating system has been developed based on a commercial patient positioning system. The purpose of this study is to investigate the ability of the gating system to reproduce normal, nongated IMRT operation and to quantify the errors produced by delivering a nongated IMRT treatment onto a moving target. A moving phantom capable of simultaneous two-dimensional motion was built, and an analytical liver motion function was used to drive the phantom. Studies were performed to assess the effect of gating window size and choice of delivery method (segmented and dynamic multileaf collimation). Additionally, two multiple field IMRT cases were delivered to quantify the error in gated and nongated IMRT with motion. Dosimetric error between nonmoving and moving deliveries is related to gating window size. By reducing the window size, the error can be reduced. Delivery error can be reduced for both dynamic and segmented delivery with gating. For the implementation of dynamic IMRT delivery in this study, dynamic delivery was found to generate larger delivery errors than segmented delivery in most cases studied. For multiple field IMRT delivery, the largest errors were generated in regions where high field modulation was present parallel to the axis of motion. Gating was found to reduce these large errors to clinically acceptable levels

Double optical gating

Science.gov (United States)

Gilbertson, Steve

The observation and control of dynamics in atomic and molecular targets requires the use of laser pulses with duration less than the characteristic timescale of the process which is to be manipulated. For electron dynamics, this time scale is on the order of attoseconds where 1 attosecond = 10 -18 seconds. In order to generate pulses on this time scale, different gating methods have been proposed. The idea is to extract or "gate" a single pulse from an attosecond pulse train and switch off all the other pulses. While previous methods have had some success, they are very difficult to implement and so far very few labs have access to these unique light sources. The purpose of this work is to introduce a new method, called double optical gating (DOG), and to demonstrate its effectiveness at generating high contrast single isolated attosecond pulses from multi-cycle lasers. First, the method is described in detail and is investigated in the spectral domain. The resulting attosecond pulses produced are then temporally characterized through attosecond streaking. A second method of gating, called generalized double optical gating (GDOG), is also introduced. This method allows attosecond pulse generation directly from a carrier-envelope phase un-stabilized laser system for the first time. Next the methods of DOG and GDOG are implemented in attosecond applications like high flux pulses and extreme broadband spectrum generation. Finally, the attosecond pulses themselves are used in experiments. First, an attosecond/femtosecond cross correlation is used for characterization of spatial and temporal properties of femtosecond pulses. Then, an attosecond pump, femtosecond probe experiment is conducted to observe and control electron dynamics in helium for the first time.

Multi detector computed tomography (MDCT) of the aortic root; ECG-gated verses non-ECG-gated examinations

International Nuclear Information System (INIS)

Kristiansen, Joanna; Guenther, Anne; Aalokken, Trond Mogens; Andersen, Rune

2011-01-01

Purpose: Motion artifacts may degrade a conventional CT examination of the ascending aorta and hinder accurate diagnosis. We quantitatively compared retrospectively electrocardiographic (ECG) -gated multi detector computed tomography (MDCT) with non-ECG-gated MDCT in order to demonstrate whether or not one of the methods should be preferred. Method: The study included seventeen patients with surgically reconstructed aortic root and reimplanted coronary arteries. All patients had undergone both non-gated MDCT and retrospectively ECG-gated MDCT employing a stringently modulated tube current with single phase image reconstruction. The incidence of motion artifacts in the left main coronary artery (LM), proximal right coronary artery (RCA), and aortic root and ascending aorta were rated using a four point scale. The effective dose for each scan was calculated and normalized to a 15 cm scan length. Statistical analysis of motion artifacts and radiation dose was performed using Wilcoxon matched pairs signed rank sum test. Results: A significant reduction in motion artifacts was found in all three vessels in images from the retrospectively ECG-gated scans (LM: P = 0.005, RCA: P = 0.015, aorta: P = 0.003). The mean normalized effective radiation dose was 3.69 mSv (±1.03) for the non-ECG-gated scans and 16.37 mSv (±2.53) for the ECG-gated scans. Conclusion: Retrospective ECG-gating with single phase reconstruction significantly reduces the incidence of motion artifacts in the aortic root and the proximal portion of the coronary arteries but at the expense of a fourfold increase in radiation dose.

Cardiac gated ventilation

International Nuclear Information System (INIS)

Hanson, C.W. III; Hoffman, E.A.

1995-01-01

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. The authors 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 50 msec scan aperture. Multi slice, 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. The authors observed an increase in cardiac output of up to 30% with inspiration gated to the systolic phase of the cardiac cycle in a non-failing model of the heart

EST Table - KAIKOcDNA | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available uences registered to public database as of September 2011. Data file File name: kaiko_cdna_main.zip File URL...: ftp://ftp.biosciencedbc.jp/archive/kaiko-cdna/LATEST/kaiko_cdna_main.zip File s...ize: 157 MB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/kaiko_cdna_main#en Data acquisition

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

SU-E-T-350: Verification of Gating Performance of a New Elekta Gating Solution: Response Kit and Catalyst System

Energy Technology Data Exchange (ETDEWEB)

Xie, X; Cao, D; Housley, D; Mehta, V; Shepard, D [Swedish Cancer Institute, Seattle, WA (United States)

2014-06-01

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.

Voltage-Gated Potassium Channels: A Structural Examination of Selectivity and Gating

Science.gov (United States)

Kim, Dorothy M.; Nimigean, Crina M.

2016-01-01

Voltage-gated potassium channels play a fundamental role in the generation and propagation of the action potential. The discovery of these channels began with predictions made by early pioneers, and has culminated in their extensive functional and structural characterization by electrophysiological, spectroscopic, and crystallographic studies. With the aid of a variety of crystal structures of these channels, a highly detailed picture emerges of how the voltage-sensing domain reports changes in the membrane electric field and couples this to conformational changes in the activation gate. In addition, high-resolution structural and functional studies of K+ channel pores, such as KcsA and MthK, offer a comprehensive picture on how selectivity is achieved in K+ channels. Here, we illustrate the remarkable features of voltage-gated potassium channels and explain the mechanisms used by these machines with experimental data. PMID:27141052

Audio-visual biofeedback for respiratory-gated radiotherapy: Impact of audio instruction and audio-visual biofeedback on respiratory-gated radiotherapy

International Nuclear Information System (INIS)

George, Rohini; Chung, Theodore D.; Vedam, Sastry S.; Ramakrishnan, Viswanathan; Mohan, Radhe; Weiss, Elisabeth; Keall, Paul J.

2006-01-01

Purpose: Respiratory gating is a commercially available technology for reducing the deleterious effects of motion during imaging and treatment. The efficacy of gating is dependent on the reproducibility within and between respiratory cycles during imaging and treatment. The aim of this study was to determine whether audio-visual biofeedback can improve respiratory reproducibility by decreasing residual motion and therefore increasing the accuracy of gated radiotherapy. Methods and Materials: A total of 331 respiratory traces were collected from 24 lung cancer patients. The protocol consisted of five breathing training sessions spaced about a week apart. Within each session the patients initially breathed without any instruction (free breathing), with audio instructions and with audio-visual biofeedback. Residual motion was quantified by the standard deviation of the respiratory signal within the gating window. Results: Audio-visual biofeedback significantly reduced residual motion compared with free breathing and audio instruction. Displacement-based gating has lower residual motion than phase-based gating. Little reduction in residual motion was found for duty cycles less than 30%; for duty cycles above 50% there was a sharp increase in residual motion. Conclusions: The efficiency and reproducibility of gating can be improved by: incorporating audio-visual biofeedback, using a 30-50% duty cycle, gating during exhalation, and using displacement-based gating

ORF Table - KAIKOcDNA | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available tion of data contents List of open reading frames of the representative ESTs. Data file File name: kaiko_cdna..._orf.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kaiko-cdna/LATEST/kaiko_cdna_orf.zip File size: 11 MB... Simple search URL http://togodb.biosciencedbc.jp/togodb/view/kaiko_cdna_orf#en D

Image quality in non-gated versus gated reconstruction of tongue motion using magnetic resonance imaging: a comparison using automated image processing

Energy Technology Data Exchange (ETDEWEB)

Alvey, Christopher; Orphanidou, C.; Coleman, J.; McIntyre, A.; Golding, S.; Kochanski, G. [University of Oxford, Oxford (United Kingdom)

2008-11-15

The use of gated or ECG triggered MR is a well-established technique and developments in coil technology have enabled this approach to be applied to areas other than the heart. However, the image quality of gated (ECG or cine) versus non-gated or real-time has not been extensively evaluated in the mouth. We evaluate two image sequences by developing an automatic image processing technique which compares how well the image represents known anatomy. Four subjects practised experimental poly-syllabic sentences prior to MR scanning. Using a 1.5 T MR unit, we acquired comparable gated (using an artificial trigger) and non-gated sagittal images during speech. We then used an image processing algorithm to model the image grey along lines that cross the airway. Each line involved an eight parameter non-linear equation to model of proton densities, edges, and dimensions. Gated and non-gated images show similar spatial resolution, with non-gated images being slightly sharper (10% better resolution, less than 1 pixel). However, the gated sequences generated images of substantially lower inherent noise, and substantially better discrimination between air and tissue. Additionally, the gated sequences demonstrate a very much greater temporal resolution. Overall, image quality is better with gated imaging techniques, especially given their superior temporal resolution. Gated techniques are limited by the repeatability of the motions involved, and we have shown that speech to a metronome can be sufficiently repeatable to allow high-quality gated magnetic resonance imaging images. We suggest that gated sequences may be useful for evaluating other types of repetitive movement involving the joints and limb motions. (orig.)

Image quality in non-gated versus gated reconstruction of tongue motion using magnetic resonance imaging: a comparison using automated image processing

International Nuclear Information System (INIS)

Alvey, Christopher; Orphanidou, C.; Coleman, J.; McIntyre, A.; Golding, S.; Kochanski, G.

2008-01-01

The use of gated or ECG triggered MR is a well-established technique and developments in coil technology have enabled this approach to be applied to areas other than the heart. However, the image quality of gated (ECG or cine) versus non-gated or real-time has not been extensively evaluated in the mouth. We evaluate two image sequences by developing an automatic image processing technique which compares how well the image represents known anatomy. Four subjects practised experimental poly-syllabic sentences prior to MR scanning. Using a 1.5 T MR unit, we acquired comparable gated (using an artificial trigger) and non-gated sagittal images during speech. We then used an image processing algorithm to model the image grey along lines that cross the airway. Each line involved an eight parameter non-linear equation to model of proton densities, edges, and dimensions. Gated and non-gated images show similar spatial resolution, with non-gated images being slightly sharper (10% better resolution, less than 1 pixel). However, the gated sequences generated images of substantially lower inherent noise, and substantially better discrimination between air and tissue. Additionally, the gated sequences demonstrate a very much greater temporal resolution. Overall, image quality is better with gated imaging techniques, especially given their superior temporal resolution. Gated techniques are limited by the repeatability of the motions involved, and we have shown that speech to a metronome can be sufficiently repeatable to allow high-quality gated magnetic resonance imaging images. We suggest that gated sequences may be useful for evaluating other types of repetitive movement involving the joints and limb motions. (orig.)

Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs.

Science.gov (United States)

Pancoska, Petr; Moravek, Zdenek; Moll, Ute M

2004-01-01

Nucleic acids are molecules of choice for both established and emerging nanoscale technologies. These technologies benefit from large functional densities of 'DNA processing elements' that can be readily manufactured. To achieve the desired functionality, polynucleotide sequences are currently designed by a process that involves tedious and laborious filtering of potential candidates against a series of requirements and parameters. Here, we present a complete novel methodology for the rapid rational design of large sets of DNA sequences. This method allows for the direct implementation of very complex and detailed requirements for the generated sequences, thus avoiding 'brute force' filtering. At the same time, these sequences have narrow distributions of melting temperatures. The molecular part of the design process can be done without computer assistance, using an efficient 'human engineering' approach by drawing a single blueprint graph that represents all generated sequences. Moreover, the method eliminates the necessity for extensive thermodynamic calculations. Melting temperature can be calculated only once (or not at all). In addition, the isostability of the sequences is independent of the selection of a particular set of thermodynamic parameters. Applications are presented for DNA sequence designs for microarrays, universal microarray zip sequences and electron transfer experiments.

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

High-fidelity gates in quantum dot spin qubits.

Science.gov (United States)

Koh, Teck Seng; Coppersmith, S N; Friesen, Mark

2013-12-03

Several logical qubits and quantum gates have been proposed for semiconductor quantum dots controlled by voltages applied to top gates. The different schemes can be difficult to compare meaningfully. Here we develop a theoretical framework to evaluate disparate qubit-gating schemes on an equal footing. We apply the procedure to two types of double-dot qubits: the singlet-triplet and the semiconducting quantum dot hybrid qubit. We investigate three quantum gates that flip the qubit state: a DC pulsed gate, an AC gate based on logical qubit resonance, and a gate-like process known as stimulated Raman adiabatic passage. These gates are all mediated by an exchange interaction that is controlled experimentally using the interdot tunnel coupling g and the detuning [Symbol: see text], which sets the energy difference between the dots. Our procedure has two steps. First, we optimize the gate fidelity (f) for fixed g as a function of the other control parameters; this yields an f(opt)(g) that is universal for different types of gates. Next, we identify physical constraints on the control parameters; this yields an upper bound f(max) that is specific to the qubit-gate combination. We show that similar gate fidelities (~99:5%) should be attainable for singlet-triplet qubits in isotopically purified Si, and for hybrid qubits in natural Si. Considerably lower fidelities are obtained for GaAs devices, due to the fluctuating magnetic fields ΔB produced by nuclear spins.

Retrospectively ECG-gated multi-detector row CT of the chest: does ECG-gating improve three-dimensional visualization of the bronchial tree?

International Nuclear Information System (INIS)

Schertler, T.; Wildermuth, S.; Willmann, J.K.; Crook, D.W.; Marincek, B.; Boehm, T.

2004-01-01

Purpose: To determine the impact of retrospectively ECG-gated multi-detector row CT (MDCT) on three-dimensional (3D) visualization of the bronchial tree and virtual bronchoscopy (VB) as compared to non-ECG-gated data acquisition. Materials and Methods: Contrast-enhanced retrospectively ECG-gated and non-ECG-gated MDCT of the chest was performed in 25 consecutive patients referred for assessment of coronary artery bypass grafts and pathology of the ascending aorta. ECG-gated MDCT data were reconstructed in diastole using an absolute reverse delay of -400 msec in all patients. In 10 patients additional reconstructions at -200 msec, -300 msec, and -500 msec prior to the R-wave were performed. Shaded surface display (SSD) and virtual bronchoscopy (VB) for visualization of the bronchial segments was performed with ECG-gated and non-ECG-gated MDCT data. The visualization of the bronchial tree underwent blinded scoring. Effective radiation dose and signal-to-noise ratio (SNR) for both techniques were compared. Results: There was no significant difference in visualizing single bronchial segments using ECG-gated compared to non-ECG-gated MDCT data. However, the total sum of scores for all bronchial segments visualized with non-ECG-gated MDCT was significantly higher compared to ECG-gated MDCT (P [de

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

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.

Comparison of gate dielectric plasma damage from plasma-enhanced atomic layer deposited and magnetron sputtered TiN metal gates

Energy Technology Data Exchange (ETDEWEB)

Brennan, Christopher J.; Neumann, Christopher M.; Vitale, Steven A., E-mail: steven.vitale@ll.mit.edu [Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, Massachusetts 02420 (United States)

2015-07-28

Fully depleted silicon-on-insulator transistors were fabricated using two different metal gate deposition mechanisms to compare plasma damage effects on gate oxide quality. Devices fabricated with both plasma-enhanced atomic-layer-deposited (PE-ALD) TiN gates and magnetron plasma sputtered TiN gates showed very good electrostatics and short-channel characteristics. However, the gate oxide quality was markedly better for PE-ALD TiN. A significant reduction in interface state density was inferred from capacitance-voltage measurements as well as a 1200× reduction in gate leakage current. A high-power magnetron plasma source produces a much higher energetic ion and vacuum ultra-violet (VUV) photon flux to the wafer compared to a low-power inductively coupled PE-ALD source. The ion and VUV photons produce defect states in the bulk of the gate oxide as well as at the oxide-silicon interface, causing higher leakage and potential reliability degradation.

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...

Gate length variation effect on performance of gate-first self-aligned In₀.₅₃Ga₀.₄₇As MOSFET.

Science.gov (United States)

Mohd Razip Wee, Mohd F; Dehzangi, Arash; Bollaert, Sylvain; Wichmann, Nicolas; Majlis, Burhanuddin Y

2013-01-01

A multi-gate n-type In₀.₅₃Ga₀.₄₇As MOSFET is fabricated using gate-first self-aligned method and air-bridge technology. The devices with different gate lengths were fabricated with the Al2O3 oxide layer with the thickness of 8 nm. In this letter, impact of gate length variation on device parameter such as threshold voltage, high and low voltage transconductance, subthreshold swing and off current are investigated at room temperature. Scaling the gate length revealed good enhancement in all investigated parameters but the negative shift in threshold voltage was observed for shorter gate lengths. The high drain current of 1.13 A/mm and maximum extrinsic transconductance of 678 mS/mm with the field effect mobility of 364 cm(2)/Vs are achieved for the gate length and width of 0.2 µm and 30 µm, respectively. The source/drain overlap length for the device is approximately extracted about 51 nm with the leakage current in order of 10(-8) A. The results of RF measurement for cut-off and maximum oscillation frequency for devices with different gate lengths are compared.

Gate Length Variation Effect on Performance of Gate-First Self-Aligned In0.53Ga0.47As MOSFET

Science.gov (United States)

Mohd Razip Wee, Mohd F.; Dehzangi, Arash; Bollaert, Sylvain; Wichmann, Nicolas; Majlis, Burhanuddin Y.

2013-01-01

A multi-gate n-type In0.53Ga0.47As MOSFET is fabricated using gate-first self-aligned method and air-bridge technology. The devices with different gate lengths were fabricated with the Al2O3 oxide layer with the thickness of 8 nm. In this letter, impact of gate length variation on device parameter such as threshold voltage, high and low voltage transconductance, subthreshold swing and off current are investigated at room temperature. Scaling the gate length revealed good enhancement in all investigated parameters but the negative shift in threshold voltage was observed for shorter gate lengths. The high drain current of 1.13 A/mm and maximum extrinsic transconductance of 678 mS/mm with the field effect mobility of 364 cm2/Vs are achieved for the gate length and width of 0.2 µm and 30µm, respectively. The source/drain overlap length for the device is approximately extracted about 51 nm with the leakage current in order of 10−8 A. The results of RF measurement for cut-off and maximum oscillation frequency for devices with different gate lengths are compared. PMID:24367548

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; Smith, Casey Eben; Harris, Harlan Rusty; Young, Chadwin; Tseng, Hsinghuang; Jammy, Rajarao

2010-01-01

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.

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.

Protected gates for topological quantum field theories

International Nuclear Information System (INIS)

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

2016-01-01

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

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.

High-Fidelity Single-Shot Toffoli Gate via Quantum Control.

Science.gov (United States)

Zahedinejad, Ehsan; Ghosh, Joydip; Sanders, Barry C

2015-05-22

A single-shot Toffoli, or controlled-controlled-not, gate is desirable for classical and quantum information processing. The Toffoli gate alone is universal for reversible computing and, accompanied by the Hadamard gate, forms a universal gate set for quantum computing. The Toffoli gate is also a key ingredient for (nontopological) quantum error correction. Currently Toffoli gates are achieved by decomposing into sequentially implemented single- and two-qubit gates, which require much longer times and yields lower overall fidelities compared to a single-shot implementation. We develop a quantum-control procedure to construct a single-shot Toffoli gate for three nearest-neighbor-coupled superconducting transmon systems such that the fidelity is 99.9% and is as fast as an entangling two-qubit gate under the same realistic conditions. The gate is achieved by a nongreedy quantum control procedure using our enhanced version of the differential evolution algorithm.

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....

Structured-gate organic field-effect transistors

International Nuclear Information System (INIS)

Aljada, Muhsen; Pandey, Ajay K; Velusamy, Marappan; Burn, Paul L; Meredith, Paul; Namdas, Ebinazar B

2012-01-01

We report the fabrication and electrical characteristics of structured-gate organic field-effect transistors consisting of a gate electrode patterned with three-dimensional pillars. The pillar gate electrode was over-coated with a gate dielectric (SiO 2 ) and solution processed organic semiconductors producing both unipolar p-type and bipolar behaviour. We show that this new structured-gate architecture delivers higher source-drain currents, higher gate capacitance per unit equivalent linear channel area, and enhanced charge injection (electrons and/or holes) versus the conventional planar structure in all modes of operation. For the bipolar field-effect transistor (FET) the maximum source-drain current enhancements in p- and n-channel mode were >600% and 28%, respectively, leading to p and n charge mobilities with the same order of magnitude. Thus, we have demonstrated that it is possible to use the FET architecture to manipulate and match carrier mobilities of material combinations where one charge carrier is normally dominant. Mobility matching is advantageous for creating organic logic circuit elements such as inverters and amplifiers. Hence, the method represents a facile and generic strategy for improving the performance of standard organic semiconductors as well as new materials and blends. (paper)

Structured-gate organic field-effect transistors

Science.gov (United States)

Aljada, Muhsen; Pandey, Ajay K.; Velusamy, Marappan; Burn, Paul L.; Meredith, Paul; Namdas, Ebinazar B.

2012-06-01

We report the fabrication and electrical characteristics of structured-gate organic field-effect transistors consisting of a gate electrode patterned with three-dimensional pillars. The pillar gate electrode was over-coated with a gate dielectric (SiO2) and solution processed organic semiconductors producing both unipolar p-type and bipolar behaviour. We show that this new structured-gate architecture delivers higher source-drain currents, higher gate capacitance per unit equivalent linear channel area, and enhanced charge injection (electrons and/or holes) versus the conventional planar structure in all modes of operation. For the bipolar field-effect transistor (FET) the maximum source-drain current enhancements in p- and n-channel mode were >600% and 28%, respectively, leading to p and n charge mobilities with the same order of magnitude. Thus, we have demonstrated that it is possible to use the FET architecture to manipulate and match carrier mobilities of material combinations where one charge carrier is normally dominant. Mobility matching is advantageous for creating organic logic circuit elements such as inverters and amplifiers. Hence, the method represents a facile and generic strategy for improving the performance of standard organic semiconductors as well as new materials and blends.

Physical Modeling of Gate-Controlled Schottky Barrier Lowering of Metal-Graphene Contacts in Top-Gated Graphene Field-Effect Transistors

Science.gov (United States)

Mao, Ling-Feng; Ning, Huansheng; Huo, Zong-Liang; Wang, Jin-Yan

2015-12-01

A new physical model of the gate controlled Schottky barrier height (SBH) lowering in top-gated graphene field-effect transistors (GFETs) under saturation bias condition is proposed based on the energy conservation equation with the balance assumption. The theoretical prediction of the SBH lowering agrees well with the experimental data reported in literatures. The reduction of the SBH increases with the increasing of gate voltage and relative dielectric constant of the gate oxide, while it decreases with the increasing of oxide thickness, channel length and acceptor density. The magnitude of the reduction is slightly enhanced under high drain voltage. Moreover, it is found that the gate oxide materials with large relative dielectric constant (>20) have a significant effect on the gate controlled SBH lowering, implying that the energy relaxation of channel electrons should be taken into account for modeling SBH in GFETs.

Physical Modeling of Gate-Controlled Schottky Barrier Lowering of Metal-Graphene Contacts in Top-Gated Graphene Field-Effect Transistors.

Science.gov (United States)

Mao, Ling-Feng; Ning, Huansheng; Huo, Zong-Liang; Wang, Jin-Yan

2015-12-17

A new physical model of the gate controlled Schottky barrier height (SBH) lowering in top-gated graphene field-effect transistors (GFETs) under saturation bias condition is proposed based on the energy conservation equation with the balance assumption. The theoretical prediction of the SBH lowering agrees well with the experimental data reported in literatures. The reduction of the SBH increases with the increasing of gate voltage and relative dielectric constant of the gate oxide, while it decreases with the increasing of oxide thickness, channel length and acceptor density. The magnitude of the reduction is slightly enhanced under high drain voltage. Moreover, it is found that the gate oxide materials with large relative dielectric constant (>20) have a significant effect on the gate controlled SBH lowering, implying that the energy relaxation of channel electrons should be taken into account for modeling SBH in GFETs.

Compound list: 1% cholesterol + 0.25% sodium cholate [Open TG-GATEs

Lifescience Database Archive (English)

Full Text Available 1% cholesterol + 0.25% sodium cholate CH+DS-Na 00161 ftp://ftp.biosciencedbc.jp/arc...hive/open-tggates/LATEST/Rat/in_vivo/Liver/Repeat/1%25_cholesterol_%2B_0.25%25_sodium_cholate.Rat.in_vivo.Liver.Repeat.zip ...

A bistable electromagnetically actuated rotary gate microvalve

International Nuclear Information System (INIS)

Luharuka, Rajesh; Hesketh, Peter J

2008-01-01

Two types of rotary gate microvalves are developed for flow modulation in microfluidic systems. These microvalves have been tested for an open flow rate of up to 100 sccm and operate under a differential pressure of 6 psig with flow modulation of up to 100. The microvalve consists of a suspended gate that rotates in the plane of the chip to regulate flow through the orifice. The gate is suspended by a novel fully compliant in-plane rotary bistable micromechanism (IPRBM) that advantageously constrains the gate in all degrees of freedom except for in-plane rotational motion. Multiple inlet/outlet orifices provide flexibility of operating the microvalve in three different flow configurations. The rotary gate microvalve is switched with an external electromagnetic actuator. The suspended gate is made of a soft magnetic material and its electromagnetic actuation is based on the operating principle of a variable-reluctance stepper motor

A Dual Repeat Cis-Element Determines Expression of GERANYL DIPHOSPHATE SYNTHASE for Monoterpene Production in Phalaenopsis Orchids

Directory of Open Access Journals (Sweden)

Yu-Chen Chuang

2018-06-01

Full Text Available Phalaenopsis bellina is a scented orchid emitting large amount of monoterpenes. GERANYL DIPHOSPHATE SYNTHASE (PbGDPS is the key enzyme for monoterpene biosynthesis, and shows concomitant expression with the emission of monoterpenes during flower development in P. bellina. Here, we identified a dual repeat cis-element in the GDPS promoter that is critical for monoterpene biosynthesis in Phalaenopsis orchids. A strong correlation between the dual repeat and the monoterpene production was revealed by examination of the GDPS promoter fragments over 12 Phalaenopsis species. Serial-deletion of the 2-kb GDPS promoter fragments demonstrated that the integrity of the dual repeat was crucial for its promoter activities. By screening the Arabidopsis transcription factors (TFs cDNA library using yeast one-hybrid assay, AtbZIP18, a member of group I of bZIP TFs, was identified to be able to bind the dual repeat. We then identified PbbZIP4 in the transcriptome of P. bellina, showing 83% identity in the DNA binding region with that of AtbZIP18, and the expression level of PbbZIP4 was higher in the scented orchids. In addition, PbbZIP4 transactivated the GDPS promoter fragment containing the dual repeat in dual luciferase assay. Furthermore, transient ectopic expression of PbbZIP4 induced a 10-fold production of monoterpenoids in the scentless orchid. In conclusion, these results indicate that the dual repeat is a real TF-bound cis-element significant for GDPS gene expression, and thus subsequent monoterpene biosynthesis in the scented Phalaenopsis orchids.

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.

Piezoconductivity of gated suspended graphene

NARCIS (Netherlands)

Medvedyeva, M.V.; Blanter, Y.M.

2011-01-01

We investigate the conductivity of graphene sheet deformed over a gate. The effect of the deformation on the conductivity is twofold: The lattice distortion can be represented as pseudovector potential in the Dirac equation formalism, whereas the gate causes inhomogeneous density redistribution. We

Restless Tuneup of High-Fidelity Qubit Gates

Science.gov (United States)

Rol, M. A.; Bultink, C. C.; O'Brien, T. E.; de Jong, S. R.; Theis, L. S.; Fu, X.; Luthi, F.; Vermeulen, R. F. L.; de Sterke, J. C.; Bruno, A.; Deurloo, D.; Schouten, R. N.; Wilhelm, F. K.; DiCarlo, L.

2017-04-01

We present a tuneup protocol for qubit gates with tenfold speedup over traditional methods reliant on qubit initialization by energy relaxation. This speedup is achieved by constructing a cost function for Nelder-Mead optimization from real-time correlation of nondemolition measurements interleaving gate operations without pause. Applying the protocol on a transmon qubit achieves 0.999 average Clifford fidelity in one minute, as independently verified using randomized benchmarking and gate-set tomography. The adjustable sensitivity of the cost function allows the detection of fractional changes in the gate error with a nearly constant signal-to-noise ratio. The restless concept demonstrated can be readily extended to the tuneup of two-qubit gates and measurement operations.

Light-effect transistor (LET with multiple independent gating controls for optical logic gates and optical amplification

Directory of Open Access Journals (Sweden)

Jason eMarmon

2016-03-01

Full Text Available Modern electronics are developing electronic-optical integrated circuits, while their electronic backbone, e.g. field-effect transistors (FETs, remains the same. However, further FET down scaling is facing physical and technical challenges. A light-effect transistor (LET offers electronic-optical hybridization at the component level, which can continue Moore’s law to quantum region without requiring a FET’s fabrication complexity, e.g. physical gate and doping, by employing optical gating and photoconductivity. Multiple independent gates are therefore readily realized to achieve unique functionalities without increasing chip space. Here we report LET device characteristics and novel digital and analog applications, such as optical logic gates and optical amplification. Prototype CdSe-nanowire-based LETs show output and transfer characteristics resembling advanced FETs, e.g. on/off ratios up to ~1.0x106 with a source-drain voltage of ~1.43 V, gate-power of ~260 nW, and subthreshold swing of ~0.3 nW/decade (excluding losses. Our work offers new electronic-optical integration strategies and electronic and optical computing approaches.

Implementation of a two-qubit controlled-rotation gate based on unconventional geometric phase with a constant gating time

International Nuclear Information System (INIS)

Yabu-uti, B.F.C.; Roversi, J.A.

2011-01-01

We propose an alternative scheme to implement a two-qubit controlled-R (rotation) gate in the hybrid atom-CCA (coupled cavities array) system. Our scheme results in a constant gating time and, with an adjustable qubit-bus coupling (atom-resonator), one can specify a particular rotation R on the target qubit. We believe that this proposal may open promising perspectives for networking quantum information processors and implementing distributed and scalable quantum computation. -- Highlights: → We propose an alternative two-qubit controlled-rotation gate implementation. → Our gate is realized in a constant gating time for any rotation. → A particular rotation on the target qubit can be specified by an adjustable qubit-bus coupling. → Our proposal may open promising perspectives for implementing distributed and scalable quantum computation.

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

Direct immobilization and hybridization of DNA on group III nitride semiconductors

Energy Technology Data Exchange (ETDEWEB)

Xu Xiaobin; Jindal, Vibhu; Shahedipour-Sandvik, Fatemeh; Bergkvist, Magnus [College of Nanoscale Science and Engineering, University at Albany (SUNY), 255 Fuller Road, Albany, NY 12203 (United States); Cady, Nathaniel C. [College of Nanoscale Science and Engineering, University at Albany (SUNY), 255 Fuller Road, Albany, NY 12203 (United States)], E-mail: ncady@uamail.albany.edu

2009-03-15

A key concern for group III-nitride high electron mobility transistor (HEMT) biosensors is the anchoring of specific capture molecules onto the gate surface. To this end, a direct immobilization strategy was developed to attach single-stranded DNA (ssDNA) to AlGaN surfaces using simple printing techniques without the need for cross-linking agents or complex surface pre-functionalization procedures. Immobilized DNA molecules were stably attached to the AlGaN surfaces and were able to withstand a range of pH and ionic strength conditions. The biological activity of surface-immobilized probe DNA was also retained, as demonstrated by sequence-specific hybridization experiments. Probe hybridization with target ssDNA could be detected by PicoGreen fluorescent dye labeling with a minimum detection limit of 2 nM. These experiments demonstrate a simple and effective immobilization approach for attaching nucleic acids to AlGaN surfaces which can further be used for the development of HEMT-based DNA biosensors.

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

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

Experimental superposition of orders of quantum gates

Science.gov (United States)

Procopio, Lorenzo M.; Moqanaki, Amir; Araújo, Mateus; Costa, Fabio; Alonso Calafell, Irati; Dowd, Emma G.; Hamel, Deny R.; Rozema, Lee A.; Brukner, Časlav; Walther, Philip

2015-01-01

Quantum computers achieve a speed-up by placing quantum bits (qubits) in superpositions of different states. However, it has recently been appreciated that quantum mechanics also allows one to ‘superimpose different operations'. Furthermore, it has been shown that using a qubit to coherently control the gate order allows one to accomplish a task—determining if two gates commute or anti-commute—with fewer gate uses than any known quantum algorithm. Here we experimentally demonstrate this advantage, in a photonic context, using a second qubit to control the order in which two gates are applied to a first qubit. We create the required superposition of gate orders by using additional degrees of freedom of the photons encoding our qubits. The new resource we exploit can be interpreted as a superposition of causal orders, and could allow quantum algorithms to be implemented with an efficiency unlikely to be achieved on a fixed-gate-order quantum computer. PMID:26250107

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

Methodology for Analysis, Modeling and Simulation of Airport Gate-waiting Delays

Science.gov (United States)

Wang, Jianfeng

This dissertation presents methodologies to estimate gate-waiting delays from historical data, to identify gate-waiting-delay functional causes in major U.S. airports, and to evaluate the impact of gate operation disruptions and mitigation strategies on gate-waiting delay. Airport gates are a resource of congestion in the air transportation system. When an arriving flight cannot pull into its gate, the delay it experiences is called gate-waiting delay. Some possible reasons for gate-waiting delay are: the gate is occupied, gate staff or equipment is unavailable, the weather prevents the use of the gate (e.g. lightning), or the airline has a preferred gate assignment. Gate-waiting delays potentially stay with the aircraft throughout the day (unless they are absorbed), adding costs to passengers and the airlines. As the volume of flights increases, ensuring that airport gates do not become a choke point of the system is critical. The first part of the dissertation presents a methodology for estimating gate-waiting delays based on historical, publicly available sources. Analysis of gate-waiting delays at major U.S. airports in the summer of 2007 identifies the following. (i) Gate-waiting delay is not a significant problem on majority of days; however, the worst delay days (e.g. 4% of the days at LGA) are extreme outliers. (ii) The Atlanta International Airport (ATL), the John F. Kennedy International Airport (JFK), the Dallas/Fort Worth International Airport (DFW) and the Philadelphia International Airport (PHL) experience the highest gate-waiting delays among major U.S. airports. (iii) There is a significant gate-waiting-delay difference between airlines due to a disproportional gate allocation. (iv) Gate-waiting delay is sensitive to time of a day and schedule peaks. According to basic principles of queueing theory, gate-waiting delay can be attributed to over-scheduling, higher-than-scheduled arrival rate, longer-than-scheduled gate-occupancy time, and reduced gate

Gate tunneling current and quantum capacitance in metal-oxide-semiconductor devices with graphene gate electrodes

Science.gov (United States)

An, Yanbin; Shekhawat, Aniruddh; Behnam, Ashkan; Pop, Eric; Ural, Ant

2016-11-01

Metal-oxide-semiconductor (MOS) devices with graphene as the metal gate electrode, silicon dioxide with thicknesses ranging from 5 to 20 nm as the dielectric, and p-type silicon as the semiconductor are fabricated and characterized. It is found that Fowler-Nordheim (F-N) tunneling dominates the gate tunneling current in these devices for oxide thicknesses of 10 nm and larger, whereas for devices with 5 nm oxide, direct tunneling starts to play a role in determining the total gate current. Furthermore, the temperature dependences of the F-N tunneling current for the 10 nm devices are characterized in the temperature range 77-300 K. The F-N coefficients and the effective tunneling barrier height are extracted as a function of temperature. It is found that the effective barrier height decreases with increasing temperature, which is in agreement with the results previously reported for conventional MOS devices with polysilicon or metal gate electrodes. In addition, high frequency capacitance-voltage measurements of these MOS devices are performed, which depict a local capacitance minimum under accumulation for thin oxides. By analyzing the data using numerical calculations based on the modified density of states of graphene in the presence of charged impurities, it is shown that this local minimum is due to the contribution of the quantum capacitance of graphene. Finally, the workfunction of the graphene gate electrode is extracted by determining the flat-band voltage as a function of oxide thickness. These results show that graphene is a promising candidate as the gate electrode in metal-oxide-semiconductor devices.

Precise linear gating circuit on integrated microcircuits

Energy Technology Data Exchange (ETDEWEB)

Butskii, V.V.; Vetokhin, S.S.; Reznikov, I.V.

Precise linear gating circuit on four microcircuits is described. A basic flowsheet of the gating circuit is given. The gating circuit consists of two input differential cascades total load of which is two current followers possessing low input and high output resistances. Follower outlets are connected to high ohmic dynamic load formed with a current source which permits to get high amplification (>1000) at one cascade. Nonlinearity amounts to <0.1% in the range of input signal amplitudes of -10-+10 V. Front duration for an output signal with 10 V amplitude amounts to 100 ns. Attenuation of input signal with a closed gating circuit is 60 db. The gating circuits described is used in the device intended for processing of scintillation sensor signals.

Bubble gate for in-plane flow control.

Science.gov (United States)

Oskooei, Ali; Abolhasani, Milad; Günther, Axel

2013-07-07

We introduce a miniature gate valve as a readily implementable strategy for actively controlling the flow of liquids on-chip, within a footprint of less than one square millimetre. Bubble gates provide for simple, consistent and scalable control of liquid flow in microchannel networks, are compatible with different bulk microfabrication processes and substrate materials, and require neither electrodes nor moving parts. A bubble gate consists of two microchannel sections: a liquid-filled channel and a gas channel that intercepts the liquid channel to form a T-junction. The open or closed state of a bubble gate is determined by selecting between two distinct gas pressure levels: the lower level corresponds to the "open" state while the higher level corresponds to the "closed" state. During closure, a gas bubble penetrates from the gas channel into the liquid, flanked by a column of equidistantly spaced micropillars on each side, until the flow of liquid is completely obstructed. We fabricated bubble gates using single-layer soft lithographic and bulk silicon micromachining procedures and evaluated their performance with a combination of theory and experimentation. We assessed the dynamic behaviour during more than 300 open-and-close cycles and report the operating pressure envelope for different bubble gate configurations and for the working fluids: de-ionized water, ethanol and a biological buffer. We obtained excellent agreement between the experimentally determined bubble gate operational envelope and a theoretical prediction based on static wetting behaviour. We report case studies that serve to illustrate the utility of bubble gates for liquid sampling in single and multi-layer microfluidic devices. Scalability of our strategy was demonstrated by simultaneously addressing 128 bubble gates.

High speed gated x-ray imagers

International Nuclear Information System (INIS)

Kilkenny, J.D.; Bell, P.; Hanks, R.; Power, G.; Turner, R.E.; Wiedwald, J.

1988-01-01

Single and multi-frame gated x-ray images with time-resolution as fast as 150 psec are described. These systems are based on the gating of microchannel plates in a stripline configuration. The gating voltage comes from the avalanche breakdown of reverse biased p-n junction producing high power voltage pulses as short as 70 psec. Results from single and four frame x-ray cameras used on Nova are described. 8 refs., 9 figs

Respiratory gating and multi field technique radiotherapy for esophageal cancer

International Nuclear Information System (INIS)

Ohta, Atsushi; Kaidu, Motoki; Tanabe, Satoshi

2017-01-01

To investigate the effects of a respiratory gating and multi field technique on the dose-volume histogram (DVH) in radiotherapy for esophageal cancer. Twenty patients who underwent four-dimensional computed tomography for esophageal cancer were included. We retrospectively created the four treatment plans for each patient, with or without the respiratory gating and multi field technique: No gating-2-field, No gating-4-field, Gating-2-field, and Gating-4-field plans. We compared the DVH parameters of the lung and heart in the No gating-2-field plan with the other three plans.Result In the comparison of the parameters in the No gating-2-field plan, there are significant differences in the Lung V 5Gy , V 20Gy , mean dose with all three plans and the Heart V 25Gy -V 40Gy with Gating-2-field plan, V 35Gy , V 40Gy , mean dose with No Gating-4-field plan and V 30Gy -V 40Gy , and mean dose with Gating-4-field plan. The lung parameters were smaller in the Gating-2-field plan and larger in the No gating-4-field and Gating-4-field plans. The heart parameters were all larger in the No gating-2-field plan. The lung parameters were reduced by the respiratory gating technique and increased by the multi field technique. The heart parameters were reduced by both techniques. It is important to select the optimal technique according to the risk of complications. (author)

Air-gating and chemical-gating in transistors and sensing devices made from hollow TiO2 semiconductor nanotubes

Science.gov (United States)

Alivov, Yahya; Funke, Hans; Nagpal, Prashant

2015-07-01

Rapid miniaturization of electronic devices down to the nanoscale, according to Moore’s law, has led to some undesirable effects like high leakage current in transistors, which can offset additional benefits from scaling down. Development of three-dimensional transistors, by spatial extension in the third dimension, has allowed higher contact area with a gate electrode and better control over conductivity in the semiconductor channel. However, these devices do not utilize the large surface area and interfaces for new electronic functionality. Here, we demonstrate air gating and chemical gating in hollow semiconductor nanotube devices and highlight the potential for development of novel transistors that can be modulated using channel bias, gate voltage, chemical composition, and concentration. Using chemical gating, we reversibly altered the conductivity of nanoscaled semiconductor nanotubes (10-500 nm TiO2 nanotubes) by six orders of magnitude, with a tunable rectification factor (ON/OFF ratio) ranging from 1-106. While demonstrated air- and chemical-gating speeds were slow here (˜seconds) due to the mechanical-evacuation rate and size of our chamber, the small nanoscale volume of these hollow semiconductors can enable much higher switching speeds, limited by the rate of adsorption/desorption of molecules at semiconductor interfaces. These chemical-gating effects are completely reversible, additive between different chemical compositions, and can enable semiconductor nanoelectronic devices for ‘chemical transistors’, ‘chemical diodes’, and very high-efficiency sensing applications.

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

Position dependent mismatch discrimination on DNA microarrays – experiments and model

Directory of Open Access Journals (Sweden)

Michel Wolfgang

2008-12-01

Full Text Available Abstract Background The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR. Yet our understanding of oligonucleotide hybridization, in particular in presence of surfaces, is rather limited. Here we use oligonucleotide microarrays made in-house by optically controlled DNA synthesis to produce probe sets comprising all possible single base mismatches and base bulges for each of 20 sequence motifs under study. Results We observe that mismatch discrimination is mostly determined by the defect position (relative to the duplex ends as well as by the sequence context. We investigate the thermodynamics of the oligonucleotide duplexes on the basis of double-ended molecular zipper. Theoretical predictions of defect positional influence as well as long range sequence influence agree well with the experimental results. Conclusion Molecular zipping at thermodynamic equilibrium explains the binding affinity of mismatched DNA duplexes on microarrays well. The position dependent nearest neighbor model (PDNN can be inferred from it. Quantitative understanding of microarray experiments from first principles is in reach.

Evolutionary and Expression Analyses of the Apple Basic Leucine Zipper Transcription Factor Family

Science.gov (United States)

Zhao, Jiao; Guo, Rongrong; Guo, Chunlei; Hou, Hongmin; Wang, Xiping; Gao, Hua

2016-01-01

Transcription factors (TFs) play essential roles in the regulatory networks controlling many developmental processes in plants. Members of the basic leucine (Leu) zipper (bZIP) TF family, which is unique to eukaryotes, are involved in regulating diverse processes, including flower and vascular development, seed maturation, stress signaling, and defense responses to pathogens. The bZIP proteins have a characteristic bZIP domain composed of a DNA-binding basic region and a Leu zipper dimerization region. In this study, we identified 112 apple (Malus domestica Borkh) bZIP TF-encoding genes, termed MdbZIP genes. Synteny analysis indicated that segmental and tandem duplication events, as well as whole genome duplication, have contributed to the expansion of the apple bZIP family. The family could be divided into 11 groups based on structural features of the encoded proteins, as well as on the phylogenetic relationship of the apple bZIP proteins to those of the model plant Arabidopsis thaliana (AtbZIP genes). Synteny analysis revealed that several paired MdbZIP genes and AtbZIP gene homologs were located in syntenic genomic regions. Furthermore, expression analyses of group A MdbZIP genes showed distinct expression levels in 10 different organs. Moreover, changes in these expression profiles in response to abiotic stress conditions and various hormone treatments identified MdbZIP genes that were responsive to high salinity and drought, as well as to different phytohormones. PMID:27066030

Evolutionary and Expression Analyses of the Apple Basic Leucine Zipper Transcription Factor Family

Directory of Open Access Journals (Sweden)

Jiao eZhao

2016-03-01

Full Text Available Transcription factors (TFs play essential roles in the regulatory networks controlling many developmental processes in plants. Members of the basic leucine (Leu zipper (bZIP TF family, which is unique to eukaryotes, are involved in regulating diverse processes, including flower and vascular development, seed maturation, stress signaling and defense responses to pathogens. The bZIP proteins have a characteristic bZIP domain composed of a DNA-binding basic region and a Leu zipper dimerization region. In this study, we identified 112 apple (Malus domestica Borkh bZIP TF-encoding genes, termed MdbZIP genes. Synteny analysis indicated that segmental and tandem duplication events, as well as whole genome duplication, have contributed to the expansion of the apple bZIP family. The family could be divided into 11 groups based on structural features of the encoded proteins, as well as on the phylogenetic relationship of the apple bZIP proteins to those of the model plant Arabidopsis thaliana (AtbZIP genes. Synteny analysis revealed that several paired MdbZIP genes and AtbZIP gene homologs were located in syntenic genomic regions. Furthermore, expression analyses of group A MdbZIP genes showed distinct expression levels in ten different organs. Moreover, changes in these expression profiles in response to abiotic stress conditions and various hormone treatments identified MdbZIP genes that were responsive to high salinity and drought, as well as to different phytohormones.

Designable DNA-binding domains enable construction of logic circuits in mammalian cells.

Science.gov (United States)

Gaber, Rok; Lebar, Tina; Majerle, Andreja; Šter, Branko; Dobnikar, Andrej; Benčina, Mojca; Jerala, Roman

2014-03-01

Electronic computer circuits consisting of a large number of connected logic gates of the same type, such as NOR, can be easily fabricated and can implement any logic function. In contrast, designed genetic circuits must employ orthogonal information mediators owing to free diffusion within the cell. Combinatorial diversity and orthogonality can be provided by designable DNA- binding domains. Here, we employed the transcription activator-like repressors to optimize the construction of orthogonal functionally complete NOR gates to construct logic circuits. We used transient transfection to implement all 16 two-input logic functions from combinations of the same type of NOR gates within mammalian cells. Additionally, we present a genetic logic circuit where one input is used to select between an AND and OR function to process the data input using the same circuit. This demonstrates the potential of designable modular transcription factors for the construction of complex biological information-processing devices.

DNA microarray revealed and RNAi plants confirmed key genes conferring low Cd accumulation in barley grains

DEFF Research Database (Denmark)

Sun, Hongyan; Chen, Zhong-Hua; Chen, Fei

2015-01-01

Background Understanding the mechanism of low Cd accumulation in crops is crucial for sustainable safe food production in Cd-contaminated soils. Results Confocal microscopy, atomic absorption spectrometry, gas exchange and chlorophyll fluorescence analyses revealed a distinct difference in Cd...... with a substantial difference between the two genotypes. Cd stress led to higher expression of genes involved in transport, carbohydrate metabolism and signal transduction in the low-grain-Cd-accumulating genotype. Novel transporter genes such as zinc transporter genes were identified as being associated with low Cd...... accumulation. Quantitative RT-PCR confirmed our microarray data. Furthermore, suppression of the zinc transporter genes HvZIP3 and HvZIP8 by RNAi silencing showed increased Cd accumulation and reduced Zn and Mn concentrations in barley grains. Thus, HvZIP3 and HvZIP8 could be candidate genes related to low...

Genotyping of single nucleotide polymorphism by probe-gated silica nanoparticles.

Science.gov (United States)

Ercan, Meltem; Ozalp, Veli C; Tuna, Bilge G

2017-11-15

The development of simple, reliable, and rapid approaches for molecular detection of common mutations is important for prevention and early diagnosis of genetic diseases, including Thalessemia. Oligonucleotide-gated mesoporous nanoparticles-based analysis is a new platform for mutation detection that has the advantages of sensitivity, rapidity, accuracy, and convenience. A specific mutation in β-thalassemia, one of the most prevalent inherited diseases in several countries, was used as model disease in this study. An assay for detection of IVS110 point mutation (A > G reversion) was developed by designing probe-gated mesoporous silica nanoparticles (MCM-41) loaded with reporter fluorescein molecules. The silica nanoparticles were characterized by AFM, TEM and BET analysis for having 180 nm diameter and 2.83 nm pore size regular hexagonal shape. Amine group functionalized nanoparticles were analysed with FTIR technique. Mutated and normal sequence probe oligonucleotides)about 12.7 nmol per mg nanoparticles) were used to entrap reporter fluorescein molecules inside the pores and hybridization with single stranded DNA targets amplified by PCR gave different fluorescent signals for mutated targets. Samples from IVS110 mutated and normal patients resulted in statistically significant differences when the assay procedure were applied. Copyright © 2017 Elsevier Inc. All rights reserved.

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

Double-disc gate valve

International Nuclear Information System (INIS)

Wheatley, S.J.

1979-01-01

The invention relates to an improvement in a conventional double-disc gate valve having a vertically movable gate assembly including a wedge, spreaders slidably engaged therewith, a valve disc carried by the spreaders. When the gate assembly is lowered to a selected point in the valve casing, the valve discs are moved transversely outward to close inlet and outlet ports in the casing. The valve includes hold-down means for guiding the disc-and-spreader assemblies as they are moved transversely outward and inward. If such valves are operated at relatively high differential pressures, they sometimes jam during opening. Such jamming has been a problem for many years in gate valves used in gaseous diffusion plants for the separation of uranium isotopes. The invention is based on the finding that the above-mentioned jamming results when the outlet disc tilts about its horizontal axis in a certain way during opening of the valve. In accordance with the invention, tilting of the outlet disc is maintained at a tolerable value by providing the disc with a rigid downwardly extending member and by providing the casing with a stop for limiting inward arcuate movement of the member to a preselected value during opening of the valve

The dynamic changes of DNA methylation and histone modifications of salt responsive transcription factor genes in soybean.

Directory of Open Access Journals (Sweden)

Yuguang Song

Full Text Available Epigenetic modification contributes to the regulation of gene expression and plant development under salinity stress. Here we describe the identification of 49 soybean transcription factors by microarray analysis as being inducible by salinity stress. A semi-quantitative RT-PCR-based expression assay confirmed the salinity stress inducibility of 45 of these 49 transcription factors, and showed that ten of them were up-regulated when seedlings were exposed to the demethylation agent 5-aza-2-deoxycytidine. Salinity stress was shown to affect the methylation status of four of these ten transcription factors (one MYB, one b-ZIP and two AP2/DREB family members using a combination of bisulfite sequencing and DNA methylation-sensitive DNA gel blot analysis. ChIP analysis indicated that the activation of three of the four DNA methylated transcription factors was correlated with an increased level of histone H3K4 trimethylation and H3K9 acetylation, and/or a reduced level of H3K9 demethylation in various parts of the promoter or coding regions. Our results suggest a critical role for some transcription factors' activation/repression by DNA methylation and/or histone modifications in soybean tolerance to salinity stress.

Rapidly reconfigurable all-optical universal logic gate

Science.gov (United States)

Goddard, Lynford L.; Bond, Tiziana C.; Kallman, Jeffrey S.

2010-09-07

A new reconfigurable cascadable all-optical on-chip device is presented. The gate operates by combining the Vernier effect with a novel effect, the gain-index lever, to help shift the dominant lasing mode from a mode where the laser light is output at one facet to a mode where it is output at the other facet. Since the laser remains above threshold, the speed of the gate for logic operations as well as for reprogramming the function of the gate is primarily limited to the small signal optical modulation speed of the laser, which can be on the order of up to about tens of GHz. The gate can be rapidly and repeatedly reprogrammed to perform any of the basic digital logic operations by using an appropriate analog optical or electrical signal at the gate selection port. Other all-optical functionality includes wavelength conversion, signal duplication, threshold switching, analog to digital conversion, digital to analog conversion, signal routing, and environment sensing. Since each gate can perform different operations, the functionality of such a cascaded circuit grows exponentially.

Spot 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 ...d_spot.zip File URL: ftp://ftp.biosciencedbc.jp/archive/rpd/LATEST/rpd_spot.zip F... cDNA. (multiple entries) About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Spot table - RPD | LSDB Archive ...

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.

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.

[Cloning and expression analysis of a zinc-regulated transporters (ZRT), iron-regulated transporter (IRT)-like protein encoding gene in Dendrobium officinale].

Science.gov (United States)

Zhang, Gang; Li, Yi-Min; Li, Biao; Zhang, Da-Wei; Guo, Shun-Xing

2015-01-01

The zinc-regulated transporters (ZRT), iron-regulated transporter (IRT)-like protein (ZIP) plays an important role in the growth and development of plant. In this study, a full length cDNA of ZIP encoding gene, designed as DoZIP1 (GenBank accession KJ946203), was identified from Dendrobium officinale using RT-PCR and RACE. Bioinformatics analysis showed that DoZIP1 consisted of a 1,056 bp open reading frame (ORF) encoded a 351-aa protein with a molecular weight of 37.57 kDa and an isoelectric point (pI) of 6.09. The deduced DoZIP1 protein contained the conserved ZIP domain, and its secondary structure was composed of 50.71% alpha helix, 11.11% extended strand, 36.18% random coil, and beta turn 1.99%. DoZIP1 protein exhibited a signal peptide and eight transmembrane domains, presumably locating in cell membrane. The amino acid sequence had high homology with ZIP proteins from Arabidopsis, alfalfa and rice. A phylogenetic tree analysis demonstrated that DoZIP1 was closely related to AtZIP10 and OsZIP3, and they were clustered into one clade. Real time quantitative PCR analysis demonstrated that the transcription level of DoZIP1 in D. officinale roots was the highest (4.19 fold higher than that of stems), followed by that of leaves (1.12 fold). Molecular characters of DoZIP1 will be useful for further functional determination of the gene involving in the growth and development of D. officinale.