Transfer-function modelling between environmental variation and mesozooplankton in the Baltic Sea [review article

NASA Astrophysics Data System (ADS)

Vuorinen, I.; Hänninen, J.; Kornilovs, G.

2003-12-01

Time series of freshwater runoff, seawater salinity, temperature and oxygen were used in transfer functions (TF) to model changes of mesozooplankton taxa in the Baltic Sea from the 1960’s to the 1990’s. The models were then compared with long term zooplankton monitoring data from the same period. The TF models for all taxa over the whole Baltic proper and at different depth layers showed statistically significant estimates in t-tests. TF models were further compared using parsimony as a criterion. We present models showing 1) r2 > 0.4, 2) the smallest residual standard error with the combination of exploratory variables, 3) the lowest number of parameters and 4) the highest proportional decrease in error term when the TF model residual standard error was compared with those of the univariate ARIMA model of the same response variable. Most often (7 taxa out of a total of 8), zooplankton taxa were dependent on freshwater runoff and/or seawater salinity. Cladocerans and estuarine copepods were more conveniently modelled through the inclusion of seawater temperature and oxygen data as independent variables. Our modelling, however, explains neither the overall increase in zooplankton abundance nor a simultaneous decrease found in the neritic copepod, Temora longicornis. Therefore, biotic controlling agents (e.g. nutrients, primary production and planktivore diets) are suggested as independent variables for further TF modelling. TF modelling enabled us to put the controlling factors in a time frame. It was then possible, despite the inherent multiple correlation among parameters studied to deduce a chain-of-events from the environmental controls and biotic feedback mechanisms to changes in zooplankton species. We suggest that the documented long-term changes in zooplankton could have been driven by climatic regulation only. The control by climate could be mediated to zooplankton through marine chemical and physical factors, as well as biotic factors if all of these were responding to the same external control, such as changes in the freshwater runoff. Increased runoff would explain both the increasing eutrophication, causing the overall increase of zooplankton, and the changes in selective predation, contributing to decline of Temora.

XML Storage for Magnetotelluric Transfer Functions: Towards a Comprehensive Online Reference Database

NASA Astrophysics Data System (ADS)

Kelbert, A.; Blum, C.

2015-12-01

Magnetotelluric Transfer Functions (MT TFs) represent most of the information about Earth electrical conductivity found in the raw electromagnetic data, providing inputs for further inversion and interpretation. To be useful for scientific interpretation, they must also contain carefully recorded metadata. Making these data available in a discoverable and citable fashion would provide the most benefit to the scientific community, but such a development requires that the metadata is not only present in the file but is also searchable. The most commonly used MT TF format to date, the historical Society of Exploration Geophysicists Electromagnetic Data Interchange Standard 1987 (EDI), no longer supports some of the needs of modern magnetotellurics, most notably accurate error bars recording. Moreover, the inherent heterogeneity of EDI's and other historic MT TF formats has mostly kept the community away from healthy data sharing practices. Recently, the MT team at Oregon State University in collaboration with IRIS Data Management Center developed a new, XML-based format for MT transfer functions, and an online system for long-term storage, discovery and sharing of MT TF data worldwide (IRIS SPUD; www.iris.edu/spud/emtf). The system provides a query page where all of the MT transfer functions collected within the USArray MT experiment and other field campaigns can be searched for and downloaded; an automatic on-the-fly conversion to the historic EDI format is also included. To facilitate conversion to the new, more comprehensive and sustainable, XML format for MT TFs, and to streamline inclusion of historic data into the online database, we developed a set of open source format conversion tools, which can be used for rotation of MT TFs as well as a general XML <-> EDI converter (https://seiscode.iris.washington.edu/projects/emtf-fcu). Here, we report on the newly established collaboration between the USGS Geomagnetism Program and the Oregon State University to gather and convert both historic and modern-day MT or related transfer functions into the searchable database at the IRIS DMC. The more complete and free access to these previously collected MT TFs will be of great value to MT scientists both in planning future surveys, and then to leverage the value of the new data at the inversion and interpretation stage.

Indications, usage, and dosage of the transfer factor.

PubMed

Berrón-Pérez, Renato; Chávez-Sánchez, Raúl; Estrada-García, Iris; Espinosa-Padilla, Sara; Cortez-Gómez, Rudyard; Serrano-Miranda, Ernestina; Ondarza-Aguilera, Rodolfo; Pérez-Tapia, Mayra; Pineda Olvera, Benjamín; Jiménez-Martínez, María del Carmen; Portugués, Abraham; Rodríguez, Azucena; Cano, Laura; Pacheco, Pedro Urcino; Barrientos, Javier; Chacón, Rommel; Serafín, Jeannet; Mendez, Patricia; Monges, Abelardo; Cervantes, Edgar; Estrada-Parra, Sergio

2007-01-01

The transfer factor (TF) was described in 1955 by S. Lawrence. In 1992 Kirkpatrick characterized the specific TF at molecular level. The TF is constituted by a group of numerous molecules, of low molecular weight, from 1.0 to 6.0 kDa. The 5 kDa fraction corresponds to the TF specific to antigens. There are a number of publications about the clinical indications of the TF for diverse diseases, in particular those where the cellular immune response is compromised or in those where there is a deficient regulation of the immune response. In this article we present our clinical and basic experiences, especially regarding the indications, usage and dosage of the TF. Our group demonstrated that the TF increases the expression of IFN-gamma and RANTES, while decreases the expression of osteopontine. Using animal models we have worked with M. tuberculosis, and with a model of glioma with good therapeutic results. In the clinical setting we have worked with herpes zoster, herpes simplex type I, herpetic keratitis, atopic dermatitis, osteosarcoma, tuberculosis, asthma, post-herpetic neuritis, anergic coccidioidomycosis, leishmaniasis, toxoplasmosis, mucocutaneous candidiasis, pediatric infections produced by diverse pathogen germs, sinusitis, pharyngitis, and otits media. All of these diseases were studied through protocols which main goals were to study the therapeutic effects of the TF, and to establish in a systematic way diverse dosage schema and time for treatment to guide the prescription of the TF.

In Vivo 18-FDG/18-Choline-Mediated Cerenkov Radiation Energy Transfer (CRET) Multiplexed Optical Imaging for Human Prostate Carcinoma Detection and Staging

DTIC Science & Technology

2017-12-01

AWARD NUMBER: W81XWH-13-1-0138 TITLE: In Vivo 18-FDG/18-Choline-Mediated Cerenkov Radiation Energy Transfer (CRET) Multiplexed Optical...18Ffluorocholine/ 18F-FDG Cerenkov radiation energy transfer (CRET) coupled with TF- and ErbB2/3- molecularly targeted nearinfrared (NIR) QDs can be used to detect...to examine whether internal illumination via 18F-fluorocholine Cerenkov radiation energy transfer (CRET) coupled with TF- and ErbB2/3- molecularly

Multi-hundred kilowatt roll ring assembly

NASA Technical Reports Server (NTRS)

Jacobson, Peter E.

1985-01-01

A program was completed to develop an evaluation unit of a high power rotary transfer device for potential application in a space environment. This device was configured around a Roll Ring concept which performs the same function as a slip ring/brush assembly with a rolling instead of sliding interface. An eight circuit Evaluation Unit (EU) and a portable Test Fixture (TF) were designed and fabricated. The EU was designed to transfer currents to 200 amperes at a potential of as high as 500 volts for an ultimate 100 kW/circuit transfer capability. The EU was evaluated in vacuum at dc transfer currents of 50 to 200 amperes at voltages to 10 volts and at 500 volts at 2 amperes. Power transfer to levels of 2 kW through each of the eight circuits was completed. Power transfer in vacuum at levels and efficiencies not previously achieved was demonstrated. The terminal-to-terminal resistance was measured to be greater than 0.42 milliohms which translates to an efficiency at 100 kW of 99.98 percent. The EU and TF have been delivered to the Lewis Research Center and are being prepared tor testing at increased power levels and for life testing, which will include both dc and ac power.

Trace element mobility and transfer to vegetation within the Ethiopian Rift Valley lake areas.

PubMed

Kassaye, Yetneberk A; Skipperud, Lindis; Meland, Sondre; Dadebo, Elias; Einset, John; Salbu, Brit

2012-10-26

To evaluate critical trace element loads in native vegetation and calculate soil-to-plant transfer factors (TFs), 11 trace elements (Cr, Co, Ni, Cu, Zn, As, Se, Mo, Cd, Pb and Mn) have been determined in leaves of 9 taxonomically verified naturally growing terrestrial plant species as well as in soil samples collected around 3 Ethiopian Rift Valley lakes (Koka, Ziway and Awassa). The Cr concentration in leaves of all the plant species was higher than the "normal" range, with the highest level (8.4 mg per kg dw) being observed in Acacia tortilis from the Lake Koka area. Caper species (Capparis fascicularis) and Ethiopian dogstooth grass (Cynodon aethiopicus) from Koka also contained exceptionally high levels of Cd (1 mg per kg dw) and Mo (32.8 mg per kg dw), respectively. Pb, As and Cu concentrations were low in the plant leaves from all sites. The low Cu level in important fodder plant species (Cynodon aethiopicus, Acacia tortilis and Opuntia ficus-indicus) implies potential deficiency in grazing and browsing animals. Compared to the Canadian environmental quality guideline and maximum allowable concentration in agricultural soils, the total soil trace element concentrations at the studied sites are safe for agricultural crop production. Enrichment factor was high for Zn in soils around Lakes Ziway and Awassa, resulting in moderate to high transfer of Zn to the studied plants. A six step sequential extraction procedure on the soils revealed a relatively high mobility of Cd, Se and Mn. Strong association of most trace elements with the redox sensitive fraction and mineral lattice was also confirmed by partial redundancy analysis. TF (mg per kg dw plants/mg per kg dw soil) values based on the total (TF(total)) and mobile fractions (TF(mobile)) of soil trace element concentrations varied widely among elements and plant species, with the averaged TF(total) and TF(mobile) values ranging from 0.01-2 and 1-60, respectively. Considering the mobile fraction in soils should be available to plants, TF(mobile) values could reflect trace elements transfer to plants in the most realistic way. However, the present study indicates that TF(total) values also reflect the transfer of elements such as Mn, Cd and Se to plants more realistically than TF(mobile) values did.

Lawrence Transfer Factor: Transference of Specific Immune Memory by Dialyzable Leukocyte Extract from a CD8+ T Cell Line.

PubMed

Wang, Jason F; Park, Andrew J; Rendini, Tina; Levis, William R

2017-12-01

Lawrence transfer factor (TF) is defined as dialyzable leukocyte extract (DLE) that can transfer antigen-specific cell-mediated immunity from a person testing positive for the antigen in a delayed type hypersensitivity skin test manner to a person negative for the same antigen. A recent article by Myles et al1 has identified a DLE isolated from an established CD8+ T cell line capable of transferring antigen-specific immunity. The DLE contains a portion of the beta chain of the T cell receptor and additional nucleotide and protein factors that are being subjected to further modern biochemical analysis. After months of study that included interviews of TF physician-scientists, we conclude that an antigen-specific TF exists for most, if not all, antigens. By working from a CD8+ T cell line with modern biochemical technology, it should be possible to identify and patent products capable of treating infectious diseases, antigen-responsive cancers, and autoimmune disorders.

Characterization of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([Emim][Tf2N])∕TX-100∕cyclohexane ternary microemulsion: investigation of photoinduced electron transfer in this RTIL containing microemulsion.

PubMed

Sarkar, Souravi; Pramanik, Rajib; Ghatak, Chiranjib; Rao, Vishal Govind; Sarkar, Nilmoni

2011-02-21

In this study we have characterized a ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethyl- sulfonyl)imide containing ternary nonaqueous microemulsion ([Emim][Tf(2)N]∕∕TX-100∕cyclo- hexane). The phase behavior and dynamic light scattering study show that the [Emim][Tf(2)N]∕TX-100∕cyclohexane three component system can form microemulsion with [Emim][Tf(2)N] as polar core at suitable condition. We have investigated photoinduced electron transfer (PET) using dimethyl aniline as electron donor and several Coumarin dyes as electron acceptor molecules at two different R values (R = [ionic liquid]∕[surfactant]) to observe how the dynamics of the PET rate is affected in this type of confined microenvironment compared to that of the PET dynamics in neat ionic liquid and other pure solvent media. The plot of observed k(q) values with the free energy change (ΔG(0)) for electron transfer reaction shows an apparent inversion in the observed rate as predicted by the Marcus theory.

Novel Antitransferrin Receptor Antibodies Improve the Blood-Brain Barrier Crossing Efficacy of Immunoliposomes.

PubMed

Gregori, Maria; Orlando, Antonina; Re, Francesca; Sesana, Silvia; Nardo, Luca; Salerno, Domenico; Mantegazza, Francesco; Salvati, Elisa; Zito, Andrea; Malavasi, Fabio; Masserini, Massimo; Cazzaniga, Emanuela

2016-01-01

Surface functionalization with antitransferrin receptor (TfR) mAbs has been suggested as the strategy to enhance the transfer of nanoparticles (NPs) across the blood-brain barrier (BBB) and to carry nonpermeant drugs from the blood into the brain. However, the efficiency of BBB crossing is currently too poor to be used in vivo. In the present investigation, we compared 6 different murine mAbs specific for different epitopes of the human TfR to identify the best performing one for the functionalization of NPs. For this purpose, we compared the ability of mAbs to cross an in vitro BBB model made of human brain capillary endothelial cells (hCMEC/D3). Liposomes functionalized with the best performing mAb (MYBE/4C1) were uptaken, crossed the BBB in vitro, and facilitated the BBB in vitro passage of doxorubicin, an anticancer drug, 3.9 folds more than liposomes functionalized with a nonspecific IgG, as assessed by confocal microscopy, radiochemical techniques, and fluorescence, and did not modify the cell monolayer structural or functional properties. These results show that MYBE/4C1 antihuman TfR mAb is a powerful resource for the enhancement of BBB crossing of NPs and is therefore potentially useful in the treatment of neurologic diseases and disorders including brain carcinomas. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Fabrication of transferrin functionalized gold nanoclusters/graphene oxide nanocomposite for turn-on near-infrared fluorescent bioimaging of cancer cells and small animals.

PubMed

Wang, Yong; Chen, Jia-Tong; Yan, Xiu-Ping

2013-02-19

Transferrin (Tf)-functionalized gold nanoclusters (Tf-AuNCs)/graphene oxide (GO) nanocomposite (Tf-AuNCs/GO) was fabricated as a turn-on near-infrared (NIR) fluorescent probe for bioimaging cancer cells and small animals. A one-step approach was developed to prepare Tf-AuNCs via a biomineralization process with Tf as the template. Tf acted not only as a stabilizer and a reducer but also as a functional ligand for targeting the transferrin receptor (TfR). The prepared Tf-AuNCs gave intense NIR fluorescence that can avoid interference from biological media such as tissue autofluorescence and scattering light. The assembly of Tf-AuNCs and GO gave the Tf-AuNCs/GO nanocomposite, a turn-on NIR fluorescent probe with negligible background fluorescence due to the super fluorescence quenching property of GO. The NIR fluorescence of the Tf-AuNCs/GO nanocomposite was effectively restored in the presence of TfR, due to the specific interaction between Tf and TfR and the competition of TfR with the GO for the Tf in Tf-AuNCs/GO composite. The developed turn-on NIR fluorescence probe offered excellent water solubility, stability, and biocompatibility, and exhibited high specificity to TfR with negligible cytotoxicity. The probe was successfully applied for turn-on fluorescent bioimaging of cancer cells and small animals.

Nanorods on surface of GaN-based thin-film LEDs deposited by post-annealing after photo-assisted chemical etching

NASA Astrophysics Data System (ADS)

Chen, Lung-Chien; Lin, Wun-Wei; Liu, Te-Yu

2017-01-01

This study investigates the optoelectronic characteristics of gallium nitride (GaN)-based thin-film light-emitting diodes (TF-LEDs) that are formed by a two-step transfer process that involves wet etching and post-annealing. In the two-step transfer process, GaN LEDs were stripped from sapphire substrates by the laser lift-off (LLO) method using a KrF laser and then transferred onto ceramic substrates. Ga-K nanorods were formed on the surface of the GaN-based TF-LEDs following photo-assisted chemical etching and photo-enhanced post-annealing at 100 °C for 1 min. As a result, the light output power of GaN-based TF-LEDs with wet etching and post-annealing was over 72% more than that of LEDs that did not undergo these treatments.

Properties of thermospheric gravity waves on earth, Venus and Mars

NASA Technical Reports Server (NTRS)

Mayr, H. G.; Harris, I.; Pesnell, W. D.

1992-01-01

A spectral model with spherical harmonics and Fourier components that can simulate atmospheric perturbations in the global geometry of a multiconstituent atmosphere is presented. The boundaries are the planetary surface where the transport velocities vanish and the exobase where molecular heat conduction and viscosity dominate. The time consuming integration of the conservation equations is reduced to computing the transfer function (TF) which describes the dynamic properties of the medium divorced from the complexities in the temporal and horizontal variations of the excitation source. Given the TF, the atmospheric response to a chosen source distribution is then obtained in short order. Theoretical studies are presented to illuminate some properties of gravity waves on earth, Venus and Mars.

Exploring lateral genetic transfer among microbial genomes using TF-IDF.

PubMed

Cong, Yingnan; Chan, Yao-Ban; Ragan, Mark A

2016-07-25

Many microbes can acquire genetic material from their environment and incorporate it into their genome, a process known as lateral genetic transfer (LGT). Computational approaches have been developed to detect genomic regions of lateral origin, but typically lack sensitivity, ability to distinguish donor from recipient, and scalability to very large datasets. To address these issues we have introduced an alignment-free method based on ideas from document analysis, term frequency-inverse document frequency (TF-IDF). Here we examine the performance of TF-IDF on three empirical datasets: 27 genomes of Escherichia coli and Shigella, 110 genomes of enteric bacteria, and 143 genomes across 12 bacterial and three archaeal phyla. We investigate the effect of k-mer size, gap size and delineation of groups on the inference of genomic regions of lateral origin, finding an interplay among these parameters and sequence divergence. Because TF-IDF identifies donor groups and delineates regions of lateral origin within recipient genomes, aggregating these regions by gene enables us to explore, for the first time, the mosaic nature of lateral genes including the multiplicity of biological sources, ancestry of transfer and over-writing by subsequent transfers. We carry out Gene Ontology enrichment tests to investigate which biological processes are potentially affected by LGT.

Accumulation and transfer of 137Cs and 90Sr in the plants of the forest ecosystem near the Ignalina Nuclear Power Plant.

PubMed

Lukšienė, B; Marčiulionienė, D; Gudelienė, I; Schönhofer, F

2013-02-01

The radioecological state of the forest ecosystem in the vicinity of the Ignalina Power Plant prior to decommissioning was analysed with specific emphasis on (137)Cs and (90)Sr activity concentrations in plant species growing in two reference sampling sites (Tilze and Grikiniskes). In the period of 1996-2008 the mean contamination of plants with (137)Cs was from 45 to 119 Bq/kg and with (90)Sr - from 3 to 42 Bq/kg. Measured (137)Cs TF values for soil-root transfer mainly ranged between 1.0-1.4, except for Calamagrostis arundinacea which had a TF value of 0.1. On average, the (137)Cs TF value from root to shoot was 1.7 fold higher than for soil to root transfer. (90)Sr TF values (soil-root) were in the range of 1.2-1.8 but for Calluna vulgaris it was 0.2. The mean root to shoot TF value for (90)Sr was 7.7 fold higher. These results indicate the higher (90)Sr bioavailability than that of (137)Cs in the forested area. The Grikiniskes reference site is located nearby the Ignalina NPP, specifically the heated water outlet channel, which results in altered microclimatic conditions. These specific microclimatic conditions result in relationships between (137)Cs TF (soil-root) values and pH, moisture and organic matter content in the soil at Grikiniskes which appear to be different to those at the Tilze reference sampling site. Copyright © 2012 Elsevier Ltd. All rights reserved.

Nanorods on surface of GaN-based thin-film LEDs deposited by post-annealing after photo-assisted chemical etching.

PubMed

Chen, Lung-Chien; Lin, Wun-Wei; Liu, Te-Yu

2017-12-01

This study investigates the optoelectronic characteristics of gallium nitride (GaN)-based thin-film light-emitting diodes (TF-LEDs) that are formed by a two-step transfer process that involves wet etching and post-annealing. In the two-step transfer process, GaN LEDs were stripped from sapphire substrates by the laser lift-off (LLO) method using a KrF laser and then transferred onto ceramic substrates. Ga-K nanorods were formed on the surface of the GaN-based TF-LEDs following photo-assisted chemical etching and photo-enhanced post-annealing at 100 °C for 1 min. As a result, the light output power of GaN-based TF-LEDs with wet etching and post-annealing was over 72% more than that of LEDs that did not undergo these treatments.

Soil-to-cassava transfer of naturally occurring radionuclides from communities along Ghana's oil and gas rich Tano Basin.

PubMed

Doyi, Israel Nutifafa Yawo; Essumang, David Kofi; Agyapong, Asare Kwaku; Asumadu-Sarkodie, Samuel

2018-02-01

Soil-to-plant transfer factor (TF) is widely used to assess the impact of soil radioactivity on agricultural crops. The root crop cassava (Manihot esculenta) provides 30%-50% of the calories consumed in Sub-Saharan Africa and is widely used in South America. γ-ray analysis was used to measure activity concentrations of 238 U, 232 Th, and 40 K in cassava root and soil. The TF values for 238 U, 232 Th, and 40 K were in the range 0.06-0.12, 0.01-0.10 and 0.04-0.28 respectively. The median transfer factors were 0.10 ( 238 U), 0.04 ( 232 Th) and 0.08 ( 40 K). For 238 U and 232 Th, the highest TF values were 0.12 and 0.10 respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

Root uptake of 137Cs by natural and semi-natural grasses as a function of texture and moisture of soils.

PubMed

Grytsyuk, N; Arapis, G; Davydchuk, V

2006-01-01

This work studies the dependence of 137Cs root uptake on the structure of landscape, especially on texture and moisture of soils, under natural conditions, on abandoned radiopolluted lands in Northern Ukraine. Researches were carried out on a wide range of landscape conditions, at various levels of 137Cs contamination (from 20 up to 5000 kBqm(-2)), with different types of soils (approx. 20 soil varieties), which differ in texture, granulometric composition, degrees of gleyization and water regime, and anthropogenic transformation. The results showed that transfer factor (TF) values of 137Cs differ 50 times for the natural grassy coenoses and 8 times for the semi-natural ones. The lowest 137Cs TF values were measured in the herbages of dry meadows at automorphous loamy soils, while the highest were observed in wetland meadows at organic soils. Finally, the correlation between 137Cs TF values and granulometric composition of soil was determined for both automorphic and hydromorphic mineral soils.

Transferrin-mediated fullerenes nanoparticles as Fe(2+)-dependent drug vehicles for synergistic anti-tumor efficacy.

PubMed

Zhang, Huijuan; Hou, Lin; Jiao, Xiaojing; Ji, Yandan; Zhu, Xiali; Zhang, Zhenzhong

2015-01-01

Artesunate (AS) is an iron-dependent drug, which has been used extensively as anti-malarial drugs worldwide with no obvious side effects. Recently, studies have shown that AS also possess profound cytotoxicity against tumor cells. However, simultaneous delivery of hydrophobic AS and Fe(2+) into tumor cells remains a major challenge. Herein, we report a new kind of active-targeting preparations which could not only specially target to tumor cells but also synchronously transfer AS and irons into tumor tissue. In this study, hyaluronic acid (HA) was grafted onto fullerene to get a water-soluble biomaterial (HA-C60) with excellent biocompatibility, and then combined with transferrin (Tf) to obtain a multi-functional drug delivery system (HA-C60-Tf) with significant tumor-targeting efficacy and powerful photodynamic therapy capacity. Finally, AS was adsorbed on HA-C60-Tf with a high loading efficacy of 162.4% (weight ratio of AS: HA-C60-Tf). Compared with free AS, remarkably enhanced antitumor efficacy of AS-loaded HA-C60-Tf nanoparticles was realized both in a cultured MCF-7 cells in vitro and in a tumor-bearing murine model in vivo, due to increased intracellular accumulation of AS in tumor and activated mechanism by co-delivery of Tf and AS analogs. Furthermore, with laser irradiation in vivo, the relative tumor volume (V/V0) of HA-C60-Tf/AS declined by half, from 1.72 ± 0.12 to 0.84 ± 0.07, suggesting a new way with multi-mechanism for tumor treatment was developed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fast Fourier Tranformation Algorithms: Experiments with Microcomputers.

DTIC Science & Technology

1986-07-01

is, functions a with a known, discrete Fourier transform A Such functions are given fn [I]. The functions, TF1 , TF2, and TF3, were used and are...the IBM PC, all with TF1 (Eq. 1). ’The compilers provided options to improve performance, as noted, for which a penalty in compiling time has to be...BASIC only. Series I In this series the procedures were as follows: (i) Calculate the input values for TF1 of ar and the modulus Iar (which is

Forecasting models for flow and total dissolved solids in Karoun river-Iran

NASA Astrophysics Data System (ADS)

Salmani, Mohammad Hassan; Salmani Jajaei, Efat

2016-04-01

Water quality is one of the most important factors contributing to a healthy life. From the water quality management point of view, TDS (total dissolved solids) is the most important factor and many water developing plans have been implemented in recognition of this factor. However, these plans have not been perfect and very successful in overcoming the poor water quality problem, so there are a good volume of related studies in the literature. We study TDS and the water flow of the Karoun river in southwest Iran. We collected the necessary time series data from the Harmaleh station located in the river. We present two Univariate Seasonal Autoregressive Integrated Movement Average (ARIMA) models to forecast TDS and water flow in this river. Then, we build up a Transfer Function (TF) model to formulate the TDS as a function of water flow volume. A performance comparison between the Seasonal ARIMA and the TF models are presented.

Plant uptake of elements in soil and pore water: field observations versus model assumptions.

PubMed

Raguž, Veronika; Jarsjö, Jerker; Grolander, Sara; Lindborg, Regina; Avila, Rodolfo

2013-09-15

Contaminant concentrations in various edible plant parts transfer hazardous substances from polluted areas to animals and humans. Thus, the accurate prediction of plant uptake of elements is of significant importance. The processes involved contain many interacting factors and are, as such, complex. In contrast, the most common way to currently quantify element transfer from soils into plants is relatively simple, using an empirical soil-to-plant transfer factor (TF). This practice is based on theoretical assumptions that have been previously shown to not generally be valid. Using field data on concentrations of 61 basic elements in spring barley, soil and pore water at four agricultural sites in mid-eastern Sweden, we quantify element-specific TFs. Our aim is to investigate to which extent observed element-specific uptake is consistent with TF model assumptions and to which extent TF's can be used to predict observed differences in concentrations between different plant parts (root, stem and ear). Results show that for most elements, plant-ear concentrations are not linearly related to bulk soil concentrations, which is congruent with previous studies. This behaviour violates a basic TF model assumption of linearity. However, substantially better linear correlations are found when weighted average element concentrations in whole plants are used for TF estimation. The highest number of linearly-behaving elements was found when relating average plant concentrations to soil pore-water concentrations. In contrast to other elements, essential elements (micronutrients and macronutrients) exhibited relatively small differences in concentration between different plant parts. Generally, the TF model was shown to work reasonably well for micronutrients, whereas it did not for macronutrients. The results also suggest that plant uptake of elements from sources other than the soil compartment (e.g. from air) may be non-negligible. Copyright © 2013 Elsevier Ltd. All rights reserved.

Encapsulate-and-peel: fabricating carbon nanotube CMOS integrated circuits in a flexible ultra-thin plastic film.

PubMed

Gao, Pingqi; Zhang, Qing

2014-02-14

Fabrication of single-walled carbon nanotube thin film (SWNT-TF) based integrated circuits (ICs) on soft substrates has been challenging due to several processing-related obstacles, such as printed/transferred SWNT-TF pattern and electrode alignment, electrical pad/channel material/dielectric layer flatness, adherence of the circuits onto the soft substrates etc. Here, we report a new approach that circumvents these challenges by encapsulating pre-formed SWNT-TF-ICs on hard substrates into polyimide (PI) and peeling them off to form flexible ICs on a large scale. The flexible SWNT-TF-ICs show promising performance comparable to those circuits formed on hard substrates. The flexible p- and n-type SWNT-TF transistors have an average mobility of around 60 cm(2) V(-1) s(-1), a subthreshold slope as low as 150 mV dec(-1), operating gate voltages less than 2 V, on/off ratios larger than 10(4) and a switching speed of several kilohertz. The post-transfer technique described here is not only a simple and cost-effective pathway to realize scalable flexible ICs, but also a feasible method to fabricate flexible displays, sensors and solar cells etc.

Improved in vivo gene transfer into tumor tissue by stabilization of pseudodendritic oligoethylenimine-based polyplexes.

PubMed

Russ, Verena; Fröhlich, Thomas; Li, Yunqiu; Halama, Anna; Ogris, Manfred; Wagner, Ernst

2010-02-01

HD O is a low molecular weight pseudodendrimer containing oligoethylenimine and degradable hexanediol diacrylate diesters. DNA polyplexes display encouraging gene transfer efficiency in vitro and in vivo but also a limited stability under physiological conditions. This limitation must be overcome for further development into more sophisticated formulations. HD O polyplexes were laterally stabilized by crosslinking surface amines via bifunctional crosslinkers, bioreducible dithiobis(succimidyl propionate) (DSP) or the nonreducible analog disuccinimidyl suberate (DSS). Optionally, in a subsequent step, the targeting ligand transferrin (Tf) was attached to DSP-linked HD O polyplexes via Schiff base formation between HD O amino groups and Tf aldehyde groups, which were introduced into Tf by periodate oxidation of the glycosylation sites. Crosslinked DNA polyplexes showed an increased stability against exchange reaction by salt or heparin. Disulfide bond containing DSP-linked polyplexes were susceptible to reducing conditions. These polyplexes displayed the highest gene expression levels in vitro and in vivo (upon intratumoral application in mice), and these were significantly elevated and prolonged over standard or DSS-stabilized HD O formulations. DSP-stabilized HD O polyplexes with or without Tf coating were well-tolerated after intravenous application. High gene expression levels were found in tumor tissue, with negligible gene expression in any other organ. Lateral stabilization of HD O polyplexes with DSP crosslinker enhanced gene transfer efficacy and was essential for the incorporation of a ligand (Tf) into a stable particle formulation.

Characterization of the interaction between diferric transferrin and transferrin receptor 2 by functional assays and atomic force microscopy*

PubMed Central

Ikuta, Katsuya; Yersin, Alexandre; Ikai, Atsushi; Aisen, Philip; Kohgo, Yutaka

2010-01-01

Transferrin receptor (TfR2), a homologue of classical transferrin receptor 1 (TfR1), is found in two isoforms, α and β. Like TfR1, TfR2α is a type II membrane protein, but the β form lacks transmembrane portions and therefore is likely to be an intracellular protein. To investigate the functional properties of TfR2α we expressed the protein with FLAG-tagging in transferrin receptor-deficient Chinese hamster ovary cells. The association constant for binding of diferric transferrin (Tf) to TfR2α is 5.6 × 106 M−1, which is about 50 times lower than that of TfR1, with correspondingly reduced rates of iron uptake. Evidence for Tf internalization and recycling via TfR2α without degradation, as in the TfR1 pathway, was also found. The interaction of TfR2α with Tf was further investigated using atomic force microscopy (AFM), a powerful tool for investigation of the interaction between ligand and receptor at the single molecule level on the living cell surface. Dynamic force microscopy reveals a difference in the interactions of Tf with TfR2α and TfR1, with Tf-TfR1 unbinding characterized by 2 energy barriers, while only one is present for Tf-TfR2. We speculate that this difference may reflect Tf binding to TfR2α by a single lobe, whereas two lobes of Tf participate in binding to TfR1. The difference in the binding properties of Tf to TfR1 and TfR2α may help account for the different physiological roles of the two receptors. PMID:20096706

Can we predict uranium bioavailability based on soil parameters? Part 2: soil solution uranium concentration is not a good bioavailability index.

PubMed

Vandenhove, H; Van Hees, M; Wannijn, J; Wouters, K; Wang, L

2007-01-01

The present study aimed to quantify the influence of soil parameters on uranium uptake by ryegrass. Ryegrass was established on eighteen distinct soils, spiked with (238)U. Uranium soil-to-plant transfer factors (TF) ranged from 0.0003 to 0.0340kgkg(-1). There was no significant relation between the U soil-to-plant transfer (or total U uptake or flux) and the uranium concentration in the soil solution or any other soil factor measured, nor with the U recovered following selective soil extractions. Multiple linear regression analysis resulted in a significant though complex model explaining up to 99% of variation in TF. The influence of uranium speciation on uranium uptake observed was featured: UO(2)(+2), uranyl carbonate complexes and UO(2)PO(4)(-) seem the U species being preferentially taken up by the roots and transferred to the shoots. Improved correlations were obtained when relating the uranium TF with the summed soil solution concentrations of mentioned uranium species.

Paddy-field contamination with 134Cs and 137Cs due to Fukushima Dai-ichi Nuclear Power Plant accident and soil-to-rice transfer coefficients.

PubMed

Endo, Satoru; Kajimoto, Tsuyoshi; Shizuma, Kiyoshi

2013-02-01

The transfer coefficient (TF) from soil to rice plants of (134)Cs and (137)Cs in the form of radioactive deposition from the Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident in March 2011 was investigated in three rice paddy fields in Minami-Soma City. Rice crops were planted in the following May and harvested at the end of September. Soil cores of 30-cm depth were sampled from rice-planted paddy fields to measure (134)Cs and (137)Cs radioactivity at 5-cm intervals. (134)Cs and (137)Cs radioactivity was also measured in rice ears (rice with chaff), straws and roots. The rice ears were subdivided into chaff, brown rice, polished rice and rice bran, and the (134)Cs and (137)Cs radioactivity concentration of each plant part was measured to calculate the respective TF from the soil. The TF of roots was highest at 0.48 ± 0.10 in the field where the (40)K concentration in the soil core was relatively low, in comparison with TF values of 0.31 and 0.38 in other fields. Similar trends could be found for the TF of whole rice plants, excluding roots. The TF of rice ears was relatively low at 0.019-0.026. The TF of chaff, rice bran, brown rice and polished rice was estimated to be 0.049, 0.10-0.16, 0.013-0.017 and 0.005-0.013, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF.

PubMed

Cong, Yingnan; Chan, Yao-Ban; Ragan, Mark A

2016-07-25

Lateral genetic transfer (LGT) plays an important role in the evolution of microbes. Existing computational methods for detecting genomic regions of putative lateral origin scale poorly to large data. Here, we propose a novel method based on TF-IDF (Term Frequency-Inverse Document Frequency) statistics to detect not only regions of lateral origin, but also their origin and direction of transfer, in sets of hierarchically structured nucleotide or protein sequences. This approach is based on the frequency distributions of k-mers in the sequences. If a set of contiguous k-mers appears sufficiently more frequently in another phyletic group than in its own, we infer that they have been transferred from the first group to the second. We performed rigorous tests of TF-IDF using simulated and empirical datasets. With the simulated data, we tested our method under different parameter settings for sequence length, substitution rate between and within groups and post-LGT, deletion rate, length of transferred region and k size, and found that we can detect LGT events with high precision and recall. Our method performs better than an established method, ALFY, which has high recall but low precision. Our method is efficient, with runtime increasing approximately linearly with sequence length.

Enhancing immune responses to inactivated porcine parvovirus oil emulsion vaccine by co-inoculating porcine transfer factor in mice.

PubMed

Wang, Rui-ning; Wang, Ya-bin; Geng, Jing-wei; Guo, Dong-hui; Liu, Fang; Chen, Hong-ying; Zhang, Hong-ying; Cui, Bao-an; Wei, Zhan-yong

2012-07-27

Inactivated porcine parvovirus (PPV) vaccines are available commercially and widely used in the breeding herds. However, inactivated PPV vaccines have deficiencies in induction of specific cellular immune response. Transfer factor (TF) is a material that obtained from the leukocytes, and is a novel immune-stimulatory reagent that as a modulator of the immune system. In this study, the immunogenicity of PPV oil emulsion vaccine and the immuno-regulatory activities of TF were investigated. The inactivated PPV oil emulsion vaccines with or without TF were inoculated into BALB/c mice by subcutaneous injection. Then humoral and cellular immune responses were evaluated by indirect enzyme-linked immunosorbent assays (ELISA), fluorescence-activated cell sorter analyses (FACS). The results showed that the PPV specific immune responses could be evoked in mice by inoculating with PPV oil emulsion vaccine alone or by co-inoculation with TF. The cellular immune response levels in the co-inoculation groups were higher than those groups receiving the PPV oil emulsion vaccine alone, with the phenomena of higher level of IFN-γ, a little IL-6 and a trace of IL-4 in serum, and a vigorous T-cell response. However, there was no significant difference in antibody titers between TF synergy inactivated vaccine and the inactivated vaccine group (P>0.05). In conclusion, these results suggest that TF possess better cellular immune-enhancing capability and would be exploited into an effective immune-adjuvant for inactivated vaccines. Copyright © 2012 Elsevier Ltd. All rights reserved.

The removal of RNA primers from DNA synthesized by the reverse transcriptase of the retrotransposon Tf1 is stimulated by Tf1 integrase.

PubMed

Herzig, Eytan; Voronin, Nickolay; Hizi, Amnon

2012-06-01

The Tf1 retrotransposon represents a group of long terminal repeat retroelements that use an RNA self-primer for initiating reverse transcription while synthesizing the minus-sense DNA strand. Tf1 reverse transcriptase (RT) was found earlier to generate the self-primer in vitro. Here, we show that this RT can remove from the synthesized cDNA the entire self-primer as well as the complete polypurine tract (PPT) sequence (serving as a second primer for cDNA synthesis). However, these primer removals, mediated by the RNase H activity of Tf1 RT, are quite inefficient. Interestingly, the integrase of Tf1 stimulated the specific Tf1 RT-directed cleavage of both the self-primer and PPT, although there was no general enhancement of the RT's RNase H activity (and the integrase by itself is devoid of any primer cleavage). The RTs of two prototype retroviruses, murine leukemia virus and human immunodeficiency virus, showed only a partial and nonspecific cleavage of both Tf1-associated primers with no stimulation by Tf1 integrase. Mutagenesis of Tf1 integrase revealed that the complete Tf1 integrase protein (excluding its chromodomain) is required for stimulating the Tf1 RT primer removal activity. Nonetheless, a double mutant integrase that has lost its integration functions can still stimulate the RT's activity, though heat-inactivated integrase cannot enhance primer removals. These findings suggest that the enzymatic activity of Tf1 integrase is not essential for stimulating the RT-mediated primer removal, while the proper folding of this protein is obligatory for this function. These results highlight possible new functions of Tf1 integrase in the retrotransposon's reverse transcription process.

The Removal of RNA Primers from DNA Synthesized by the Reverse Transcriptase of the Retrotransposon Tf1 Is Stimulated by Tf1 Integrase

PubMed Central

Herzig, Eytan; Voronin, Nickolay

2012-01-01

The Tf1 retrotransposon represents a group of long terminal repeat retroelements that use an RNA self-primer for initiating reverse transcription while synthesizing the minus-sense DNA strand. Tf1 reverse transcriptase (RT) was found earlier to generate the self-primer in vitro. Here, we show that this RT can remove from the synthesized cDNA the entire self-primer as well as the complete polypurine tract (PPT) sequence (serving as a second primer for cDNA synthesis). However, these primer removals, mediated by the RNase H activity of Tf1 RT, are quite inefficient. Interestingly, the integrase of Tf1 stimulated the specific Tf1 RT-directed cleavage of both the self-primer and PPT, although there was no general enhancement of the RT's RNase H activity (and the integrase by itself is devoid of any primer cleavage). The RTs of two prototype retroviruses, murine leukemia virus and human immunodeficiency virus, showed only a partial and nonspecific cleavage of both Tf1-associated primers with no stimulation by Tf1 integrase. Mutagenesis of Tf1 integrase revealed that the complete Tf1 integrase protein (excluding its chromodomain) is required for stimulating the Tf1 RT primer removal activity. Nonetheless, a double mutant integrase that has lost its integration functions can still stimulate the RT's activity, though heat-inactivated integrase cannot enhance primer removals. These findings suggest that the enzymatic activity of Tf1 integrase is not essential for stimulating the RT-mediated primer removal, while the proper folding of this protein is obligatory for this function. These results highlight possible new functions of Tf1 integrase in the retrotransposon's reverse transcription process. PMID:22491446

Radiocaesium transfer from volcanic soils to Swiss chard, cabbage and sweet corn.

PubMed

Schuller, Paulina; Castillo, Alejandra; Voigt, Gabriele; Semioshkina, Natalia

2018-06-18

The root uptake of radiocaesium by different plant parts of Swiss chard (Beta vulgaris L. var. cicla), cabbage (Brassica oleracea L. var. capitata) and sweet corn (Zea mays L. var. saccharata) and the potential influence of K-fertilising on the transfer behaviour was studied in allophanic volcanic soils (umbric andosol and dystric fluvisol) in Chile under temperate climate and heavy rainfall conditions (∼2660 mm y -1 ) over several vegetation periods. The soils were spiked homogeneously to 0.20 m depth with 100 kBq 134 Cs m -2 and activity concentrations measured. The transfer factor (TF, on a dry mass basis) to Swiss chard had a clear exponential decrease within each crop year for both soil types, either K-fertilised or unfertilised. The highest values of the TFs to Swiss chard were at the beginning of the harvests, and the half-times of TF decrease ranged between 52 and 137 d for umbric andosol and between 40 and 164 d for dystric fluvisol. Over the five seasons there was no consistent ageing effect based on TF in either soil types for the three studied crops. The effect of 134 Cs foliar uptake by Swiss chard from resuspended soil was estimated to account for about 70% (external leaves) and 30% (internal leaves) increase in the TF for the K-unfertilised umbric andosol, and showed an ambiguous behaviour for the K-fertilised umbric andosol. Consequently foliar uptake does not explain the 370 and 500% increase of the TF to Swiss chard leaves determined during the third growing period in the umbric andosol without and with K-fertilisation, respectively. Therefore an uncertainty factor of 3-5 is recommended to be taken into account when using this parameter for dose calculations. The TF to Swiss chard was found to be higher than previously reported values. The TF to cabbage and sweet corn plant parts was found to be within the range of previously reported values. Normal K-fertilisation resulted in about 2.4-fold reduction in 134 Cs TF to Swiss chard, 2.3-fold to sweet corn and 3.0-fold to cabbage. Copyright © 2018 Elsevier Ltd. All rights reserved.

Workload, Performance, and Reliability of Digital Computing Systems.

DTIC Science & Technology

1980-12-01

maximized is then P()(tf, ...... , ad .[[. P(ts) h( tf1 ),) (0 42.33) Note that this problem is equivalent to minimazing the function En Jn ,l~~f,) (-X) 1...have been observed at times tf1 , after observing the system since tsl. Take, for instance, the case of the distribution obtained from the simplified...represented by a set of pairs [ts,, tf1 ] i 1 ...... n the maximum likelihood values of a,y,P are these values that maximize the function p(n)( tf1 -ts 1 . . ts

Uptake of 137Cs by Leafy Vegetables and Grains from Calcareous Soils

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

Robison, W; Hamilton, T; Conrado, C

2004-04-19

Cesium-137 was deposited on Bikini Island at Bikini Atoll in 1954 as a result of nuclear testing and has been transported and cycled in the ecosystem ever since. Atoll soils are of marine origin and are almost pure CaCO{sub 3} with high concentrations of organic matter in the top 40 cm. Data from previous experiments with mature fruit trees show very high transfer factors (TF's), [Bq g{sup -1} plant/ Bq g{sup -1} soil, both in dry weight] into fruits from atoll calcareous soil. These TF's are much higher than reported for continental, silica-based soils. In this report TF's for 5more » types of leafy vegetable crops and 2 types of grain crops are provided for use in predictive dose assessments and for comparison with other data from other investigators working with other types of soil in the IAEA CRP ''The Classification of Soil Systems on the Basis of Transfer Factors of Radionuclides from Soil to Reference Plants''. Transfer factors for plants grown on calcareous soil are again very high relative to clay-containing soils and range from 23 to 39 for grain crops and 21 to 113 for leafy vegetables. Results from these experiments, in this unique, high pH, high organic content, low potassium (K) soil, provide a boundary condition for models relating soil properties to TF.« less

Potential of Melastoma malabathricum as bio-accumulator for uranium and thorium from soil

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

Saat, Ahmad, E-mail: ahmad183@salam.uitm.edu.my; Faculty of Applied Sciences, Universiti Teknologi MARA, 40450 Shah Alam; Kamsani, Ain Shaqina

2015-04-29

Uranium and Thorium are naturally occuring radionuclides. However, due to anthropogenic activities in some locations their concentrations in the soils could be elevated. This study explores the potential of Melastoma malabathricum (locally known as ‘pokok senduduk’) as bio-accumulator of uranium and thorium from soils of three different study areas, namely former tin mining, industrial and residential/commercial areas in Peninsular Malaysia. The study found elevated concentrations of uranium and thorium in former tin mining soils as compared to natural abundance. However in industral and residential/commercial areas the concentrations are within the range of natural abundance. In terms of transfer factor (TF),more » in ex-mining areas TF > 1 for uranium in the leaf, stem and roots, indicating accumulation of uranium from soil. However for thorium TF < 1, indicating the occurence of transfer from soil to root, stem and leaf, but no accumulation. For other areas only transfer of uranium and thorium were observed. The results indicated the potential of Melastoma malabathricum to be used as bio-accumulatior of uranium, especially in areas of elevated concentration.« less

Molecular Screening Tools to Study Arabidopsis Transcription Factors

PubMed Central

Wehner, Nora; Weiste, Christoph; Dröge-Laser, Wolfgang

2011-01-01

In the model plant Arabidopsis thaliana, more than 2000 genes are estimated to encode transcription factors (TFs), which clearly emphasizes the importance of transcriptional control. Although genomic approaches have generated large TF open reading frame (ORF) collections, only a limited number of these genes is functionally characterized, yet. This review evaluates strategies and methods to identify TF functions. In particular, we focus on two recently developed TF screening platforms, which make use of publically available GATEWAY®-compatible ORF collections. (1) The Arabidopsis thaliana TF ORF over-Expression (AtTORF-Ex) library provides pooled collections of transgenic lines over-expressing HA-tagged TF genes, which are suited for screening approaches to define TF functions in stress defense and development. (2) A high-throughput microtiter plate based protoplast trans activation (PTA) system has been established to screen for TFs which are regulating a given promoter:Luciferase construct in planta. PMID:22645547

Kinetics of ATP hydrolysis catalyzed by isolated TF1 and reconstituted TF0F1 ATPase.

PubMed

Rögner, M; Gräber, P

1986-09-01

The rate of ATP hydrolysis catalyzed by isolated TF1 and reconstituted TF0F1 was measured as a function of the ATP concentration in the presence of inhibitors [ADP, Pi and 3'-O-(1-naphthoyl)ATP]. ATP hydrolysis can be described by Michaelis-Menten kinetics with Km(TF1) = 390 microM and Km (TF0F1) = 180 microM. The inhibition constants are for ADP Ki(TF1) = 20 microM and Ki(TF0F1) = 100 microM, for 3'-O-(1-naphthoyl)ATP Ki(TF1) = 150 microM and Ki(TF0F1) = 3 microM, and for Pi Ki(TF1) = 60 mM. From these results it is concluded that upon binding of TF0 to TF1 the mechanism of ATP hydrolysis catalyzed by TF1 is not changed qualitatively; however, the kinetic constants differ quantitatively.

The nuclear orphan receptors COUP-TF and ARP-1 positively regulate the trout estrogen receptor gene through enhancing autoregulation.

PubMed Central

Lazennec, G; Kern, L; Valotaire, Y; Salbert, G

1997-01-01

The rainbow trout estrogen receptor (rtER) is a positively autoregulated gene in liver cells. In a previous report, we showed that upregulation is mediated by an estrogen response element (ERE) located in the proximal promoter of the gene and that a half binding site for nuclear receptors (5'-TGACCT-3') located 15 bp upstream of the ERE is involved in the magnitude of the estrogen response. We now report that the human orphan receptor COUP-TF and a COUP-TF-like protein from trout liver are able to bind to the consensus half-site. When cotransfected with the rtER gene proximal promoter, COUP-TF had no regulatory functions on its own. Interestingly, COUP-TF enhanced rtER transactivation properties in the presence of estradiol in a dose-dependent manner when cotransfected with the rtER gene promoter. Unliganded retinoid receptor heterodimers had the same helper function as COUP-TF in the presence of estradiol but were switched to repressors when the ligand all-trans-retinoic acid was added. Mutation of the consensus half-site only slightly reduced COUP-TF helper function, suggesting that it actually results from a complex mechanism that probably involves both DNA binding of COUP-TF to the promoter and protein-protein interaction with another transcription factor bound to the promoter. Nevertheless, a DNA-binding-defective mutant of COUP-TF was also defective in ER helper function. Competition footprinting analysis suggested that COUP-TF actually establishes contacts with the consensus upstream half-site and the downstream ERE half-site that would form a DR-24-like response element. Interaction of COUP-TF with the DR-24 element was confirmed in footprinting assays by using nuclear extracts from Saccharomyces cerevisiae expressing COUP-TF. Finally, interaction of COUP-TF with mutants of the rtER gene promoter showed that COUP-TF recognizes the ERE when the upstream half-site is mutated. These data show that COUP-TF may activate transcription through interaction with other nuclear receptors. This cross-talk between liganded nuclear receptors and orphan receptors is likely to modulate the spectrum of action of a particular ligand-receptor complex and may participate in the cell-type specificity of the ligand effect. PMID:9271383

Systemic p53 gene therapy of cancer with immunolipoplexes targeted by anti-transferrin receptor scFv.

PubMed Central

Xu, L.; Tang, W. H.; Huang, C. C.; Alexander, W.; Xiang, L. M.; Pirollo, K. F.; Rait, A.; Chang, E. H.

2001-01-01

BACKGROUND: A long-standing goal in genetic therapy for cancer is a systemic gene delivery system that selectively targets tumor cells, including metastases. Here we describe a novel cationic immunolipoplex system that shows high in vivo gene transfer efficiency and anti- tumor efficacy when used for systemic p53 gene therapy of cancer. MATERIALS AND METHODS: A cationic immunolipoplex incorporating a biosynthetically lipid-tagged, anti-transferrin receptor single-chain antibody (TfRscFv), was designed to target tumor cells both in vitro and in vivo. A human breast cancer metastasis model was employed to evaluate the in vivo efficacy of systemically administered, TfRscFv-immunolipoplex-mediated, p53 gene therapy in combination with docetaxel. RESULTS: The TfRscFv-targeting cationic immunolipoplex had a size of 60-100 nm, showed enhanced tumor cell binding, and improved targeted gene delivery and transfection efficiencies, both in vitro and in vivo. The p53 tumor suppressor gene was not only systemically delivered by the immunolipoplex to human tumor xenografts in nude mice but also functionally expressed. In the nude mouse breast cancer metastasis model, the combination of the p53 gene delivered by the systemic administration of the TfRscFv-immunolipoplex and docetaxel resulted in significantly improved efficacy with prolonged survival. CONCLUSIONS: This is the first report using scFv-targeting immunolipoplexes for systemic gene therapy. The TfRscFv has a number of advantages over the transferrin (Tf) molecule itself: (1) scFv has a much smaller size than Tf producing a smaller immunolipoplex giving better penetration into solid tumors; (2) unlike Tf, the scFv is a recombinant protein, not a blood product; (3) large scale production and strict quality control of the recombinant scFv, as well as scFv-immunolipoplex, are feasible. The sensitization of tumors to chemotherapy by this tumor-targeted and efficient p53 gene delivery method could lower the effective dose of the drug, correspondingly lessening the severe side effects, while decreasing the possibility of recurrence. Moreover, this approach is applicable to both primary and recurrent tumors, and more significantly, metastatic disease. The TfRscFv-targeting of cationic immunolipoplexes is a promising method of tumor targeted gene delivery that can be used for systemic gene therapy of cancer with the potential to critically impact the clinical management of cancer. PMID:11713371

Effect of viscosity on steady-state voltammetry and scanning electrochemical microscopy in room temperature ionic liquids.

PubMed

Lovelock, Kevin R J; Cowling, Frances N; Taylor, Alasdair W; Licence, Peter; Walsh, Darren A

2010-04-08

The electrochemical properties of a series of room temperature ionic liquids (RTILs) were studied using voltammetric methods and scanning electrochemical microscopy (SECM). The RTILs consisted of 1-alkyl-3-methylimidazolium cations, [C(n)C(1)Im](+), and either bis[(trifluoromethyl)sulfonyl]imide anions, [Tf(2)N](-), or hexafluorophosphate anions, [PF(6)](-). The effect of RTIL viscosity on mass transfer dynamics within each RTIL was studied electrochemically using ferrocene as a redox probe. In the case of the [C(n)C(1)Im][Tf(2)N] RTILs, the viscosity was altered by changing the alkyl chain length. [C(4)C(1)Im][PF(6)] was used for comparison as its viscosity is significantly higher than that of the [C(n)C(1)Im][Tf(2)N] RTILs. The RTIL viscosity affected the ability to record steady-state voltammograms at ultramicroelectrodes (UMEs). For example, it was possible to record steady-state voltammograms at scan rates up to 10 mV s(-1) in [C(2)C(1)Im][Tf(2)N] using 1.5 mum radius disk UMEs, but non-steady-state behavior was observed at 50 mV s(-1). However, at 12.5 microm radius UMEs, steady-state voltammetry was only observed at 1 mV s(-1) in [C(2)C(1)Im][Tf(2)N]. The RTIL viscosity also affected the ability to record SECM feedback approach curves that agreed with conventional SECM theory. In the most viscous [C(n)C(1)Im][Tf(2)N] RTILs, feedback approach curves agreed with conventional theory only when very slow tip approach speeds were used (0.1 microm s(-1)). These observations were interpreted using the Peclet number, which describes the relative contributions of convective and diffusive mass transfer to the tip surface. By recording feedback approach curves in each RTIL at a range of tip approach speeds, we describe the experimental conditions that must be met to perform SECM in imidazolium-based RTILs. The rate of heterogeneous electron transfer across the RTIL/electrode interface was also studied using SECM and the standard heterogeneous electron transfer rate constant, k(0), for ferrocene oxidation recorded in each RTIL was higher than that determined previously using voltammetric methods.

The Influence of Team Functioning and Workload on Sustainability of Trauma-Focused Evidence-Based Psychotherapies.

PubMed

Mohr, David C; Rosen, Craig S; Schnurr, Paula P; Orazem, Robert J; Noorbaloochi, Siamak; Clothier, Barbara A; Eftekhari, Afsoon; Bernardy, Nancy C; Chard, Kathleen M; Crowley, Jill J; Cook, Joan M; Kehle-Forbes, Shannon M; Ruzek, Josef I; Sayer, Nina A

2018-05-25

It has been over a decade since the U.S. Department of Veterans Affairs (VA) began formal dissemination and implementation of two trauma-focused evidence-based psychotherapies (TF-EBPs). The objective of this study was to examine the sustainability of the TF-EBPs and determine whether team functioning and workload were associated with TF-EBP sustainability. This observational study used VA administrative data for 6,251 patients with posttraumatic stress disorder (PTSD) and surveys from 78 providers from 10 purposefully selected PTSD clinical teams located in nine VA medical centers. The outcome was sustainability of TF-EBPs, which was based on British National Health System Sustainability Index scores (possible scores range from 0 to 100.90). Primary predictors included team functioning, workload, and TB-EBP reach to patients with PTSD. Multiple linear regression models were used to examine the influence of team functioning and workload on TF-EBP sustainability after adjustment for covariates that were significantly associated with sustainability. Sustainability Index scores ranged from 53.15 to 100.90 across the 10 teams. Regression models showed that after adjustment for patient and facility characteristics, team functioning was positively associated (B=9.16, p<.001) and workload was negatively associated (B=-.28, p<.05) with TF-EBP sustainability. There was considerable variation across teams in TF-EBP sustainability. The contribution of team functioning and workload to the sustainability of evidence-based mental health care warrants further study.

Using the international classification of functioning to examine the impact of trigger finger.

PubMed

Langer, Danit; Maeir, Adina; Michailevich, Michael; Applebaum, Yael; Luria, Shai

2016-12-01

To evaluate the impact of trigger finger (TF) on hand motor function, activity and participation (A&P) and quality of life (QOL), and to evaluate the association between personal factors (age and gender, disease severity) and body functions (dexterity and strength) with A&P and QOL in patients with TF. Sixty-six patients with TF (study group) and 66 healthy volunteers (control group) participated in the study. TF symptoms were graded using the Quinnell classification. A&P was evaluated using the Disabilities of Arm Shoulder and Hand questionnaire and the QOL using the World Health Organization Quality of Life questionnaire. Dexterity was evaluated using the Functional Dexterity Test and the Purdue Pegboard Test; hand strength was evaluated using the Jamar Dynamometer and Pinch Gauge. The comparisons between the study and control groups revealed significant differences in all measures. The study group reported lower perceived QOL, A&P and reduced hand strength and dexterity. Hierarchical regression analyses revealed that (a) the severity of TF contributed significantly to the explained variance of QOL, while demographics and hand functioning did not; (b) demographics, TF severity and hand function all contributed significantly to the explained variance of A&P. The findings of the study point to the importance of addressing the functional implications and QOL of individuals with TF. Implications for Rehabilitation Although trigger finger is considered to be a mild hand pathology, it has a wide-ranging impact on hand functioning, daily activities and quality of life. Clinicians should include assessments of these outcomes in the treatment of individuals with trigger finger. Treatment efficacy should be evaluated with International Classification of Functioning outcomes, and not limited to symptomatology.

Expression of Tissue Factor by Melanoma Cells Promotes Efficient Hematogenous Metastasis

NASA Astrophysics Data System (ADS)

Mueller, Barbara M.; Reisfeld, Ralph A.; Edgington, Thomas S.; Ruf, Wolfram

1992-12-01

Metastasis is a multistep process which requires highly adapted interactions of tumor cells with host target organs. Compared with nonmetastatic cells, metastatic human melanoma cells express 1000-fold higher levels of tissue factor (TF), the major cellular initiator of the plasma coagulation protease cascades. To explore whether TF may contribute to metastatic tumor dissemination, we analyzed the effect of specific inhibition of TF function on human melanoma metastasis in severe combined immunodeficient (SCID) mice. Using species-specific antibodies to TF, we demonstrate that initial adherence is insufficient for successful tumor cell implantation in a target organ. Rapid arrest of human tumor cells in the lungs of mice was not diminished by inhibition of TF. However, inhibition of TF receptor function and consequent reduction in local protease generation abolished prolonged adherence of tumor cells, resulting in significantly reduced numbers of tumor cells retained in the vasculature of the lungs. The growth of pulmonary metastases was also significantly inhibited by a blocking anti-TF monoclonal antibody and Fab fragments thereof, whereas a noninhibitory antibody lacked antimetastatic effects. Cell surface expression of functional TF thus contributes to melanoma progression by allowing metastatic cells to provide requisite signals for prolonged adhesive interactions and/or transmigration of tumor cells across the endothelium, resulting in successful metastatic tumor implantation.

ATP-dependent potassium channels and mitochondrial permeability transition pores play roles in the cardioprotection of theaflavin in young rat.

PubMed

Ma, Huijie; Huang, Xinli; Li, Qian; Guan, Yue; Yuan, Fang; Zhang, Yi

2011-07-01

Previous studies have confirmed that tea polyphenols possess a broad spectrum of biological functions such as anti-oxidative, anti-bacterial, anti-tumor, anti-inflammatory, anti-viral and cardiovascular protection activities, as well as anti-cerebral ischemia-reperfusion injury properties. But the effect of tea polyphenols on ischemia/reperfusion heart has not been well elucidated. The aim of this study was to investigate the protective effect of theaflavin (TF1) and its underlying mechanism. Young male Sprague-Dawley (SD) rats were randomly divided into five groups: (1) the control group; (2) TF1 group; (3) glibenclamide + TF1 group; (4) 5-hydroxydecanoate (5-HD) + TF1 group; and (5) atractyloside + TF1 group. The Langendorff technique was used to record cardiac function in isolated rat heart before and after 30 min of global ischemia followed by 60 min of reperfusion. The parameters of cardiac function, including left ventricular developing pressure (LVDP), left ventricular end-diastolic pressure (LVEDP), maximal differentials of LVDP (± LVdP/dt (max)) and coronary flow (CF), were measured. The results showed: (1) compared with the control group, TF1 (10, 20, 40 μmol/l) displayed a better recovery of cardiac function after ischemia/reperfusion in a concentration-dependent manner. At 60 min of reperfusion, LVDP, ± LVdP/dt (max) and CF in the TF1 group were much higher than those in the control group, whereas left ventricular end-diastolic pressure (LVEDP) in the TF1 group was lower than that in the control group (P < 0.01). (2) Pretreatment with glibenclamide (10 μmol/l), a K(ATP) antagonist, completely abolished the cardioprotective effects of TF1 (20 μmol/l). Also, most of the effects of TF1 (20 μmol/l) on cardiac function after 60 min of reperfusion were reversed by 5-HD (100 μmol/l), a selective mitochondria K(ATP) antagonist. (3) Atractyloside (20 μmol/l), a mitochondrial permeability transition pore (mPTP) opener, administered at the beginning of 15 min of reperfusion completely abolished the cardioprotection of TF1 (20 μmol/l). The results indicate that TF1 protects the rat heart against ischemia/reperfusion injury through the opening of K(ATP) channels, particularly on the mitochondrial membrane, and inhibits mPTP opening.

Novel gene expression mechanism in a fission yeast retroelement: Tf1 proteins are derived from a single primary translation product.

PubMed

Levin, H L; Weaver, D C; Boeke, J D

1993-12-01

In sharp contrast to the single ORF of the Schizosaccharomyces pombe retrotransposon Tf1, retroviruses and most retrotransposons employ two different ORFs to separately encode the Gag and Pol proteins. The different ORFs are thought to allow for overexpression of the Gag protein relative to Pol protein presumed necessary for the assembly of functional retrovirus particles and virus-like particles (VLPs). The results of in vivo experiments designed to detect the transposition of Tf1 show that Tf1 is indeed active and can insert itself into the host genome via a true retrotransposition process. Thus, a paradox emerged between the lack of any obvious means of overexpressing Tf1 Gag protein and the demonstrated functionality of the element. Epitope tagging experiments described here confirm that the Tf1 large ORF is intact and that there is no translational or transcriptional mechanism used to overexpress the Tf1 Gag protein. In addition, we used sucrose gradients and antisera specific for Tf1 capsid (CA) and integrase (IN) to show that the Tf1 proteins do assemble into uniform populations of macromolecular particles that also cosediment with Tf1 reverse transcription products. This evidence suggests that Tf1 proteins form VLPs without using the previously described mechanisms that retroviruses and retrotransposons require to overexpress Gag proteins.

The impact of transfer from hemodialysis on peritoneal dialysis technique survival.

PubMed

Nessim, Sharon J; Bargman, Joanne M; Jassal, S Vanita; Oliver, Matthew J; Na, Yingbo; Perl, Jeffrey

2015-01-01

A significant proportion of peritoneal dialysis (PD) patients receive an initial period of hemodialysis (HD) before transitioning to PD ("PD-switch"). We sought to better understand the risks of PD technique failure (TF) and mortality for those patients compared with patients starting with PD as their first dialysis modality ("PD-first"). Using Canadian Organ Replacement Register data, we compared the risk of PD TF between PD-first and PD-switch patients within the first year after HD initiation. In a secondary analysis, the PD-switch patients were stratified into three groups based on timing of the switch from initial HD to PD as follows: 0 - 90 days, 91 - 180 days, and 181 - 365 days. Each group was compared with PD-first patients for risk of PD TF and death. Between 2001 and 2010, 9404 patients initiated PD as their first renal replacement therapy, and 3757 switched from HD to PD. After multivariable adjustment, the risk of PD TF was higher among PD-switch patients than among PD-first patients [adjusted hazard ratio (AHR): 1.37; 95% confidence interval (CI): 1.26 to 1.49], particularly within the first year after the switch from HD to PD (AHR: 1.51; 95% CI: 1.36 to 1.68). There was no association between time on HD within the first year and subsequent risk of PD TF. For all the stratified PD-switch groups, death rates were higher than those for PD-first patients. Compared with patients who start renal replacement therapy with PD, those who transfer from HD to PD within the first year on dialysis experience higher rates of PD TF and death, with the highest risk being observed in the initial year after the switch to PD. Copyright © 2015 International Society for Peritoneal Dialysis.

Structural, functional and evolutionary characterization of major drought transcription factors families in maize

NASA Astrophysics Data System (ADS)

Mittal, Shikha; Banduni, Pooja; Mallikarjuna, Mallana G.; Rao, Atmakuri R.; Jain, Prashant A.; Dash, Prasanta K.; Thirunavukkarasu, Nepolean

2018-05-01

Drought is one of the major threats to maize production. In order to improve the production and to breed tolerant hybrids, understanding the genes and regulatory mechanisms during drought stress is important. Transcription factors (TFs) play a major role in gene regulation and many TFs have been identified in response to drought stress. In our experiment, a set of 15 major TF families comprising 1436 genes was structurally and functionally characterized using in-silico tools and a gene expression assay. All 1436 genes were mapped on 10 chromosome of maize. The functional annotation indicated the involvement of these genes in ABA signaling, ROS scavenging, photosynthesis, stomatal regulation, and sucrose metabolism. Duplication was identified as the primary force in divergence and expansion of TF families. Phylogenetic relationship was developed individually for each TF family as well as combined TF families. Phylogenetic analysis grouped the TF family of genes into TF-specific and mixed groups. Phylogenetic analysis of genes belonging to various TF families suggested that the origin of TFs occurred in the lineage of maize evolution. Gene structure analysis revealed that more number of genes were intron-rich as compared to intronless genes. Drought-responsive CRE’s such as ABREA, ABREB, DRE1 and DRECRTCOREAT have been identified. Expression and interaction analyses identified leaf-specific bZIP TF, GRMZM2G140355, as a potential contributor toward drought tolerance in maize. We also analyzed protein-protein interaction network of 269 drought-responsive genes belonging to different drought-related TFs. The information generated on structural and functional characteristics, expression and interaction of the drought-related TF families will be useful to decipher the drought tolerance mechanisms and to derive drought-tolerant genotypes in maize.

The Microbiota Is Essential for the Generation of Black Tea Theaflavins-Derived Metabolites

PubMed Central

Chen, Huadong; Hayek, Saeed; Rivera Guzman, Javier; Gillitt, Nicholas D.; Ibrahim, Salam A.; Jobin, Christian; Sang, Shengmin

2012-01-01

Background Theaflavins including theaflavin (TF), theaflavin-3-gallate (TF3G), theaflavin-3′-gallate (TF3′G), and theaflavin-3,3′-digallate (TFDG), are the most important bioactive polyphenols in black tea. Because of their poor systemic bioavailability, it is still unclear how these compounds can exert their biological functions. The objective of this study is to identify the microbial metabolites of theaflavins in mice and in humans. Methods and Findings In the present study, we gavaged specific pathogen free (SPF) mice and germ free (GF) mice with 200 mg/kg TFDG and identified TF, TF3G, TF3′G, and gallic acid as the major fecal metabolites of TFDG in SPF mice. These metabolites were absent in TFDG- gavaged GF mice. The microbial bioconversion of TFDG, TF3G, and TF3′G was also investigated in vitro using fecal slurries collected from three healthy human subjects. Our results indicate that TFDG is metabolized to TF, TF3G, TF3′G, gallic acid, and pyrogallol by human microbiota. Moreover, both TF3G and TF3′G are metabolized to TF, gallic acid, and pyrogallol by human microbiota. Importantly, we observed interindividual differences on the metabolism rate of gallic acid to pyrogallol among the three human subjects. In addition, we demonstrated that Lactobacillus plantarum 299v and Bacillus subtilis have the capacity to metabolize TFDG. Conclusions The microbiota is important for the metabolism of theaflavins in both mice and humans. The in vivo functional impact of microbiota-generated theaflavins-derived metabolites is worthwhile of further study. PMID:23227227

Quantitative in vivo imaging of tissue factor expression in glioma using dynamic contrast-enhanced MRI derived parameters.

PubMed

Chen, Xiao; Xie, Tian; Fang, Jingqin; Xue, Wei; Tong, Haipeng; Kang, Houyi; Wang, Sumei; Yang, Yizeng; Xu, Minhui; Zhang, Weiguo

2017-08-01

Tissue Factor (TF) has been well established in angiogenesis, invasion, metastasis, and prognosis in glioma. A noninvasive assessment of TF expression status in glioma is therefore of obvious clinical relevance. Dynamic contrast-enhanced (DCE) MRI parameters have been used to evaluate microvascular characteristics and predict molecular expression status in tumors. Our aim is to investigate whether quantitative DCE-MRI parameters could assess TF expression in glioma. Thirty-two patients with histopathologically diagnosed supratentorial glioma who underwent DCE-MRI were retrospectively recruited. Extended Tofts linear model was used for DCE-MRI post-processing. Hot-spot, whole tumor cross-sectional approaches, and histogram were used for analysis of model based parameters. Four serial paraffin sections of each case were stained with TF, CD105, CD34 and α-Sooth Muscle Actin, respectively for evaluating the association of TF and microvascular properties. Pearson correlation was performed between percentage of TF expression area and DCE-MRI parameters, multiple microvascular indexes. Volume transfer constant (K trans ) hot-spot value best correlated with TF (r=0.886, p<0.001), followed by 90th percentile K trans value (r=0.801, p<0.001). Moreover, histogram analysis of K trans value demonstrated that weak TF expression was associated with less heterogeneous and positively skewed distribution. Finally, pathology analysis revealed TF was associated with glioma grade and significantly correlated with these two dynamic angiogenic indexes which could be used to explain the strong correlation between K trans and TF expression. Our results indicate that K trans may serve as a potential clinical imaging biomarker to predict TF expression status preoperatively in gliomas. Copyright © 2017 Elsevier B.V. All rights reserved.

Systematic Analysis of Zn2Cys6 Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus

PubMed Central

Huang, Pengyun; Lin, Fucheng

2014-01-01

Because of great challenges and workload in deleting genes on a large scale, the functions of most genes in pathogenic fungi are still unclear. In this study, we developed a high-throughput gene knockout system using a novel yeast-Escherichia-Agrobacterium shuttle vector, pKO1B, in the rice blast fungus Magnaporthe oryzae. Using this method, we deleted 104 fungal-specific Zn2Cys6 transcription factor (TF) genes in M. oryzae. We then analyzed the phenotypes of these mutants with regard to growth, asexual and infection-related development, pathogenesis, and 9 abiotic stresses. The resulting data provide new insights into how this rice pathogen of global significance regulates important traits in the infection cycle through Zn2Cys6TF genes. A large variation in biological functions of Zn2Cys6TF genes was observed under the conditions tested. Sixty-one of 104 Zn2Cys6 TF genes were found to be required for fungal development. In-depth analysis of TF genes revealed that TF genes involved in pathogenicity frequently tend to function in multiple development stages, and disclosed many highly conserved but unidentified functional TF genes of importance in the fungal kingdom. We further found that the virulence-required TF genes GPF1 and CNF2 have similar regulation mechanisms in the gene expression involved in pathogenicity. These experimental validations clearly demonstrated the value of a high-throughput gene knockout system in understanding the biological functions of genes on a genome scale in fungi, and provided a solid foundation for elucidating the gene expression network that regulates the development and pathogenicity of M. oryzae. PMID:25299517

Addressing safety liabilities of TfR bispecific antibodies that cross the blood-brain barrier.

PubMed

Couch, Jessica A; Yu, Y Joy; Zhang, Yin; Tarrant, Jacqueline M; Fuji, Reina N; Meilandt, William J; Solanoy, Hilda; Tong, Raymond K; Hoyte, Kwame; Luk, Wilman; Lu, Yanmei; Gadkar, Kapil; Prabhu, Saileta; Ordonia, Benjamin A; Nguyen, Quyen; Lin, Yuwen; Lin, Zhonghua; Balazs, Mercedesz; Scearce-Levie, Kimberly; Ernst, James A; Dennis, Mark S; Watts, Ryan J

2013-05-01

Bispecific antibodies using the transferrin receptor (TfR) have shown promise for boosting antibody uptake in brain. Nevertheless, there are limited data on the therapeutic properties including safety liabilities that will enable successful development of TfR-based therapeutics. We evaluate TfR/BACE1 bispecific antibody variants in mouse and show that reducing TfR binding affinity improves not only brain uptake but also peripheral exposure and the safety profile of these antibodies. We identify and seek to address liabilities of targeting TfR with antibodies, namely, acute clinical signs and decreased circulating reticulocytes observed after dosing. By eliminating Fc effector function, we ameliorated the acute clinical signs and partially rescued a reduction in reticulocytes. Furthermore, we show that complement mediates a residual decrease in reticulocytes observed after Fc effector function is eliminated. These data raise important safety concerns and potential mitigation strategies for the development of TfR-based therapies that are designed to cross the blood-brain barrier.

How gene order is influenced by the biophysics of transcription regulation

PubMed Central

Kolesov, Grigory; Wunderlich, Zeba; Laikova, Olga N.; Gelfand, Mikhail S.; Mirny, Leonid A.

2007-01-01

What are the forces that shape the structure of prokaryotic genomes: the order of genes, their proximity, and their orientation? Coregulation and coordinated horizontal gene transfer are believed to promote the proximity of functionally related genes and the formation of operons. However, forces that influence the structure of the genome beyond the level of a single operon remain unknown. Here, we show that the biophysical mechanism by which regulatory proteins search for their sites on DNA can impose constraints on genome structure. Using simulations, we demonstrate that rapid and reliable gene regulation requires that the transcription factor (TF) gene be close to the site on DNA the TF has to bind, thus promoting the colocalization of TF genes and their targets on the genome. We use parameters that have been measured in recent experiments to estimate the relevant length and times scales of this process and demonstrate that the search for a cognate site may be prohibitively slow if a TF has a low copy number and is not colocalized. We also analyze TFs and their sites in a number of bacterial genomes, confirm that they are colocalized significantly more often than expected, and show that this observation cannot be attributed to the pressure for coregulation or formation of selfish gene clusters, thus supporting the role of the biophysical constraint in shaping the structure of prokaryotic genomes. Our results demonstrate how spatial organization can influence timing and noise in gene expression. PMID:17709750

Insect transferrin functions as an antioxidant protein in a beetle larva.

PubMed

Kim, Bo Yeon; Lee, Kwang Sik; Choo, Young Moo; Kim, Iksoo; Je, Yeon Ho; Woo, Soo Dong; Lee, Sang Mong; Park, Hyun Cheol; Sohn, Hung Dae; Jin, Byung Rae

2008-06-01

In insects transferrin is known as an iron transporter, an antibiotic agent, a vitellogenin, and a juvenile hormone regulated protein. Here, a novel functional role for insect transferrin as an antioxidant protein is demonstrated. Stressors, such as heat shock, fungal challenge, and H(2)O(2) exposure, cause upregulation of the white-spotted flower chafer Protaetia brevitarsis (Coleoptera: Scarabaeidae) transferrin (PbTf) mRNA in the fat body and increases PbTf protein levels in the hemolymph. RNA interference (RNAi) treated PbTf reduction causes increased iron and H(2)O(2) levels in the hemolymph and results in induction of apoptotic cell death in the fat body during exposure to stress. The observed effects of PbTf RNAi suggest that PbTf inhibits stress-induced apoptosis by diminishing the Fenton reaction via the binding of iron, thus supporting an antioxidant role for PbTf in stress responses.

The prokaryotic thermophilic TF1-ATPase is functionally compatible with the eukaryotic CFo-part of the chloroplast ATP-synthase.

PubMed

Galmiche, J M; Pezennec, S; Zhao, R; Girault, G; Baeuerlein, E

1994-01-31

The ATP synthase from chloroplasts, CFo.F1, was reconstituted into liposomes, from which most of CF1 was removed by a short treatment with guanidinium chloride. ATP-dependent proton uptake was restored with these CFo-liposomes even better by the addition of the bacterial TF1-than of the related CF1-part. This proton uptake was prevented by tentoxin, a specific inhibitor of the CF1-ATPase, in these CFo.F1-liposomes, but not in the hybrid CFo.TF1-liposomes. Venturicidin, a specific inhibitor of proton flow through CFo, was able to block it in both the hybrid CFo.TF1-liposomes and reconstituted CFo.F1-liposomes. These results indicate that the bacterial TF1-part binds to the eukaryotic CFo-part of four subunits forming a functional CFo.TF1-ATPase.

Soil-to-crop transfer factors of tellurium.

PubMed

Yang, Guosheng; Zheng, Jian; Tagami, Keiko; Uchida, Shigeo

2014-09-01

Stable tellurium (Te) concentrations in 148 sets of agricultural soil and associated crop samples were measured in this study to obtain soil-to-crop transfer factor (TF) of Te. We used a recently developed simple method that applies digestion of samples with aqua regia and sector field inductively coupled plasma mass spectrometry to measure low Te levels in these samples. Geometric mean (GM) concentrations of Te in soil and crops were 75μgkg(-1)-dry (range: 15-850μgkg(-1)-dry) and 1.8μgkg(-1)-dry (range: 0.1-120μgkg(-1)-dry), respectively; the Te concentration range was significantly wider in crops than in soil. Using these data, we calculated TFs and obtained their range from 1.3×10(-3) to 1.1×10(-1). The GM of TF for upland field crops was calculated to be 2.0×10(-2) and for brown rice was 3.1×10(-2); all crop types had the similar GMs of their TF values. Data comparison for TF of Te was carried out with six elements, which are present in anionic forms in soil environment like Te is, i.e. P, Br, As, Se, Mo, and I. TFs of Te and I showed the highest correlation factor for upland field crops by t-test (r=0.577, p<0.001), but no correlation was found for brown rice. We considered it likely that different water management practices in upland fields and paddy fields affected the Te transfer from soil to crops. Copyright © 2014 Elsevier Ltd. All rights reserved.

Human operator identification model and related computer programs

NASA Technical Reports Server (NTRS)

Kessler, K. M.; Mohr, J. N.

1978-01-01

Four computer programs which provide computational assistance in the analysis of man/machine systems are reported. The programs are: (1) Modified Transfer Function Program (TF); (2) Time Varying Response Program (TVSR); (3) Optimal Simulation Program (TVOPT); and (4) Linear Identification Program (SCIDNT). The TV program converts the time domain state variable system representative to frequency domain transfer function system representation. The TVSR program computes time histories of the input/output responses of the human operator model. The TVOPT program is an optimal simulation program and is similar to TVSR in that it produces time histories of system states associated with an operator in the loop system. The differences between the two programs are presented. The SCIDNT program is an open loop identification code which operates on the simulated data from TVOPT (or TVSR) or real operator data from motion simulators.

Schizosaccharomyces pombe Retrotransposon Tf2 Mobilizes Primarily through Homologous cDNA Recombination

PubMed Central

Hoff, Eleanor F.; Levin, Henry L.; Boeke, Jef D.

1998-01-01

The Tf2 retrotransposon, found in the fission yeast Schizosaccharomyces pombe, is nearly identical to its sister element, Tf1, in its reverse transcriptase-RNase H and integrase domains but is very divergent in the gag domain, the protease, the 5′ untranslated region, and the U3 domain of the long terminal repeats. It has now been demonstrated that a neo-marked copy of Tf2 overexpressed from a heterologous promoter can mobilize into the S. pombe genome and produce true transposition events. However, the Tf2-neo mobilization frequency is 10- to 20-fold lower than that of Tf1-neo, and 70% of the Tf2-neo events are homologous recombination events generated independently of a functional Tf2 integrase. Thus, the Tf2 element is primarily dependent on homologous recombination with preexisting copies of Tf2 for its propagation. Finally, production of Tf2-neo proteins and cDNA was also analyzed; surprisingly, Tf2 was found to produce its reverse transcriptase as a single species in which it is fused to protease, unlike all other retroviruses and retrotransposons. PMID:9774697

Evaluation of Nonferrous Metals as Potential In Vivo Tracers of Transferrin-Based Therapeutics

NASA Astrophysics Data System (ADS)

Zhao, Hanwei; Wang, Shunhai; Nguyen, Son N.; Elci, S. Gokhan; Kaltashov, Igor A.

2016-02-01

Transferrin (Tf) is a promising candidate for targeted drug delivery. While development of such products is impossible without the ability to monitor biodistribution of Tf-drug conjugates in tissues and reliable measurements of their levels in blood and other biological fluids, the presence of very abundant endogenous Tf presents a significant impediment to such efforts. Several noncognate metals have been evaluated in this work as possible tracers of exogenous transferrin in complex biological matrices using inductively coupled plasma mass spectrometry (ICP MS) as a detection tool. Placing Ni(II) on a His-tag of recombinant Tf resulted in formation of a marginally stable protein-metal complex, which readily transfers the metal to ubiquitous physiological scavengers, such as serum albumin. An alternative strategy targeted iron-binding pockets of Tf, where cognate Fe(III) was replaced by metal ions known to bind this protein. Both Ga(III) and In(III) were evaluated, with the latter being vastly superior as a tracer (stronger binding to Tf unaffected by the presence of metal scavengers and the retained ability to associate with Tf receptor). Spiking serum with indium-loaded Tf followed by ICP MS detection demonstrated that protein quantities as low as 0.04 nM can be readily detected in animal blood. Combining laser ablation with ICP MS detection allows distribution of exogenous Tf to be mapped within animal tissue cross-sections with spatial resolution exceeding 100 μm. The method can be readily extended to a range of other therapeutics where metalloproteins are used as either carriers or payloads.

Transfer Rates of 238U and 232Th for E. globulus, A. mearnsii, H. filipendula and Hazardous Effects of the Usage of Medicinal Plants From Around Gold Mine Dump Environs

PubMed Central

Tshivhase, Victor M.; Njinga, Raymond L.; Mathuthu, Manny; Dlamini, Thulani C.

2015-01-01

Medicinal plant consumption can be a source of human exposure to radioactive elements such as 238U and 232Th, which can lead to internal radiation doses. The uptake of 238U and 232Th from soils to the leaf samples of three different medicinal plant species (Eucalyptus globulus, Acacia mearnsii and Hyparrhenia filipendula) from the purlieu of the Princess gold mine dump, an abandoned contaminated tailings storage site (TSS), located at longitude 27°55′00″E and latitude 26°09′30″S in Davidsonville (Roodepoort, west of Johannesburg, South Africa) was measured. This was done using ICP-MS spectrometry and substantial differences were observed in the soil-plant transfer factor (TF) values between these radionuclides. The plant species E. globulus exhibited the highest uptake of 238U, with an average TF of 3.97, while that of H. filipendula was 0.01 and the lowest TF of 0.15 × 10−2 was measured for A. mearnsii. However, in the case of 232Th, the highest average TF was observed for A. mearnsii (0.29), followed by E. globulus (0.10) and lowest was measured for H. filipendula (0.27 × 10−2). The ratio of TF average value i.e., 238U to 232Th in the soil-plant leaves was 38.05 for E. globulus, 0.01 for A. mearnsii and 4.38 for H. filipendula. PMID:26690462

Transcriptome-wide profiling and expression analysis of transcription factor families in a liverwort, Marchantia polymorpha

PubMed Central

2013-01-01

Background Transcription factors (TFs) are vital elements that regulate transcription and the spatio-temporal expression of genes, thereby ensuring the accurate development and functioning of an organism. The identification of TF-encoding genes in a liverwort, Marchantia polymorpha, offers insights into TF organization in the members of the most basal lineages of land plants (embryophytes). Therefore, a comparison of Marchantia TF genes with other land plants (monocots, dicots, bryophytes) and algae (chlorophytes, rhodophytes) provides the most comprehensive view of the rates of expansion or contraction of TF genes in plant evolution. Results In this study, we report the identification of TF-encoding transcripts in M. polymorpha for the first time, as evidenced by deep RNA sequencing data. In total, 3,471 putative TF encoding transcripts, distributed in 80 families, were identified, representing 7.4% of the generated Marchantia gametophytic transcriptome dataset. Overall, TF basic functions and distribution across families appear to be conserved when compared to other plant species. However, it is of interest to observe the genesis of novel sequences in 24 TF families and the apparent termination of 2 TF families with the emergence of Marchantia. Out of 24 TF families, 6 are known to be associated with plant reproductive development processes. We also examined the expression pattern of these TF-encoding transcripts in six male and female developmental stages in vegetative and reproductive gametophytic tissues of Marchantia. Conclusions The analysis highlighted the importance of Marchantia, a model plant system, in an evolutionary context. The dataset generated here provides a scientific resource for TF gene discovery and other comparative evolutionary studies of land plants. PMID:24365221

Calculation of Coupled Vibroacoustics Response Estimates from a Library of Available Uncoupled Transfer Function Sets

NASA Technical Reports Server (NTRS)

Smith, Andrew; LaVerde, Bruce; Hunt, Ron; Fulcher, Clay; Towner, Robert; McDonald, Emmett

2012-01-01

The design and theoretical basis of a new database tool that quickly generates vibroacoustic response estimates using a library of transfer functions (TFs) is discussed. During the early stages of a launch vehicle development program, these response estimates can be used to provide vibration environment specification to hardware vendors. The tool accesses TFs from a database, combines the TFs, and multiplies these by input excitations to estimate vibration responses. The database is populated with two sets of uncoupled TFs; the first set representing vibration response of a bare panel, designated as H(sup s), and the second set representing the response of the free-free component equipment by itself, designated as H(sup c). For a particular configuration undergoing analysis, the appropriate H(sup s) and H(sup c) are selected and coupled to generate an integrated TF, designated as H(sup s +c). This integrated TF is then used with the appropriate input excitations to estimate vibration responses. This simple yet powerful tool enables a user to estimate vibration responses without directly using finite element models, so long as suitable H(sup s) and H(sup c) sets are defined in the database libraries. The paper discusses the preparation of the database tool and provides the assumptions and methodologies necessary to combine H(sup s) and H(sup c) sets into an integrated H(sup s + c). An experimental validation of the approach is also presented.

BOREAS TF-11 SSA-Fen 1996 Water Surface Film Capping Data

NASA Technical Reports Server (NTRS)

Billesbach, David P.; Hall, Forrest G. (Editor); Knapp, David E. (Editor)

2000-01-01

The BOREAS TF-11 team gathered a variety of data to complement its tower flux measurements collected at the SSA-Fen site. The data described in this document were made by the TF-11 team at the SSA-Fen site to quantify the effect that the films observed to form on open water surfaces had on the transfer of carbon dioxide and methane from the water to the air. Measurements of fluxes of carbon dioxide and methane were made in 1994 and in 1996 using the chamber flux method. A gas chromatograph and a LI-COR LI-6200 were used to measure concentrations and to calculate the fluxes. The data are stored in tabular ASCII files.

Drivers of U.S. toxicological footprints trajectory 1998-2013

NASA Astrophysics Data System (ADS)

Koh, S. C. L.; Ibn-Mohammed, T.; Acquaye, A.; Feng, K.; Reaney, I. M.; Hubacek, K.; Fujii, H.; Khatab, K.

2016-12-01

By exploiting data from the Toxic Release Inventory of the United States, we have established that the toxicological footprint (TF) increased by 3.3% (88.4 Mt) between 1998 and 1999 and decreased by 39% (1088.5 Mt) between 1999 and 2013. From 1999 to 2006, the decreasing TF was driven by improvements in emissions intensity (i.e. gains in production efficiency) through toxic chemical management options: cleaner production; end of pipe treatment; transfer for further waste management; and production scale. In particular, the mining sector reduced its TF through outsourcing processes. Between 2006 and 2009, decreasing TF was due to decrease in consumption volume triggered by economic recession. Since 2009, the economic recovery increased TF, overwhelming the influence of improved emissions intensity through population growth, consumption and production structures. Accordingly, attaining a less-toxic economy and environment will be influenced by a combination of gains in production efficiency through improvement in emissions mitigation technologies and changes in consumption patterns. Overall, the current analysis highlights the structural dynamics of toxic chemical release and would inform future formulation of effective mitigation standards and management protocols towards the detoxification of the environment.

Verification of radionuclide transfer factors to domestic-animal food products, using indigenous elements and with emphasis on iodine.

PubMed

Sheppard, S C; Long, J M; Sanipelli, B

2010-11-01

Recent reviews have established benchmark values for transfer factors that describe radionuclide transfer from plants to animal food product such as milk, eggs and meat. They also illustrate the paucity of data for some elements and some food products. The present study quantified transfer data using indigenous elements measured in dairy, poultry and other livestock farms in Canada. Up to 62 elements are reported, with particular emphasis on iodine (I) because of the need to accurately assess the behaviour of (129)I from disposal of nuclear fuel waste. There was remarkable agreement with the literature values, and for many elements the present study involved many more observations than were previously available. Perhaps the most important observation was that product/substrate concentration ratios (CR) were quite consistent across species, whereas the traditional fractional transfer factors (TF, units of d kg(-1) or d L(-1)) necessarily vary with body mass (feed intake). This suggests that for long-term assessments, it may be advisable to change the models to use CR rather than TF.

Influence of the nonexchangeable potassium of mica on radiocesium uptake by paddy rice.

PubMed

Eguchi, Tetsuya; Ohta, Takeshi; Ishikawa, Tetsuya; Matsunami, Hisaya; Takahashi, Yoshihiko; Kubo, Katashi; Yamaguchi, Noriko; Kihou, Nobuharu; Shinano, Takuro

2015-09-01

A pot cultivation experiment was conducted to elucidate the influence of the nonexchangeable potassium (K) of mica on radiocesium ((137)Cs) uptake by paddy rice (Oryza sativa L. cv. Koshihikari), and to evaluate the potential of mica application as a countermeasure to reduce radiocesium transfer from soil to paddy rice. The increase in the exchangeable K concentrations of soils, measured before planting, due to mica (muscovite, biotite, and phlogopite) application was negligible. However, in trioctahedral mica (biotite and phlogopite)-treated soil, the release of nonexchangeable K from the mica interlayer maintained the soil-solution K at a higher level during the growing season in comparison to the control, and consequently decreased the (137)Cs transfer factor for brown rice (TF). The sodium tetraphenylboron (TPB)-extractable K concentration of the soils, measured before planting, was strongly negatively correlated with the TF, whereas the exchangeable K concentration of the soils, also measured before planting, was not correlated with the TF. Therefore, we conclude that TPB-extractable K is more reliable than exchangeable K as a basis of fertilizer recommendations for radiocesium-contaminated paddy fields. Phlogopite-treated soils exhibited higher TPB-extractable K concentrations and lower TF values than biotite-treated soils. We thus conclude that phlogopite application is an effective countermeasure to reduce radiocesium uptake in paddy rice. Copyright © 2015 Elsevier Ltd. All rights reserved.

Promoter selection in human mitochondria involves binding of a transcription factor to orientation-independent upstream regulatory elements.

PubMed

Fisher, R P; Topper, J N; Clayton, D A

1987-07-17

Selective transcription of human mitochondrial DNA requires a transcription factor (mtTF) in addition to an essentially nonselective RNA polymerase. Partially purified mtTF is able to sequester promoter-containing DNA in preinitiation complexes in the absence of mitochondrial RNA polymerase, suggesting a DNA-binding mechanism for factor activity. Functional domains, required for positive transcriptional regulation by mtTF, are identified within both major promoters of human mtDNA through transcription of mutant promoter templates in a reconstituted in vitro system. These domains are essentially coextensive with DNA sequences protected from nuclease digestion by mtTF-binding. Comparison of the sequences of the two mtTF-responsive elements reveals significant homology only when one sequence is inverted; the binding sites are in opposite orientations with respect to the predominant direction of transcription. Thus mtTF may function bidirectionally, requiring additional protein-DNA interactions to dictate transcriptional polarity. The mtTF-responsive elements are arrayed as direct repeats, separated by approximately 80 bp within the displacement-loop region of human mitochondrial DNA; this arrangement may reflect duplication of an ancestral bidirectional promoter, giving rise to separate, unidirectional promoters for each strand.

Transfer of (40)K, (238)U, (210)Pb, and (210)Po from soil to plant in various locations in south of Syria.

PubMed

Al-Masri, M S; Al-Akel, B; Nashawani, A; Amin, Y; Khalifa, K H; Al-Ain, F

2008-02-01

Transfer factors of (40)K, (238)U, (210)Pb, and (210)Po from soil to some agriculture crops in various locations in south of Syria (Dara'a and Assuwaydaa districts) have been determined. Soil and vegetable crops (green pepper, cucumber, tomato, and eggplant), legumes crops (lentil, chickpea, and broad bean), fruit trees (apple, grape, and olives) and cereals (barley and wheat) were collected and analyzed for (238)U, (210)Pb, and (210)Po. The results have shown that higher transfer factors (calculated as Bqkg(-1) dry wt. plant material per Bqkg(-1) dry wt. soil) for (210)Po, (210)Pb and (238)U were observed in vegetable leaves than fruits and cereals leaves; the highest values of transfer factor (TF) for (238)U were found to be 0.1 for straw of chickpea. Transfer factors for (210)Po varied between 2.8x10(-2) and 2 in fruits of eggplant and grain of barley, respectively. In addition, several parameters affecting transfer factors of the radionuclides were evaluated. The results can be considered as base values for TF of natural radionuclides in the region.

[Changes of iron metabolism indices in children with various genotypes of thalassema].

PubMed

Huang, Yu-Jun; Wu, Shao-Guo; Ou, Xiao-Bing; Zhang, Li

2010-02-01

To study the value of iron metabolism indices, serum iron (SI), total iron blinding capacity (TIBC) and transferring (Tf), in thalassema. The serum samples from 9 children with silent alpha thalassema, 56 with standard alpha thalassema, 26 with HbH disease, 40 with beta+ thalassema, 56 with beta0 thalassema, 45 with iron deficiency anemia (IDA) and 70 healthy children were detected for SI, TIBC and Tf levels. The SI level increased (p<0.01), while the TIBC level decreased significantly in the beta0 thalassema group compared with those in the other groups (p<0.05 or 0.01), but the Tf level was not different. The Tf level of both the silent alpha thalassema and the standard alpha thalassema groups was statistically lower than that of the healthy group (p<0.01), but the levels of SI and TIBC were similar to the healthy group. Though the SI level of the HbH disease group was similar to the healthy group, the TIBC and Tf levels were statistically lower (p<0.01). Compared with Tf, SI and TIBC are better indices for monitoring iron loading in children with thalassema. The increased SI level and decreased TIBC level are two indices for the diagnosis of beta(0) thalassema in children with cellule anaemia.

The functionally conserved nucleoporins Nup124p from fission yeast and the human Nup153 mediate nuclear import and activity of the Tf1 retrotransposon and HIV-1 Vpr.

PubMed

Varadarajan, Padmapriya; Mahalingam, Sundarasamy; Liu, Peiyun; Ng, Sarah Boon Hsi; Gandotra, Sheetal; Dorairajoo, Desmond Suresh Kumar; Balasundaram, David

2005-04-01

We report that the fission yeast nucleoporin Nup124p is required for the nuclear import of both, retrotransposon Tf1-Gag as well as the retroviral HIV-1 Vpr. Failure to import Tf1-Gag into the nucleus in a nup124 null mutant resulted in complete loss of Tf1 transposition. Similarly, nuclear import of HIV-1 Vpr was impaired in nup124 null mutant strains and cells became resistant to Vpr's cell-killing activity. On the basis of protein domain similarity, the human nucleoporin Nup153 was identified as a putative homolog of Nup124p. We demonstrate that in vitro-translated Nup124p and Nup153 coimmunoprecipitate Tf1-Gag or HIV-1 Vpr. Though full-length Nup153 was unable to complement the Tf1 transposition defect in a nup124 null mutant, we provide evidence that both nucleoporins share a unique N-terminal domain, Nup124p(AA264-454) and Nup153(AA448-634) that is absolutely essential for Tf1 transposition. Epigenetic overexpression of this domain in a wild-type (nup124(+)) background blocked Tf1 activity implying that sequences from Nup124p and the human Nup153 challenged the same pathway affecting Tf1 transposition. Our results establish a unique relationship between two analogous nucleoporins Nup124p and Nup153 wherein the function of a common domain in retrotransposition is conserved.

Natural radionuclides in plants, soils and sediments affected by U-rich coal mining activities in Brazil.

PubMed

Galhardi, Juliana Aparecida; García-Tenorio, Rafael; Bonotto, Daniel Marcos; Díaz Francés, Inmaculada; Motta, João Gabriel

2017-10-01

Mining activities can increase the mobility of metals by accelerating the dissolution and leaching of minerals from the rocks and tailing piles to the environment and, consequently, their availability for plants and subsequent transfer to the food chain. The weathering of minerals and the disposal of coal waste in tailing piles can accelerate the generation of acid mine drainage (AMD), which is responsible for the higher dissolution of metals in mining areas. In this context, the behavior of U, Th and K in soils and sediment, and the transfer factor (TF) of 238 U, 234 U and 210 Po for soybean, wheat, pine and eucalyptus cultivated around a coal mine in southern Brazil was evaluated. Alpha and gamma spectrometry were used for the measurements of the activity concentration of the radioelements. 210 Po was the radionuclide that is most accumulated in the plants, especially in the leaves. When comparing the plant species, pine showed the highest TF values for 234 U (0.311 ± 0.420) for leaves, while eucalyptus showed the highest TF for 238 U (0.344 ± 0.414) for leaves. In general, TF were higher for the leaves of soybean and wheat when compared to the grains, and grains of wheat showed higher TF for 210 Po and 238 U than grains of soybean. Deviations from the natural U isotopic ratio were recorded at all investigated areas, indicating possible industrial and mining sources of U for the vegetables. A safety assessment of transport routes and accumulation of radionuclides in soils with a potential for cultivation is important, mainly in tropical areas contaminated with solid waste and effluents from mines and industry. Copyright © 2017 Elsevier Ltd. All rights reserved.

137Cs soil-to-plant transfer for individual species in a semi-natural grassland. Influence of potassium soil content.

PubMed

Ciuffo, Liliana; Velasco, Hugo; Belli, Mar; Sansone, Umberto

2003-09-01

In the present study we assessed the radiocaesium uptake by plants in order to piece together information on factors affecting the uptake processes, particularly K supply and plant species differences. Vegetation uptake from soil contaminated by the Chernobyl accident was compared at two semi-natural grasslands. The Cs/K discrimination factor (DF), which is often used to evaluate a plant's efficiency in absorbing nutrients from soil, was estimated. The obtained DF values (0.01 to 0.8) vary with K soil concentrations and plant species, indicating that the (40)K is more efficiently absorbed than (137)Cs. The soil-to-plant relationship was evaluated by means of the transfer factor (TF). The (137)Cs TF(sp) values obtained from separated plant species varied within the range of 0.016 to 0.400 (site 1) and 0.017 to 0.171 (site 2). When mixed grass samples were considered a large variation was observed, mainly for site 1. The (137)Cs TF(mix) ranges were: 0.018 to 0.250 for site 1 and 0.017 to 0.167 for site 2. These values fall within the range of TFs commonly reported (0.0001-1). Our present data suggest that these pastures are apt for forage use. Different plant species presented different individual behavior regarding their (137)Cs TF(sp) when the (40)K soil activity concentration was taken in account. For most of the species analyzed, we observed a gradual decrease in the individual (137)Cs TF(sp) when the (40)K soil activity concentration was increased, with the exception of Taraxacum officinale at one of the sampling sites.

Auditory Time-Frequency Masking for Spectrally and Temporally Maximally-Compact Stimuli

PubMed Central

Laback, Bernhard; Savel, Sophie; Ystad, Sølvi; Balazs, Peter; Meunier, Sabine; Kronland-Martinet, Richard

2016-01-01

Many audio applications perform perception-based time-frequency (TF) analysis by decomposing sounds into a set of functions with good TF localization (i.e. with a small essential support in the TF domain) using TF transforms and applying psychoacoustic models of auditory masking to the transform coefficients. To accurately predict masking interactions between coefficients, the TF properties of the model should match those of the transform. This involves having masking data for stimuli with good TF localization. However, little is known about TF masking for mathematically well-localized signals. Most existing masking studies used stimuli that are broad in time and/or frequency and few studies involved TF conditions. Consequently, the present study had two goals. The first was to collect TF masking data for well-localized stimuli in humans. Masker and target were 10-ms Gaussian-shaped sinusoids with a bandwidth of approximately one critical band. The overall pattern of results is qualitatively similar to existing data for long maskers. To facilitate implementation in audio processing algorithms, a dataset provides the measured TF masking function. The second goal was to assess the potential effect of auditory efferents on TF masking using a modeling approach. The temporal window model of masking was used to predict present and existing data in two configurations: (1) with standard model parameters (i.e. without efferents), (2) with cochlear gain reduction to simulate the activation of efferents. The ability of the model to predict the present data was quite good with the standard configuration but highly degraded with gain reduction. Conversely, the ability of the model to predict existing data for long maskers was better with than without gain reduction. Overall, the model predictions suggest that TF masking can be affected by efferent (or other) effects that reduce cochlear gain. Such effects were avoided in the experiment of this study by using maximally-compact stimuli. PMID:27875575

Auditory Time-Frequency Masking for Spectrally and Temporally Maximally-Compact Stimuli.

PubMed

Necciari, Thibaud; Laback, Bernhard; Savel, Sophie; Ystad, Sølvi; Balazs, Peter; Meunier, Sabine; Kronland-Martinet, Richard

2016-01-01

Many audio applications perform perception-based time-frequency (TF) analysis by decomposing sounds into a set of functions with good TF localization (i.e. with a small essential support in the TF domain) using TF transforms and applying psychoacoustic models of auditory masking to the transform coefficients. To accurately predict masking interactions between coefficients, the TF properties of the model should match those of the transform. This involves having masking data for stimuli with good TF localization. However, little is known about TF masking for mathematically well-localized signals. Most existing masking studies used stimuli that are broad in time and/or frequency and few studies involved TF conditions. Consequently, the present study had two goals. The first was to collect TF masking data for well-localized stimuli in humans. Masker and target were 10-ms Gaussian-shaped sinusoids with a bandwidth of approximately one critical band. The overall pattern of results is qualitatively similar to existing data for long maskers. To facilitate implementation in audio processing algorithms, a dataset provides the measured TF masking function. The second goal was to assess the potential effect of auditory efferents on TF masking using a modeling approach. The temporal window model of masking was used to predict present and existing data in two configurations: (1) with standard model parameters (i.e. without efferents), (2) with cochlear gain reduction to simulate the activation of efferents. The ability of the model to predict the present data was quite good with the standard configuration but highly degraded with gain reduction. Conversely, the ability of the model to predict existing data for long maskers was better with than without gain reduction. Overall, the model predictions suggest that TF masking can be affected by efferent (or other) effects that reduce cochlear gain. Such effects were avoided in the experiment of this study by using maximally-compact stimuli.

The Application of a Homologous Recombination Assay Revealed Amino Acid Residues in an LTR-Retrotransposon That Were Critical for Integration

PubMed Central

Atwood, Angela; Choi, Jeannie; Levin, Henry L.

1998-01-01

Retroviruses and their relatives, the LTR-retrotransposons, possess an integrase protein (IN) that is required for the insertion of reverse transcripts into the genome of host cells. Schizosaccharomyces pombe is the host of Tf1, an LTR-retrotransposon with integration activity that can be studied by using techniques of yeast genetics. In this study, we sought to identify amino acid substitutions in Tf1 that specifically affected the integration step of transposition. In addition to seeking amino acid substitutions in IN, we also explored the possibility that other Tf1 proteins contributed to integration. By comparing the results of genetic assays that monitored both transposition and reverse transcription, we were able to seek point mutations throughout Tf1 that blocked transposition but not the synthesis of reverse transcripts. These mutant versions of Tf1 were candidates of elements that possessed defects in the integration step of transposition. Five mutations in Tf1 that resulted in low levels of integration were found to be located in the IN protein: two substitutions in the N-terminal Zn domain, two in the catalytic core, and one in the C-terminal domain. These results suggested that each of the three IN domains was required for Tf1 transposition. The potential role of these five amino acid residues in the function of IN is discussed. Two of the mutations that reduced integration mapped to the RNase H (RH) domain of Tf1 reverse transcriptase. The Tf1 elements with the RH mutations produced high levels of reverse transcripts, as determined by recombination and DNA blot analysis. These results indicated that the RH of Tf1 possesses a function critical for transposition that is independent of the accumulation of reverse transcripts. PMID:9445033

Structural modulation of factor VIIa by full-length tissue factor (TF1-263): implication of novel interactions between EGF2 domain and TF.

PubMed

Prasad, Ramesh; Sen, Prosenjit

2018-02-01

Tissue factor (TF)-mediated factor VII (FVII) activation and a subsequent proteolytic TF-FVIIa binary complex formation is the key step initiating the coagulation cascade, with implications in various homeostatic and pathologic scenarios. TF binding allosterically modifies zymogen-like free FVIIa to its highly catalytically active form. As a result of unresolved crystal structure of the full-length TF 1-263 -FVIIa binary complex and free FVIIa, allosteric alterations in FVIIa following its binding to full-length TF and the consequences of these on function are not entirely clear. The present study aims to map and identify structural alterations in FVIIa and TF resulting from full-length TF binding to FVIIa and the key events responsible for enhanced FVIIa activity in coagulation. We constructed the full-length TF 1-263 -FVIIa membrane bound complex using computational modeling and subjected it to molecular dynamics (MD) simulations. MD simulations showed that TF alters the structure of each domain of FVIIa and these combined alterations contribute to enhanced TF-FVIIa activity. Detailed, domain-wise investigation revealed several new non-covalent interactions between TF and FVIIa that were not found in the truncated soluble TF-FVIIa crystal structure. The structural modulation of each FVIIa domain imparted by TF indicated that both inter and intra-domain communication is crucial for allosteric modulation of FVIIa. Our results suggest that these newly formed interactions can provide additional stability to the protease domain and regulate its activity profile by governing catalytic triad (CT) orientation and localization. The unexplored newly formed interactions between EGF2 and TF provides a possible explanation for TF-induced allosteric activation of FVIIa.

Drivers of U.S. toxicological footprints trajectory 1998–2013

PubMed Central

Koh, S. C. L.; Ibn-Mohammed, T.; Acquaye, A.; Feng, K.; Reaney, I. M.; Hubacek, K.; Fujii, H.; Khatab, K.

2016-01-01

By exploiting data from the Toxic Release Inventory of the United States, we have established that the toxicological footprint (TF) increased by 3.3% (88.4 Mt) between 1998 and 1999 and decreased by 39% (1088.5 Mt) between 1999 and 2013. From 1999 to 2006, the decreasing TF was driven by improvements in emissions intensity (i.e. gains in production efficiency) through toxic chemical management options: cleaner production; end of pipe treatment; transfer for further waste management; and production scale. In particular, the mining sector reduced its TF through outsourcing processes. Between 2006 and 2009, decreasing TF was due to decrease in consumption volume triggered by economic recession. Since 2009, the economic recovery increased TF, overwhelming the influence of improved emissions intensity through population growth, consumption and production structures. Accordingly, attaining a less-toxic economy and environment will be influenced by a combination of gains in production efficiency through improvement in emissions mitigation technologies and changes in consumption patterns. Overall, the current analysis highlights the structural dynamics of toxic chemical release and would inform future formulation of effective mitigation standards and management protocols towards the detoxification of the environment. PMID:28000739

Thermal analysis of the cryostat feed through for the ITER Tokamak TF feeder

NASA Astrophysics Data System (ADS)

Zhang, Shanwen; Song, Yuntao; Lu, Kun; Wang, Zhongwei; Zhang, Jianfeng; Qin, Yongfa

2017-04-01

In Tokamaks, the toroidal field (TF) coil feeder is an important component that is used to supply the cryogens and electrical power for the TF coils. As a part of the TF feeder, the cryostat-feed through (CFT) is subject to low temperatures of 9 and 80 K inside and room temperature of 300 K outside. Based on the features of the International Thermonuclear Experimental Reactor TF feeder, the thermal performance of the CFT under the nominal conditions is studied. Taking into account the conductive, convective and radiation heat transfer, the finite element model of the CFT is built. Transient thermal analysis is performed to determine the temperatures of the CFT on the 9th day of cooldown. The model is assessed by comparing the cooling curves of the CFT after 9 days. If the simulation and experimental results are the same, the finite element model can be considered as calibrated. The model predicts that the cooling time will be approximately 26 days and the temperature distribution and heat load of the main components are obtained when the CFT reaches thermal equilibrium. This study provides a valid quantitative characterization of the CFT design.

The Functionally Conserved Nucleoporins Nup124p from Fission Yeast and the Human Nup153 Mediate Nuclear Import and Activity of the Tf1 Retrotransposon and HIV-1 VprV⃞

PubMed Central

Varadarajan, Padmapriya; Mahalingam, Sundarasamy; Liu, Peiyun; Ng, Sarah Boon Hsi; Gandotra, Sheetal; Dorairajoo, Desmond Suresh Kumar; Balasundaram, David

2005-01-01

We report that the fission yeast nucleoporin Nup124p is required for the nuclear import of both, retrotransposon Tf1-Gag as well as the retroviral HIV-1 Vpr. Failure to import Tf1-Gag into the nucleus in a nup124 null mutant resulted in complete loss of Tf1 transposition. Similarly, nuclear import of HIV-1 Vpr was impaired in nup124 null mutant strains and cells became resistant to Vpr's cell-killing activity. On the basis of protein domain similarity, the human nucleoporin Nup153 was identified as a putative homolog of Nup124p. We demonstrate that in vitro–translated Nup124p and Nup153 coimmunoprecipitate Tf1-Gag or HIV-1 Vpr. Though full-length Nup153 was unable to complement the Tf1 transposition defect in a nup124 null mutant, we provide evidence that both nucleoporins share a unique N-terminal domain, Nup124pAA264–454 and Nup153AA448–634 that is absolutely essential for Tf1 transposition. Epigenetic overexpression of this domain in a wild-type (nup124+) background blocked Tf1 activity implying that sequences from Nup124p and the human Nup153 challenged the same pathway affecting Tf1 transposition. Our results establish a unique relationship between two analogous nucleoporins Nup124p and Nup153 wherein the function of a common domain in retrotransposition is conserved. PMID:15659641

The COUP-TFs compose a family of functionally related transcription factors

PubMed Central

Wang, Lee-Ho; Ing, Nancy H.; Tsai, Sophia Y.; O’Malley, Bert W.; Tsai, Ming-Jer

1991-01-01

The chicken ovalbumin upstream promoter transcription factors (COUP-TFs) are members of the steroid/thyroid hormone receptor superfamily and function in transcriptional regulation of a wide variety of genes. The COUP-TFs purified from HeLa nuclear extract by COUP-affinity chromatography are composed of multiple Mr forms. The Low Mr COUP-TFs (43,000, 44,000, 46,000, and 47,000 Mr) produce a relatively fast migrating complex (Cl) with DNA in electrophoresis mobility shift assays, while the high Mr forms (66,000, 68,000, 72,000, and 74,000 Mr) produce a slower migrating (C2) complex. The high Mr COUP-TFs were purified by gel filtration chromatography and independently formed the C2 DNA complex, probably acting as dimers. The high Mr forms are indistinguishable from the low Mr COUP-TFs in DNA binding and in enhancement of in vitro transcription from the ovalbumin promoter. The finding of multiple COUP-TF forms led us to clone a second low Mr COUP-TF, “COUP-TF2.” The COUP-TF2 sequence has very strong homology with COUP-TF1. The N-termini of COUP-TF1 and COUP-TF2 are least similar, but both contain glutamine-rich and proline-rich motifs, putative activation domains. PMID:1820218

Could transformation mechanisms of acetylase-harboring pMdT1 plasmid be evaluated through proteomic tools in Escherichia coli?

PubMed

Magalhães, Pedro; Pinto, Luís; Gonçalves, Alexandre; Araújo, José Eduardo; Santos, Hugo M; Capelo, José Luis; Saénz, Yolanda; de Toro, María; Torres, Carmen; Chambon, Christophe; Hébraud, Michel; Poeta, Patrícia; Igrejas, Gilberto

2016-08-11

Escherichia coli is a commensal microorganism of the gastrointestinal tract of animals and humans and it is an excellent model organism for the study of antibiotic resistance mechanisms. The resistance transmission and other characteristics of bacteria are based on different types of gene transfer occurring throughout the bacterial evolution. One of which is horizontal gene transfer that allows us to understand the ability of bacteria to acquire new genes. One dimensional and two dimensional electrophoresis (2-DE) techniques were performed in order to identify and characterize the proteome of two E. coli strains: Electromax DH10B, a transformation-ready strain; and TF-Se20, the Electromax DH10B that contains the aac(6')-Ib-cr4-harboring pMdT1 plasmid. After 2-DE and subsequent analysis by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), it was possible to identify 76 distinct proteins on the TF-Se20 strain, whereas 71 had a known function. From Electromax DH10B strain, 72 different proteins were identified of which 71 were associated with a biological process. The protein of interest, aminoglycoside N-(6')-acetyltransferase type 1, was identified by MALDI-TOF MS. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique was performed to determine its sequence. Seventy six percent of the acetylase sequence was reconstructed only in the TF-Se20 strain, representing the single protein associated to antibiotic resistance. MALDI-TOF MS and LC-MS/MS approaches allowed us to determine the total proteome of both strains, as well as the acetylase sequence. Both of them enhance the ability to obtain more accurate information about the mechanisms of antimicrobial resistance. The pMdT1 plasmid brings a new perspective in understanding the metabolic processes that lead to antibiotic resistance. This study highlights the importance of proteomics and bioinformatics in understanding mechanisms of gene transfer and antibiotic resistance. These two approaches allow to compare the protein expression in different samples, as well as different biological processes related to each protein. Copyright © 2016 Elsevier B.V. All rights reserved.

The clinical value of tissue factor assays.

PubMed

Francis, J L; Carvalho, M; Francis, D A

1995-06-01

Tissue factor (TF) is now considered to be the primary physiologic activator of the blood coagulation system. Coupled with recent advances in our understanding of the biochemistry of TF this has heightened interest in measuring aspects of TF activity in disease states. Expression of TF by blood monocytes in various diseases is an established trigger for intravascular coagulation and there is now a considerable body of experience with its measurement. This has considerable clinical potential although more widespread application awaits a consensus on the most appropriate methodologic approach to its measurement. TF can be detected in urine and may reflect the activation state of renal macrophages. Urinary TF is increased in cancer and could have diagnostic and prognostic value in a variety of malignant diseases. Finally, it is now possible to measure soluble TF in plasma. One such assay is commercially available and is technically simple to perform. The clinical value of such assays, however, must await better understanding of the source and function of soluble TF in plasma.

No effect of digestate amendment on Cs-137 and Sr-90 translocation in lysimeter experiments.

PubMed

Mehmood, Khalid; Berns, Anne E; Pütz, Thomas; Burauel, Peter; Vereecken, Harry; Opitz, Thorsten; Zoriy, Myroslav; Hofmann, Diana

2017-04-01

The soil-plant transfer of Cs-137 and Sr-90 in different crops was determined with respect to the present-day amendment practice of using digestate from biogas fermenters. The studies were performed using large lysimeters filled with undisturbed luvisol monoliths. In contrast to the conservative tracer, Br - , neither of the studied radionuclides showed a significant vertical translocation nor effect of the applied digestate amendment compared to a non-amended control was found. Furthermore, no significant plant uptake was measured for both nuclides in wheat or oat as indicated by the low transfer factors between soil-shoot for Cs-137 (TF 0.001-0.010) and for Sr-90 (0.10-0.51). The transfer into nutritionally relevant plant parts was even lower with transfer factors for soil-grain for Cs-137 (TF 0.000-0.001) and for Sr-90 (0.01-0.06). Hence, the amendment with biogas digestate is unfortunately not an option to further reduce plant uptake of these radionuclides in agricultural crops, but it does not increase plant uptake either. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface

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

Lisal, Martin; Department of Physics, Faculty of Science, J. E. Purkinje University, 400 96 Usti n. Lab.; Izak, Pavel

Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf{sub 2}N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 {mu}mol/m{sup 2} at 300 K. For [bmim][Tf{sub 2}N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are {+-}0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and itsmore » value decreases with increase of the n-hexane surface density. The [bmim][Tf{sub 2}N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.« less

Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface.

PubMed

Lísal, Martin; Izák, Pavel

2013-07-07

Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf2N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 μmol/m(2) at 300 K. For [bmim][Tf2N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are ±0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and its value decreases with increase of the n-hexane surface density. The [bmim][Tf2N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.

In Vivo 18-FDG/18-Choline-Mediated Cerenkov Radiation Energy Transfer (CRET) Multiplexed Optical Imaging for Human Prostate Carcinoma Detection and Staging

DTIC Science & Technology

2014-10-01

Transfer ( CRET ) Multiplexed Optical Imaging for Human Prostate Carcinoma Detection and Staging PRINCIPAL INVESTIGATOR: Susan L. Deutscher...SUBTITLE 5a. CONTRACT NUMBER In Vivo 18-FDG/18-Choline-Mediated Cerenkov Radiation Energy Transfer ( CRET ) Multiplexed Optical Imaging for Human...internal illumination via 18F-fluorocholine Cerenkov radiation energy transfer ( CRET ) coupled with TF- and ErbB2/3- molecularly targeted near-infrared

Rapid freeze-drying cycle optimization using computer programs developed based on heat and mass transfer models and facilitated by tunable diode laser absorption spectroscopy (TDLAS).

PubMed

Kuu, Wei Y; Nail, Steven L

2009-09-01

Computer programs in FORTRAN were developed to rapidly determine the optimal shelf temperature, T(f), and chamber pressure, P(c), to achieve the shortest primary drying time. The constraint for the optimization is to ensure that the product temperature profile, T(b), is below the target temperature, T(target). Five percent mannitol was chosen as the model formulation. After obtaining the optimal sets of T(f) and P(c), each cycle was assigned with a cycle rank number in terms of the length of drying time. Further optimization was achieved by dividing the drying time into a series of ramping steps for T(f), in a cascading manner (termed the cascading T(f) cycle), to further shorten the cycle time. For the purpose of demonstrating the validity of the optimized T(f) and P(c), four cycles with different predicted lengths of drying time, along with the cascading T(f) cycle, were chosen for experimental cycle runs. Tunable diode laser absorption spectroscopy (TDLAS) was used to continuously measure the sublimation rate. As predicted, maximum product temperatures were controlled slightly below the target temperature of -25 degrees C, and the cascading T(f)-ramping cycle is the most efficient cycle design. In addition, the experimental cycle rank order closely matches with that determined by modeling.

Biophysical Fitness Landscapes for Transcription Factor Binding Sites

PubMed Central

Haldane, Allan; Manhart, Michael; Morozov, Alexandre V.

2014-01-01

Phenotypic states and evolutionary trajectories available to cell populations are ultimately dictated by complex interactions among DNA, RNA, proteins, and other molecular species. Here we study how evolution of gene regulation in a single-cell eukaryote S. cerevisiae is affected by interactions between transcription factors (TFs) and their cognate DNA sites. Our study is informed by a comprehensive collection of genomic binding sites and high-throughput in vitro measurements of TF-DNA binding interactions. Using an evolutionary model for monomorphic populations evolving on a fitness landscape, we infer fitness as a function of TF-DNA binding to show that the shape of the inferred fitness functions is in broad agreement with a simple functional form inspired by a thermodynamic model of two-state TF-DNA binding. However, the effective parameters of the model are not always consistent with physical values, indicating selection pressures beyond the biophysical constraints imposed by TF-DNA interactions. We find little statistical support for the fitness landscape in which each position in the binding site evolves independently, indicating that epistasis is common in the evolution of gene regulation. Finally, by correlating TF-DNA binding energies with biological properties of the sites or the genes they regulate, we are able to rule out several scenarios of site-specific selection, under which binding sites of the same TF would experience different selection pressures depending on their position in the genome. These findings support the existence of universal fitness landscapes which shape evolution of all sites for a given TF, and whose properties are determined in part by the physics of protein-DNA interactions. PMID:25010228

Transverse heat transfer coefficient in the dual channel ITER TF CICCs Part II. Analysis of transient temperature responses observed during a heat slug propagation experiment

NASA Astrophysics Data System (ADS)

Lewandowska, Monika; Herzog, Robert; Malinowski, Leszek

2015-01-01

A heat slug propagation experiment in the final design dual channel ITER TF CICC was performed in the SULTAN test facility at EPFL-CRPP in Villigen PSI. We analyzed the data resulting from this experiment to determine the equivalent transverse heat transfer coefficient hBC between the bundle and the central channel of this cable. In the data analysis we used methods based on the analytical solutions of a problem of transient heat transfer in a dual-channel cable, similar to Renard et al. (2006) and Bottura et al. (2006). The observed experimental and other limits related to these methods are identified and possible modifications proposed. One result from our analysis is that the hBC values obtained with different methods differ by up to a factor of 2. We have also observed that the uncertainties of hBC in both methods considered are much larger than those reported earlier.

Improvement of COBRA-TF for modeling of PWR cold- and hot-legs during reactor transients

NASA Astrophysics Data System (ADS)

Salko, Robert K.

COBRA-TF is a two-phase, three-field (liquid, vapor, droplets) thermal-hydraulic modeling tool that has been developed by the Pacific Northwest Laboratory under sponsorship of the NRC. The code was developed for Light Water Reactor analysis starting in the 1980s; however, its development has continued to this current time. COBRA-TF still finds wide-spread use throughout the nuclear engineering field, including nuclear-power vendors, academia, and research institutions. It has been proposed that extension of the COBRA-TF code-modeling region from vessel-only components to Pressurized Water Reactor (PWR) coolant-line regions can lead to improved Loss-of-Coolant Accident (LOCA) analysis. Improved modeling is anticipated due to COBRA-TF's capability to independently model the entrained-droplet flow-field behavior, which has been observed to impact delivery to the core region[1]. Because COBRA-TF was originally developed for vertically-dominated, in-vessel, sub-channel flow, extension of the COBRA-TF modeling region to the horizontal-pipe geometries of the coolant-lines required several code modifications, including: • Inclusion of the stratified flow regime into the COBRA-TF flow regime map, along with associated interfacial drag, wall drag and interfacial heat transfer correlations, • Inclusion of a horizontal-stratification force between adjacent mesh cells having unequal levels of stratified flow, and • Generation of a new code-input interface for the modeling of coolant-lines. The sheer number of COBRA-TF modifications that were required to complete this work turned this project into a code-development project as much as it was a study of thermal-hydraulics in reactor coolant-lines. The means for achieving these tasks shifted along the way, ultimately leading the development of a separate, nearly completely independent one-dimensional, two-phase-flow modeling code geared toward reactor coolant-line analysis. This developed code has been named CLAP, for Coolant-Line-Analysis Package. Versions were created that were both coupled to COBRA-TF and standalone, with the most recent version being a standalone code. This code performs a separate, simplified, 1-D solution of the conservation equations while making special considerations for coolant-line geometry and flow phenomena. The end of this project saw a functional code package that demonstrates a stable numerical solution and that has gone through a series of Validation and Verification tests using the Two-Phase Testing Facility (TPTF) experimental data[2]. The results indicate that CLAP is under-performing RELAP5-MOD3 in predicting the experimental void of the TPTF facility in some cases. There is no apparent pattern, however, to point to a consistent type of case that the code fails to predict properly (e.g., low-flow, high-flow, discharging to full vessel, or discharging to empty vessel). Pressure-profile predictions are sometimes unrealistic, which indicates that there may be a problem with test-case boundary conditions or with the coupling of continuity and momentum equations in the solution algorithm. The code does predict the flow regime correctly for all cases with the stratification-force model off. Turning the stratification model on can cause the low-flow case void profiles to over-react to the force and the flow regime to transition out of stratified flow. The code would benefit from an increased amount of Validation & Verification testing. The development of CLAP was significant, as it is a cleanly written, logical representation of the reactor coolant-line geometry. It is stable and capable of modeling basic flow physics in the reactor coolant-line. Code development and debugging required the temporary removal of the energy equation and mass-transfer terms in governing equations. The reintroduction of these terms will allow future coupling to RELAP and re-coupling with COBRA-TF. Adding in more applicable entrainment and de-entrainment models would allow the capture of more advanced physics in the coolant-line that can be expected during Loss-of-Coolant Accident. One of the package's benefits is its ability to be used as a platform for future coolant-line model development and implementation, including capturing of the important de-entrainment behavior in reactor hot-legs (steam-binding effect) and flow convection in the upper-plenum region of the vessel.

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants.

PubMed

Jin, Jinpu; Tian, Feng; Yang, De-Chang; Meng, Yu-Qi; Kong, Lei; Luo, Jingchu; Gao, Ge

2017-01-04

With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements. In addition, we upgraded previous TF prediction server, and set up four novel tools for regulation prediction and functional enrichment analyses. Finally, we set up a novel companion portal PlantRegMap (http://plantregmap.cbi.pku.edu.cn) for users to access the regulation resource and analysis tools conveniently. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Conformational dynamics of bacterial trigger factor in apo and ribosome-bound states.

PubMed

Can, Mehmet Tarik; Kurkcuoglu, Zeynep; Ezeroglu, Gokce; Uyar, Arzu; Kurkcuoglu, Ozge; Doruker, Pemra

2017-01-01

The chaperone trigger factor (TF) binds to the ribosome exit tunnel and helps cotranslational folding of nascent chains (NC) in bacterial cells and chloroplasts. In this study, we aim to investigate the functional dynamics of fully-atomistic apo TF and its complex with 50S. As TF accomodates a high percentage of charged residues on its surface, the effect of ionic strength on TF dynamics is assessed here by performing five independent molecular dynamics (MD) simulations (total of 1.3 micro-second duration) at 29 mM and 150 mM ionic strengths. At both concentrations, TF exhibits high inter- and intra-domain flexibility related to its binding (BD), core (CD), and head (HD) domains. Even though large oscillations in gyration radius exist during each run, we do not detect the so-called 'fully collapsed' state with both HD and BD collapsed upon the core. In fact, the extended conformers with relatively open HD and BD are highly populated at the physiological concentration of 150 mM. More importantly, extended TF snapshots stand out in terms of favorable docking onto the 50S subunit. Elastic network modeling (ENM) indicates significant changes in TF's functional dynamics and domain decomposition depending on its conformation and positioning on the 50S. The most dominant slow motions are the lateral sweeping and vertical opening/closing of HD relative to 50S. Finally, our ENM-based efficient technique -ClustENM- is used to sample atomistic conformers starting with an extended TF-50S complex. Specifically, BD and CD motions are restricted near the tunnel exit, while HD is highly mobile. The atomistic conformers generated without an NC are in agreement with the cryo-EM maps available for TF-ribosome-NC complex.

In Vivo 18 FDG/18 Choline Mediated Cerenkov Radiation Energy Transfer (CRET) Multiplexed Optical Imaging for Human Prostate Carcinoma Detection and Staging

DTIC Science & Technology

2016-10-01

human prostate cancer xenografts. We have selected peptides from bacteriophage display libraries that target TF and ErbB2/ErbB3. The peptides have been...facilitate biomarker-specific diagnosis. The specific aims of the proposal are to: 1) select peptides that target the ErbB2/3 heterodimer using novel...parallel in vitro/in vivo phage display techniques; 2) generate NIR-QDs decorated with TF- and ErbB2/3-avid peptides for in vivo molecular

Understanding the Formation of Kinetically Stable Compounds and the Development of Thin Film Pair Distribution Function Analysis

NASA Astrophysics Data System (ADS)

Wood, Suzannah Rebecca

Navigating the synthesis landscape poses many challenges when developing novel solid state materials. Advancements in both synthesis and characterization are necessary to facilitate the targeting of specific materials. This dissertation discusses the formation of chalcogenide heterostructures and their properties in the first part and the development of thin film pair distribution function analysis (tfPDF) in the second part. The heterostructures were formed by the self-assembly of designed precursors deposited by physical vapor deposition in a modulated elemental reactants approach, which provides the control and predictability to synthesis. Specifically, a series of (BiSe)1+delta(TiSe2) n, where n = 2,3,&4, were synthesized to explore the extent of charge transfer from the BiSe to TiSe2 layers. To further explore the role Bi plays in charge donation, a family of structurally similar compounds, (Bix Sn1-xSe)1+deltaTiSe2, where 0≥x≥1, were synthesized and characterized. Electrical measurements show doping efficiency decreases as x increases, correlated with the structural distortion and the formation of periodic antiphase boundaries containing Bi-Bi pairs. The first heterostructures composed of three unique structural types were synthesized and Bi2Se3 layer thickness was used to tune electrical properties and further explore charge transfer. To better understand the potential energy landscape on which these kinetically stable compounds exist, two investigations were undertaken. The first was a study of the formation and subsequent decomposition of [(BiSe)1+delta]n(TiSe2)n compounds, where n= 2&3, the second an investigation of precursor structure for thermodynamically stable FeSb2 and kinetically stable FeSb3. The second section describes the development of thin film pair distribution function analysis, a technique in which total scattering data for pair distribution function (PDF) analysis is obtained from thin films, suitable for local structure analysis. This study illustrates how analysis of the local structure in amorphous precursor films can help to understand the crystallization processes of metastable phases and enables a range of new local structure studies of thin films. tfPDF was then demonstrated on In-Ga-O film materials and compared to traditional powder PDF analysis. This highlights differences between the products, and the utility of tfPDF to determined structural features of amorphous materials. This dissertation includes previously published and unpublished co-authored materials.

A proximity-based graph clustering method for the identification and application of transcription factor clusters.

PubMed

Spadafore, Maxwell; Najarian, Kayvan; Boyle, Alan P

2017-11-29

Transcription factors (TFs) form a complex regulatory network within the cell that is crucial to cell functioning and human health. While methods to establish where a TF binds to DNA are well established, these methods provide no information describing how TFs interact with one another when they do bind. TFs tend to bind the genome in clusters, and current methods to identify these clusters are either limited in scope, unable to detect relationships beyond motif similarity, or not applied to TF-TF interactions. Here, we present a proximity-based graph clustering approach to identify TF clusters using either ChIP-seq or motif search data. We use TF co-occurrence to construct a filtered, normalized adjacency matrix and use the Markov Clustering Algorithm to partition the graph while maintaining TF-cluster and cluster-cluster interactions. We then apply our graph structure beyond clustering, using it to increase the accuracy of motif-based TFBS searching for an example TF. We show that our method produces small, manageable clusters that encapsulate many known, experimentally validated transcription factor interactions and that our method is capable of capturing interactions that motif similarity methods might miss. Our graph structure is able to significantly increase the accuracy of motif TFBS searching, demonstrating that the TF-TF connections within the graph correlate with biological TF-TF interactions. The interactions identified by our method correspond to biological reality and allow for fast exploration of TF clustering and regulatory dynamics.

Molecular mechanism and structure of Trigger Factor bound to the translating ribosome

PubMed Central

Merz, Frieder; Boehringer, Daniel; Schaffitzel, Christiane; Preissler, Steffen; Hoffmann, Anja; Maier, Timm; Rutkowska, Anna; Lozza, Jasmin; Ban, Nenad; Bukau, Bernd; Deuerling, Elke

2008-01-01

Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions of Escherichia coli TF and nascent chains during translation. Furthermore, we provide the first full-length structure of TF associated with ribosome–nascent chain complexes by using cryo-electron microscopy. In its active state, TF arches over the ribosomal exit tunnel accepting nascent chains in a protective void. The growing nascent chain initially follows a predefined path through the entire interior of TF in an unfolded conformation, and even after folding into a domain it remains accommodated inside the protective cavity of ribosome-bound TF. The adaptability to accept nascent chains of different length and folding states may explain how TF is able to assist co-translational folding of all kinds of nascent polypeptides during ongoing synthesis. Moreover, we suggest a model of how TF's chaperoning function can be coordinated with the co-translational processing and membrane targeting of nascent polypeptides by other ribosome-associated factors. PMID:18497744

VASCOMP II. The V/STOL Aircraft Sizing and Performance Computer Program. Volume VI. User’s Manual. Revision 3

DTIC Science & Technology

1980-05-01

idlers, etc. Main hydraulic systems including pumps, reservoirs, accumulators, filters, valves , lines, fluid, and supports (Figure 4-40). 4-159 -4...SPEED CORRECTION Ny DN-(VALUES OF N. v VALUES OF KPR VALUES OF *111OPT VALUES OF KPN 4.OC VAL.UE LOC VALVE LOC VALU~E LOC VALUE 1207 _______ 1225...TCVT (t/c)qT 0131 TENN NUMBER OF M 0309 TF REFERRED THRUST AS A 1609 - 1616 FUNCTION OF (T/0) TF1 REFERRED N1 AS A FUNCTION 16k1 - 1648 OF (T/e) TF2

Does minimalist transfemoral transcatheter aortic valve replacement produce better survival in patients with severe chronic obstructive pulmonary disease?

PubMed

Condado, Jose F; Haider, Moosa N; Lerakis, Stamatios; Keegan, Patricia; Caughron, Hope; Thourani, Vinod H; Devireddy, Chandan; Leshnower, Bradley; Mavromatis, Kreton; Sarin, Eric L; Stewart, James; Guyton, Robert; Forcillo, Jessica; Patel, Ateet; Simone, Amy; Block, Peter C; Babaliaros, Vasilis

2017-03-01

To compare outcomes after minimalist and standard transfemoral transcatheter aortic valve replacement (TF-TAVR) in patients with severe chronic obstructive pulmonary disease (COPD). TF-TAVR is increasingly performed with conscious sedation and transthoracic echocardiography guidance (minimalist). The safety/efficacy of this technique in patients with severe COPD is unknown. We compared demographics, 30-day outcomes and 1-year survival of patients with severe COPD (FEV1% ≤50) who underwent minimalist vs. standard TF-TAVR between 2008 and 2015 at our institution. Of 88 patients with severe COPD, 46 underwent minimalist and 42 underwent standard TF-TAVR. There were no differences on baseline characteristics, except for more history of coronary artery bypass grafting (45.5% vs. 20.6%, P = 0.03) and less history of cerebrovascular disease (16.7% vs. 45.5%, P = 0.03) in the standard TF-TAVR. Seventeen minimalist TF-TAVR patients (41.0%) were transferred directly to the general medical ward with telemetry monitoring (without ICU stay); all standard TF-TAVR patients went to the ICU. Minimalist TF-TAVR patients had shorter procedure time (97 vs. 129 min, P < 0.001), ICU time (21.8 vs. 29.8 hr, P = 0.001) and length of stay (2 vs. 5 days, P = 0.001). There were no differences in procedure complications and 30-day mortality between groups. In our multivariate analysis, minimalist TF-TAVR (HR 0.28, 95%CI 0.08-0.97) and previous coronary revascularization (HR 0.24, 95%CI 0.09-0.65) were associated with increased 1-year survival. In contrast, moderate paravalvular leak (HR 7.73, 95%CI 1.94-30.84) was associated with decreased 1-year survival. In patients with severe COPD, Minimalist TF-TAVR results in less resource utilization and improved 1-year survival compared to standard approach. Our findings should be validated in a larger cohort of patients with severe COPD. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Parameterization of Photon Tunneling with Application to Ice Cloud Optical Properties at Terrestrial Wavelengths

NASA Astrophysics Data System (ADS)

Mitchell, D. L.

2006-12-01

Sometimes deep physical insights can be gained through the comparison of two theories of light scattering. Comparing van de Hulst's anomalous diffraction approximation (ADA) with Mie theory yielded insights on the behavior of the photon tunneling process that resulted in the modified anomalous diffraction approximation (MADA). (Tunneling is the process by which radiation just beyond a particle's physical cross-section may undergo large angle diffraction or absorption, contributing up to 40% of the absorption when wavelength and particle size are comparable.) Although this provided a means of parameterizing the tunneling process in terms of the real index of refraction and size parameter, it did not predict the efficiency of the tunneling process, where an efficiency of 100% is predicted for spheres by Mie theory. This tunneling efficiency, Tf, depends on particle shape and ranges from 0 to 1.0, with 1.0 corresponding to spheres. Similarly, by comparing absorption efficiencies predicted by the Finite Difference Time Domain Method (FDTD) with efficiencies predicted by MADA, Tf was determined for nine different ice particle shapes, including aggregates. This comparison confirmed that Tf is a strong function of ice crystal shape, including the aspect ratio when applicable. Tf was lowest (< 0.36) for aggregates and plates, and largest (> 0.9) for quasi- spherical shapes. A parameterization of Tf was developed in terms of (1) ice particle shape and (2) mean particle size regarding the large mode (D > 70 mm) of the ice particle size distribution. For the small mode, Tf is only a function of ice particle shape. When this Tf parameterization is used in MADA, absorption and extinction efficiency differences between MADA and FDTD are within 14% over the terrestrial wavelength range 3-100 mm for all size distributions and most crystal shapes likely to be found in cirrus clouds. Using hyperspectral radiances, it is demonstrated that Tf can be retrieved from ice clouds. Since Tf is a function of ice particle shape, this may provide a means of retrieving qualitative information on ice particle shape.

Transferrin receptors and the targeted delivery of therapeutic agents against cancer

PubMed Central

Daniels, Tracy R.; Bernabeu, Ezequiel; Rodríguez, José A.; Patel, Shabnum; Kozman, Maggie; Chiappetta, Diego A.; Holler, Eggehard; Ljubimova, Julia Y.; Helguera, Gustavo; Penichet, Manuel L.

2012-01-01

Background Traditional cancer therapy can be successful in destroying tumors, but can also cause dangerous side effects. Therefore, many targeted therapies are in development. The transferrin receptor (TfR) functions in cellular iron uptake through its interaction with transferrin. This receptor is an attractive molecule for the targeted therapy of cancer since it is upregulated on the surface of many cancer types and is efficiently internalized. This receptor can be targeted in two ways: 1) for the delivery of therapeutic molecules into malignant cells or 2) to block the natural function of the receptor leading directly to cancer cell death. Scope of review In the present article we discuss the strategies used to target the TfR for the delivery of therapeutic agents into cancer cells. We provide a summary of the vast types of anti-cancer drugs that have been delivered into cancer cells employing a variety of receptor binding molecules including Tf, anti-TfR antibodies, or TfR-binding peptides alone or in combination with carrier molecules including nanoparticles and viruses. Major conclusions Targeting the TfR has been shown to be effective in delivering many different therapeutic agents and causing cytotoxic effects in cancer cells in vitro and in vivo. General significance The extensive use of TfR for targeted therapy attests to the versatility of targeting this receptor for therapeutic purposes against malignant cells. More advances in this area are expected to further improve the therapeutic potential of targeting the TfR for cancer therapy leading to an increase in the number of clinical trials of molecules targeting this receptor. PMID:21851850

Tissue Factor-Factor VII Complex As a Key Regulator of Ovarian Cancer Phenotypes.

PubMed

Koizume, Shiro; Miyagi, Yohei

2015-01-01

Tissue factor (TF) is an integral membrane protein widely expressed in normal human cells. Blood coagulation factor VII (fVII) is a key enzyme in the extrinsic coagulation cascade that is predominantly secreted by hepatocytes and released into the bloodstream. The TF-fVII complex is aberrantly expressed on the surface of cancer cells, including ovarian cancer cells. This procoagulant complex can initiate intracellular signaling mechanisms, resulting in malignant phenotypes. Cancer tissues are chronically exposed to hypoxia. TF and fVII can be induced in response to hypoxia in ovarian cancer cells at the gene expression level, leading to the autonomous production of the TF-fVII complex. Here, we discuss the roles of the TF-fVII complex in the induction of malignant phenotypes in ovarian cancer cells. The hypoxic nature of ovarian cancer tissues and the roles of TF expression in endometriosis are discussed. Arguments will be extended to potential strategies to treat ovarian cancers based on our current knowledge of TF-fVII function.

Study on the interaction of a cyanine dye with human serum transferrin.

PubMed

Zhang, Xiu-feng; Chen, Lei; Yang, Qian-fan; Li, Qian; Sun, Xiao-ran; Chen, Hong-bo; Yang, Guang; Tang, Ya-lin

2015-12-01

Complexation between the primary carrier of ligands in blood plasma, human serum transferrin (Tf), and a cyanine dye, 3,3'-di(3-sulfopropyl)-4,5,4',5'-dibenzo-9-phenyl-thiacarbocyanine-triethylam monium salt (PTC) was investigated using fluorescence spectra, UV/Vis absorption spectra, synchronous fluorescence spectra, circular dichroism (CD) and molecular dynamic docking. The experimental results demonstrate that the formation of PTC-Tf complex is stabilized by van der Waal's interactions and hydrogen bonds, and the binding constants were found to be 8.55 × 10(6), 8.19 × 10(6) and 1.75 × 10(4) M(-1). Moreover, fluorescence experiments prove that the operational mechanism for the fluorescence quenching is static quenching and non-radiative energy transfer. Structural investigation of the PTC-Tf complexes via synchronous fluorescence spectra and CD showed that the structure of Tf became more stable with a major increase in the α-helix content and increased polarity around the tryptophan residues after PTC binding. In addition, molecular modeling highlights the residues located in the N-lobe, which retain high affinity for PTC. The mode of action of the PTC-Tf complex is illustrated by these results, and may provide an effective pathway for the transport and targeted delivery of antitumor agents. Copyright © 2015 John Wiley & Sons, Ltd.

Characterization of iron uptake from transferrin by murine endothelial cells.

PubMed

Hallmann, R; Savigni, D L; Morgan, E H; Baker, E

2000-01-01

Iron is required by the brain for normal function, however, the mechanisms by which it crosses the blood-brain barrier (BBB) are poorly understood. The uptake and efflux of transferrin (Tf) and Fe by murine brain-derived (bEND3) and lymph node-derived (m1END1) endothelial cell lines was compared. The effects of iron chelators, metabolic inhibitors and the cellular activators, lipopolysaccharide (LPS) and tumour necrosis factor-alpha (TNF-alpha), on Tf and Fe uptake were investigated. Cells were incubated with 59Fe-125I-Tf; Fe uptake was shown to increase linearly over time for both cell lines, while Tf uptake reached a plateau within 2 h. Both Tf and Fe uptake were saturable. bEND3 cells were shown to have half as many Tf receptors as m1END1 cells, but the mean cycling times of a Tf molecule were the same. Tf and Fe efflux from the cells were measured over time, revealing that after 2 h only 25% of the Tf but 80% of the Fe remained associated with the cells. Of 7 iron chelators, only deferriprone (L1) markedly decreased Tf uptake. However, Fe uptake was reduced by more than 50% by L1, pyridoxal isonicotinoyl hydrazone (PIH) and desferrithiocin (DFT). The cellular activators TNF-alpha or LPS had little effect on Tf turnover, but they accelerated Fe uptake in both endothelial cell types. Phenylarsenoxide (PhAsO) and N-ethyl maleimide (NEM), inhibitors of Tf endocytosis, reduced both Tf and Fe uptake in both cell lines, while bafilomycin A1, an inhibitor of endosomal acidification, reduced Fe uptake but did not affect Tf uptake. The results suggest that Tf and Fe uptake by both bEND3 and m1END1 is via receptor-mediated endocytosis with release of Fe from Tf within the cell and recycling of apo-Tf. On the basis of Tf- and Fe-metabolism both cell lines are similar and therefore well suited for use in in vitro models for Fe transport across the BBB.

Coup-TF1 and Coup-TF2 control subtype and laminar identity of MGE-derived neocortical interneurons.

PubMed

Hu, Jia Sheng; Vogt, Daniel; Lindtner, Susan; Sandberg, Magnus; Silberberg, Shanni N; Rubenstein, John L R

2017-08-01

Distinct cortical interneuron (CIN) subtypes have unique circuit functions; dysfunction in specific subtypes is implicated in neuropsychiatric disorders. Somatostatin- and parvalbumin-expressing (SST + and PV + ) interneurons are the two major subtypes generated by medial ganglionic eminence (MGE) progenitors. Spatial and temporal mechanisms governing their cell-fate specification and differential integration into cortical layers are largely unknown. We provide evidence that Coup-TF1 and Coup-TF2 ( Nr2f1 and Nr2f2 ) transcription factor expression in an arc-shaped progenitor domain within the MGE promotes time-dependent survival of this neuroepithelium and the time-dependent specification of layer V SST + CINs. Coup-TF1 and Coup-TF2 autonomously repress PV + fate in MGE progenitors, in part through directly driving Sox6 expression. These results have identified, in mouse, a transcriptional pathway that controls SST-PV fate. © 2017. Published by The Company of Biologists Ltd.

Transferrin receptor regulates pancreatic cancer growth by modulating mitochondrial respiration and ROS generation

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

Jeong, Seung Min, E-mail: smjeong@catholic.ac.kr; Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul 137-701; Hwang, Sunsook

2016-03-11

The transferrin receptor (TfR1) is upregulated in malignant cells and its expression is associated with cancer progression. Because of its pre-eminent role in cell proliferation, TfR1 has been an important target for the development of cancer therapy. Although TfR1 is highly expressed in pancreatic cancers, what it carries out in these refractory cancers remains poorly understood. Here we report that TfR1 supports mitochondrial respiration and ROS production in human pancreatic ductal adenocarcinoma (PDAC) cells, which is required for their tumorigenic growth. Elevated TfR1 expression in PDAC cells contributes to oxidative phosphorylation, which allows for the generation of ROS. Importantly, mitochondrial-derivedmore » ROS are essential for PDAC growth. However, exogenous iron supplement cannot rescue the defects caused by TfR1 knockdown. Moreover, we found that TfR1 expression determines PDAC cells sensitivity to oxidative stress. Together, our findings reveal that TfR1 can contribute to the mitochondrial respiration and ROS production, which have essential roles in growth and survival of pancreatic cancer. - Highlights: • Pancreatic ductal adenocarcinoma (PDAC) exhibits an elevated transferrin receptor (TfR1) expression in comparison with non-transformed pancreatic cells. • TfR1 is required for PDAC growth by regulating mitochondrial respiration and ROS production. • TfR1 functions as a determinant of cell viability to oxidative stress in PDAC cells.« less

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

Robison, W L; Hamilton, T F; Bogen, K

Inter-plant concentration ratios (IPCR), [Bq g{sup -1} {sup 137}Cs in coral atoll tree food-crops/Bq g{sup -1} {sup 137}Cs in leaves of native plant species whose roots share a common soil volume], can replace transfer factors (TF) to predict {sup 137}Cs concentration in tree food-crops in a contaminated area with an aged source term. The IPCR strategy has significant benefits relative to TF strategy for such purposes in the atoll ecosystem. IPCR strategy applied to specific assessments takes advantage of the fact tree roots naturally integrate 137Cs over large volumes of soil. Root absorption of {sup 137}Cs replaces large-scale, expensive soilmore » sampling schemes to reduce variability in {sup 137}Cs concentration due to inhomogeneous radionuclide distribution. IPCR [drinking-coconut meat (DCM)/Scaevola (SCA) and Tournefortia (TOU) leaves (native trees growing on all atoll islands)] are log normally distributed (LND) with geometric standard deviation (GSD) = 1.85. TF for DCM from Enewetak, Eneu, Rongelap and Bikini Atolls are LND with GSD's of 3.5, 3.0, 2.7, and 2.1, respectively. TF GSD for Rongelap copra coconut meat is 2.5. IPCR of Pandanus fruit to SCA and TOU leaves are LND with GSD = 1.7 while TF GSD is 2.1. Because IPCR variability is much lower than TF variability, relative sampling error of an IPCR field sample mean is up 6- to 10-fold lower than that of a TF sample mean if sample sizes are small (10 to 20). Other IPCR advantages are that plant leaf samples are collected and processed in far less time with much less effort and cost than soil samples.« less

Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach

PubMed Central

Ye, Yusen; Gao, Lin; Zhang, Shihua

2017-01-01

Transcription factors play a key role in transcriptional regulation of genes and determination of cellular identity through combinatorial interactions. However, current studies about combinatorial regulation is deficient due to lack of experimental data in the same cellular environment and extensive existence of data noise. Here, we adopt a Bayesian CANDECOMP/PARAFAC (CP) factorization approach (BCPF) to integrate multiple datasets in a network paradigm for determining precise TF interaction landscapes. In our first application, we apply BCPF to integrate three networks built based on diverse datasets of multiple cell lines from ENCODE respectively to predict a global and precise TF interaction network. This network gives 38 novel TF interactions with distinct biological functions. In our second application, we apply BCPF to seven types of cell type TF regulatory networks and predict seven cell lineage TF interaction networks, respectively. By further exploring the dynamics and modularity of them, we find cell lineage-specific hub TFs participate in cell type or lineage-specific regulation by interacting with non-specific TFs. Furthermore, we illustrate the biological function of hub TFs by taking those of cancer lineage and blood lineage as examples. Taken together, our integrative analysis can reveal more precise and extensive description about human TF combinatorial interactions. PMID:29033978

Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach.

PubMed

Ye, Yusen; Gao, Lin; Zhang, Shihua

2017-01-01

Transcription factors play a key role in transcriptional regulation of genes and determination of cellular identity through combinatorial interactions. However, current studies about combinatorial regulation is deficient due to lack of experimental data in the same cellular environment and extensive existence of data noise. Here, we adopt a Bayesian CANDECOMP/PARAFAC (CP) factorization approach (BCPF) to integrate multiple datasets in a network paradigm for determining precise TF interaction landscapes. In our first application, we apply BCPF to integrate three networks built based on diverse datasets of multiple cell lines from ENCODE respectively to predict a global and precise TF interaction network. This network gives 38 novel TF interactions with distinct biological functions. In our second application, we apply BCPF to seven types of cell type TF regulatory networks and predict seven cell lineage TF interaction networks, respectively. By further exploring the dynamics and modularity of them, we find cell lineage-specific hub TFs participate in cell type or lineage-specific regulation by interacting with non-specific TFs. Furthermore, we illustrate the biological function of hub TFs by taking those of cancer lineage and blood lineage as examples. Taken together, our integrative analysis can reveal more precise and extensive description about human TF combinatorial interactions.

Solution of Volterra and Fredholm Classes of Equations via Triangular Orthogonal Function (A Combination of Right Hand Triangular Function and Left Hand Triangular Function) and Hybrid Orthogonal Function (A Combination of Sample Hold Function and Right Hand Triangular Function)

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Anirban; Ganguly, Anindita; Chatterjee, Saumya Deep

2018-04-01

In this paper the authors have dealt with seven kinds of non-linear Volterra and Fredholm classes of equations. The authors have formulated an algorithm for solving the aforementioned equation types via Hybrid Function (HF) and Triangular Function (TF) piecewise-linear orthogonal approach. In this approach the authors have reduced integral equation or integro-differential equation into equivalent system of simultaneous non-linear equation and have employed either Newton's method or Broyden's method to solve the simultaneous non-linear equations. The authors have calculated the L2-norm error and the max-norm error for both HF and TF method for each kind of equations. Through the illustrated examples, the authors have shown that the HF based algorithm produces stable result, on the contrary TF-computational method yields either stable, anomalous or unstable results.

Reverse Transcription of a Self-Primed Retrotransposon Requires an RNA Structure Similar to the U5-IR Stem-Loop of Retroviruses

PubMed Central

Lin, Jia-Hwei; Levin, Henry L.

1998-01-01

An inverted repeat (IR) within the U5 region of the Rous sarcoma virus (RSV) mRNA forms a structure composed of a 7-bp stem and a 5-nucleotide (nt) loop. This U5-IR structure has been shown to be required for the initiation of reverse transcription. The mRNA of Tf1, long terminal repeat-containing retrotransposon from fission yeast (Schizosaccharomyces pombe) contains nucleotides with the potential to form a U5-IR stem-loop that is strikingly similar to that of RSV. The putative U5-IR stem-loop of Tf1 consists of a 7-bp stem and a 25-nt loop. Results from mutagenesis studies indicate that the U5-IR stem-loop in the mRNA of Tf1 does form and that it is required for Tf1 transposition. Although the loop is required for transposition, we were surprised that the specific sequence of the nucleotides within the loop was unimportant for function. Additional investigation indicates that the loss of transposition activity due to a reduction in the loop size to 6 nt could be rescued by increasing the GC content of the stem. This result indicates that the large loop in the Tf1 mRNA relative to that of the RSV allows the formation of the relatively weak U5-IR stem. The levels of Tf1 proteins expressed and the amounts of Tf1 RNA packaged into the virus-like particles were not affected by mutations in the U5-IR structure. However, all of the mutations in the U5-IR structure that caused defects in transposition produced low amounts of reverse transcripts. A unique feature in the initiation of Tf1 reverse transcription is that, instead of a tRNA, the first 11 nt of the Tf1 mRNA serve as the minus-strand primer. Analysis of the 5′ end of Tf1 mRNA revealed that the mutations in the U5-IR stem-loop that resulted in defects in reverse transcription caused a reduction in the cleavage activity required to generate the Tf1 primer. Our results indicate that the U5-IR stems of Tf1 and RSV are conserved in size, position, and function. PMID:9774699

When it is too hot for photosynthesis: heat-induced instability of photosynthesis in relation to respiratory burst, cell permeability changes and H₂O₂ formation.

PubMed

Hüve, Katja; Bichele, Irina; Rasulov, Bahtijor; Niinemets, Ulo

2011-01-01

Photosynthesis rate (A(n)) becomes unstable above a threshold temperature, and the recovery upon return to low temperature varies because of reasons not fully understood. We investigated responses of A(n), dark respiration and chlorophyll fluorescence to supraoptimal temperatures of varying duration and kinetics in Phaseolus vulgaris asking whether the instability of photosynthesis under severe heat stress is associated with cellular damage. Cellular damage was assessed by Evans blue penetration (enhanced membrane permeability) and by H₂O₂ generation [3,3'-diaminobenzidine 4HCl (DAB)-staining]. Critical temperature for dark fluorescence (F(0) ) rise (T(F)) was at 46-48 °C, and a burst of respiration was observed near T(F). However, A(n) was strongly inhibited already before T(F) was reached. Membrane permeability increased with temperature according to a switch-type response, with enhanced permeability observed above 48 °C. Experiments with varying heat pulse lengths and intensities underscored the threshold-type loss of photosynthetic function, and indicated that the degree of photosynthetic deterioration and cellular damage depended on accumulated heat-dose. Beyond the 'point of no return', propagation of cellular damage and reduction of photosynthesis continued upon transfer to lower temperatures and photosynthetic recovery was slow or absent. We conclude that instability of photosynthesis under severe heat stress is associated with time-dependent propagation of cellular lesions. © 2010 Blackwell Publishing Ltd.

The Dependence of Solar Flare Limb Darkening on Emission Peak Formation Temperature

NASA Astrophysics Data System (ADS)

Thiemann, Edward; Epp, Luke; Eparvier, Francis; Chamberlin, Phillip C.

2017-08-01

Solar limb effects are local brightening or darkening of an emission that depend on where in the Sun's atmosphere it forms. Near the solar limb, optically thick (thin) emissions will darken (brighten) as the column of absorbers (emitters) along the line-of-sight increases. Note that in limb brightening, emission sources are re-arranged whereas in limb darkening they are obscured. Thus, only limb darkening is expected to occur in disk integrated observations. Limb darkening also results in center-to-limb variations of disk-integrated solar flare spectra, with important consequences for how planetary atmospheres are affected by flares. Flares are typically characterized by their flux in the optically thin 0.1-0.8 nm band measured by the X-ray Sensor (XRS) on board the Geostationary Operational Environmental Satellite (GOES). On the other hand, Extreme Ultraviolet (EUV) line emissions can limb darken because they are sensitive to resonant scattering, resulting in a flare's location on the solar disk controlling the amount of ionizing radiation that reaches a planet. For example, an X-class flare originating from disk center may significantly heat a planet's thermosphere, whereas the same flare originating near the limb may have no effect because much of the effective emissions are scattered in the solar corona.To advance the relatively poor understanding of flare limb darkening, we use over 300 M-class or larger flares observed by the EUV Variability Experiment (EVE) onboard the Solar Dynamics Observatory (SDO) to characterize limb darkening as a function of emission peak formation temperature, Tf. For hot coronal emissions (Tf>2 MK), these results show a linear relationship between the degree of limb darkening and Tf where lines with Tf=2 MK darken approximately 7 times more than lines with Tf=16 MK. Because the extent of limb darkening is dependent on the height of the source plasma, we use simple Beer-Lambert radiative transfer analysis to interpret these results and characterize the average thermal structure of the flares considered. As such, these results can be used to constrain both empirical flare irradiance models and more sophisticated flare loop hydrodynamic models.

Non-linear transfer characteristics of stimulation and recording hardware account for spurious low-frequency artifacts during amplitude modulated transcranial alternating current stimulation (AM-tACS).

PubMed

Kasten, Florian H; Negahbani, Ehsan; Fröhlich, Flavio; Herrmann, Christoph S

2018-05-31

Amplitude modulated transcranial alternating current stimulation (AM-tACS) has been recently proposed as a possible solution to overcome the pronounced stimulation artifact encountered when recording brain activity during tACS. In theory, AM-tACS does not entail power at its modulating frequency, thus avoiding the problem of spectral overlap between brain signal of interest and stimulation artifact. However, the current study demonstrates how weak non-linear transfer characteristics inherent to stimulation and recording hardware can reintroduce spurious artifacts at the modulation frequency. The input-output transfer functions (TFs) of different stimulation setups were measured. Setups included recordings of signal-generator and stimulator outputs and M/EEG phantom measurements. 6 th -degree polynomial regression models were fitted to model the input-output TFs of each setup. The resulting TF models were applied to digitally generated AM-tACS signals to predict the frequency of spurious artifacts in the spectrum. All four setups measured for the study exhibited low-frequency artifacts at the modulation frequency and its harmonics when recording AM-tACS. Fitted TF models showed non-linear contributions significantly different from zero (all p < .05) and successfully predicted the frequency of artifacts observed in AM-signal recordings. Results suggest that even weak non-linearities of stimulation and recording hardware can lead to spurious artifacts at the modulation frequency and its harmonics. These artifacts were substantially larger than alpha-oscillations of a human subject in the MEG. Findings emphasize the need for more linear stimulation devices for AM-tACS and careful analysis procedures, taking into account low-frequency artifacts to avoid confusion with effects of AM-tACS on the brain. Copyright © 2018 Elsevier Inc. All rights reserved.

The Reverse Transcriptase of the Tf1 Retrotransposon Has a Specific Novel Activity for Generating the RNA Self-Primer That Is Functional in cDNA Synthesis▿

PubMed Central

Hizi, Amnon

2008-01-01

The Tf1 retrotransposon of Schizosaccharomyces pombe represents a group of eukaryotic long terminal repeat (LTR) retroelements that, based on their sequences, were predicted to use an RNA self-primer for initiating reverse transcription while synthesizing the negative-sense DNA strand. This feature is substantially different from the one typical to retroviruses and other LTR retrotransposons that all exhibit a tRNA-dependent priming mechanism. Genetic studies have suggested that the self-primer of Tf1 can be generated by a cleavage between the 11th and 12th bases of the Tf1 RNA transcript. The in vitro data presented here show that recombinant Tf1 reverse transcriptase indeed introduces a nick at the end of a duplexed region at the 5′ end of Tf1 genomic RNA, substantiating the prediction that this enzyme is responsible for generating this RNA self-primer. The 3′ end of the primer, generated in this manner, can then be extended upon the addition of deoxynucleoside triphosphates by the DNA polymerase activity of the same enzyme, synthesizing the negative-sense DNA strand. This functional primer must have been generated by the RNase H activity of Tf1 reverse transcriptase, since a mutant enzyme lacking this activity has lost its ability to generate the self-primer. It was also found here that the reverse transcriptases of human immunodeficiency virus type 1 and of murine leukemia virus do not exhibit this specific cleavage activity. In all, it is likely that the observed unique mechanism of self-priming in Tf1 represents an early advantageous form of initiating reverse transcription in LTR retroelements without involving cellular tRNAs. PMID:18753200

The reverse transcriptase of the Tf1 retrotransposon has a specific novel activity for generating the RNA self-primer that is functional in cDNA synthesis.

PubMed

Hizi, Amnon

2008-11-01

The Tf1 retrotransposon of Schizosaccharomyces pombe represents a group of eukaryotic long terminal repeat (LTR) retroelements that, based on their sequences, were predicted to use an RNA self-primer for initiating reverse transcription while synthesizing the negative-sense DNA strand. This feature is substantially different from the one typical to retroviruses and other LTR retrotransposons that all exhibit a tRNA-dependent priming mechanism. Genetic studies have suggested that the self-primer of Tf1 can be generated by a cleavage between the 11th and 12th bases of the Tf1 RNA transcript. The in vitro data presented here show that recombinant Tf1 reverse transcriptase indeed introduces a nick at the end of a duplexed region at the 5' end of Tf1 genomic RNA, substantiating the prediction that this enzyme is responsible for generating this RNA self-primer. The 3' end of the primer, generated in this manner, can then be extended upon the addition of deoxynucleoside triphosphates by the DNA polymerase activity of the same enzyme, synthesizing the negative-sense DNA strand. This functional primer must have been generated by the RNase H activity of Tf1 reverse transcriptase, since a mutant enzyme lacking this activity has lost its ability to generate the self-primer. It was also found here that the reverse transcriptases of human immunodeficiency virus type 1 and of murine leukemia virus do not exhibit this specific cleavage activity. In all, it is likely that the observed unique mechanism of self-priming in Tf1 represents an early advantageous form of initiating reverse transcription in LTR retroelements without involving cellular tRNAs.

Interferon-alpha and transfer factor in the treatment of multiple sclerosis: a double-blind, placebo-controlled trial. AUSTIMS Research Group.

PubMed Central

1989-01-01

The role of interferon-alpha (IFN-alpha) and transfer factor (TF) in the treatment of multiple sclerosis was investigated in a prospective, multi-centric, three year, double-blind, placebo-controlled trial. One hundred and eighty two patients with clinically definite multiple sclerosis were randomised into three treatment groups whose compositions were found to be similar for demographic and prognostic variables including HLA status. Subcutaneous injections of IFN-alpha (3 x 10(6) units), TF (0.5 units) manufactured from leucocytes of cohabiting donors, or placebo were given twice weekly for two months, once weekly for 10 months then fortnightly for 24 months. One hundred and fifty three patients completed the injection regimen. There was no significant difference in the progression of disability for multiple sclerosis patients in either the IFN-alpha or TF-treated groups compared with the placebo group. Similarly, change in visual evoked responses (VER), and in number of oligoclonal bands (OCB) and the level of myelin basic protein (MBP) in the cerebrospinal fluid (CSF) over the trial period did not differ significantly between the three groups. However, the IFN-alpha-treated group had significantly more reported adverse drug reactions and patient withdrawals than either of the other two groups. PMID:2659737

Protein functionalized tramadol-loaded PLGA nanoparticles: preparation, optimization, stability and pharmacodynamic studies.

PubMed

Lalani, Jigar; Rathi, Mohan; Lalan, Manisha; Misra, Ambikanandan

2013-06-01

Poly (d,l-lactide-co-glycolide acid) (PLGA) Nanoparticles (NPs) with sustained drug release and enhanced circulation time presents widely explored non-invasive approach for drug delivery to brain. However, blood-brain barrier (BBB) limits the drug delivery to brain. This can be overcome by anchoring endogenous ligand like Transferrin (Tf) and Lactoferrin (Lf) on the surface of NPs, allowing efficient brain delivery via receptor-mediated endocytosis. The aim of the present investigation was preparation, optimization, characterization and comparative evaluation of targeting efficiency of Tf- vs. Lf-conjugated NPs. Tramadol-loaded PLGA NPs were prepared by nanoprecipitation techniques and optimized using 3(3) factorial design. The effect of polymer concentration, stabilizer concentration and organic:aqueous phase ratio were evaluated on particle size (PS) and entrapment efficiency (EE). The formulation was optimized based on desirability for lower PS (<150 nm) and higher EE (>70%). Optimized PLGA NPs were conjugated with Tf and Lf, characterized and evaluated for stability study. Pharmacodynamic study was performed in rat after intravenous administration. The optimized formulation had 100 mg of PLGA, 1% polyvinyl alcohol (PVA) and 1:2 acetone:water ratio. The Lf and Tf conjugation to PLGA NPs was estimated to 186 Tf and 185 Lf molecules per NPs. Lyophilization was optimized at 1:2 ratio of NPs:trehalose. The NPs were found stable for 6 months at refrigerated condition. Pharmacodynamic study demonstrated enhanced efficacy of ligand-conjugated NPs against unconjugated NPs. Conjugated NPs demonstrated significantly higher pharmacological effect over a period of 24 h. Furthermore Lf functionalized NPs exhibited better antinociceptive effect as compared to Tf functionalized NPs.

Robust Regression Procedures for Predictor Variable Outliers.

DTIC Science & Technology

1982-03-01

space of probability dis- tributions. Then the influence function of the estimator is defined to be the derivative of the functional evaluated at the...measure of the impact of an outlier x0 on the estimator . . . . . .0 10 T(F) is the " influence function " which is defined to be T(F) - lirT(F")-T(F...positive and negative directions. An em- pirical influence function can be defined in a similar fashion simply by replacing F with F in eqn. (3.4).n

Repressor- and Activator-Type Ethylene Response Factors Functioning in Jasmonate Signaling and Disease Resistance Identified via a Genome-Wide Screen of Arabidopsis Transcription Factor Gene Expression[w

PubMed Central

McGrath, Ken C.; Dombrecht, Bruno; Manners, John M.; Schenk, Peer M.; Edgar, Cameron I.; Maclean, Donald J.; Scheible, Wolf-Rüdiger; Udvardi, Michael K.; Kazan, Kemal

2005-01-01

To identify transcription factors (TFs) involved in jasmonate (JA) signaling and plant defense, we screened 1,534 Arabidopsis (Arabidopsis thaliana) TFs by real-time quantitative reverse transcription-PCR for their altered transcript at 6 h following either methyl JA treatment or inoculation with the incompatible pathogen Alternaria brassicicola. We identified 134 TFs that showed a significant change in expression, including many APETALA2/ethylene response factor (AP2/ERF), MYB, WRKY, and NAC TF genes with unknown functions. Twenty TF genes were induced by both the pathogen and methyl JA and these included 10 members of the AP2/ERF TF family, primarily from the B1a and B3 subclusters. Functional analysis of the B1a TF AtERF4 revealed that AtERF4 acts as a novel negative regulator of JA-responsive defense gene expression and resistance to the necrotrophic fungal pathogen Fusarium oxysporum and antagonizes JA inhibition of root elongation. In contrast, functional analysis of the B3 TF AtERF2 showed that AtERF2 is a positive regulator of JA-responsive defense genes and resistance to F. oxysporum and enhances JA inhibition of root elongation. Our results suggest that plants coordinately express multiple repressor- and activator-type AP2/ERFs during pathogen challenge to modulate defense gene expression and disease resistance. PMID:16183832

Endothelial connexin 32 regulates tissue factor expression induced by inflammatory stimulation and direct cell-cell interaction with activated cells.

PubMed

Okamoto, Takayuki; Akita, Nobuyuki; Hayashi, Tatsuya; Shimaoka, Motomu; Suzuki, Koji

2014-10-01

Endothelial cell (EC) interacts with adjacent EC through gap junction, and abnormal expression or function of Cxs is associated with cardiovascular diseases. In patients with endothelial dysfunction, the up-regulation of tissue factor (TF) expression promotes the pathogenic activation of blood coagulation, however the relationship between gap junctions and TF expression in ECs remains uncharacterized. ECs express the gap junction (GJ) proteins connexin32 (Cx32), Cx37, Cx40 and Cx43. We investigated the role of endothelial gap junctions, particularly Cx32, in modulating TF expression during vascular inflammation. Human umbilical vein endothelial cells (HUVECs) were stimulated with tumor necrosis factor-α (TNF-α) and TF activity was assessed in the presence of GJ blockers and an inhibitory anti-Cx32 monoclonal antibody. Treatment with GJ blockers and anti-Cx32 monoclonal antibody enhanced the TNF-α-induced TF activity and mRNA expression in HUVECs. TNF-α-activated effector HUVECs or mouse MS-1 cells were co-cultured with non-stimulated acceptor HUVECs and TF expression in acceptor HUVECs was detected. Effector EC induced TF expression in adjacent acceptor HUVECs through direct cell-cell interaction. Cell-cell interaction induced TF expression was reduced by anti-intercellular adhesion molecule-1 (ICAM1) monoclonal antibody. Soluble ICAM1-Fc fusion protein promotes TF expression. GJ blockers and anti-Cx32 monoclonal antibody enhanced TF expression induced by cell-cell interaction and ICAM1-Fc treatment. Blockade of endothelial Cx32 increased TF expression induced by TNF-α stimulation and cell-cell interaction which was at least partly dependent upon ICAM1. These results suggest that direct Cx32-mediated interaction modulates TF expression in ECs during vascular inflammation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Unusual solvatochromic absorbance probe behaviour within mixtures of poly(ethylene glycol)-400 + ionic liquid, [bmim][Tf2N

NASA Astrophysics Data System (ADS)

Ali, Anwar; Ali, Maroof; Malik, Nisar Ahmad; Uzair, Sahar

2014-03-01

The potentially green solvents made up of ionic liquids (ILs) and poly(ethylene glycols) may have wide range of the applications in many chemical and biochemical fields. In the present work, solvatochromic absorbance probe behaviour is used to assess the physicochemical properties of the mixtures composed of PEG-400 + IL, 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [bmim][Tf2N]. Lowest energy intramolecular charge-transfer absorbance maxima of a betaine dye, i.e., ETN , indicates the dipolarity/polarizability and/or hydrogen-bond donating (HBD) acidity of the [bmim][Tf2N] + PEG-400 mixtures to be even higher than that of neat [bmim][Tf2N], the solution component with higher dipolarity/polarizability and/or HBD acidity. Dipolarity/polarizability (π∗) obtained separately from the electronic absorbance response of probe N,N-diethyl-4-nitroaniline, and the HBD acidity (α) of PEG-400 + [bmim][Tf2N] mixtures are also observed to be anomalously high. A comparative study of the PEG + IL mixtures has also been done with PEG-400 + molecular organic solvents (protic polar [methanol], aprotic polar [N,N-dimethylformamide], and non polar, [benzene]) mixtures, but these mixtures do not show this type of unusual behaviour. A four-parameter simplified combined nearly ideal binary solvent/Redlich-Kister (CNIBS/R-K) equation is shown to satisfactorily predict the solvatochromic parameters within PEG-400 + different solvent mixtures.

Extending amulti-scale parameter regionalization (MPR) method by introducing parameter constrained optimization and flexible transfer functions

NASA Astrophysics Data System (ADS)

Klotz, Daniel; Herrnegger, Mathew; Schulz, Karsten

2015-04-01

A multi-scale parameter-estimation method, as presented by Samaniego et al. (2010), is implemented and extended for the conceptual hydrological model COSERO. COSERO is a HBV-type model that is specialized for alpine-environments, but has been applied over a wide range of basins all over the world (see: Kling et al., 2014 for an overview). Within the methodology available small-scale information (DEM, soil texture, land cover, etc.) is used to estimate the coarse-scale model parameters by applying a set of transfer-functions (TFs) and subsequent averaging methods, whereby only TF hyper-parameters are optimized against available observations (e.g. runoff data). The parameter regionalisation approach was extended in order to allow for a more meta-heuristical handling of the transfer-functions. The two main novelties are: 1. An explicit introduction of constrains into parameter estimation scheme: The constraint scheme replaces invalid parts of the transfer-function-solution space with valid solutions. It is inspired by applications in evolutionary algorithms and related to the combination of learning and evolution. This allows the consideration of physical and numerical constraints as well as the incorporation of a priori modeller-experience into the parameter estimation. 2. Spline-based transfer-functions: Spline-based functions enable arbitrary forms of transfer-functions: This is of importance since in many cases the general relationship between sub-grid information and parameters are known, but not the form of the transfer-function itself. The contribution presents the results and experiences with the adopted method and the introduced extensions. Simulation are performed for the pre-alpine/alpine Traisen catchment in Lower Austria. References: Samaniego, L., Kumar, R., Attinger, S. (2010): Multiscale parameter regionalization of a grid-based hydrologic model at the mesoscale, Water Resour. Res., doi: 10.1029/2008WR007327 Kling, H., Stanzel, P., Fuchs, M., and Nachtnebel, H. P. (2014): Performance of the COSERO precipitation-runoff model under non-stationary conditions in basins with different climates, Hydrolog. Sci. J., doi: 10.1080/02626667.2014.959956.

The Development of Protein Microarrays and Their Applications in DNA-Protein and Protein-Protein Interaction Analyses of Arabidopsis Transcription Factors

PubMed Central

Gong, Wei; He, Kun; Covington, Mike; Dinesh-Kumar, S. P.; Snyder, Michael; Harmer, Stacey L.; Zhu, Yu-Xian; Deng, Xing Wang

2009-01-01

We used our collection of Arabidopsis transcription factor (TF) ORFeome clones to construct protein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both protein-DNA and protein-protein interaction analyses. For protein-DNA interaction studies, we examined AP2/ERF family TFs and their cognate cis-elements. By careful comparison of the DNA-binding specificity of 13 TFs on the protein microarray with previous non-microarray data, we showed that protein microarrays provide an efficient and high throughput tool for genome-wide analysis of TF-DNA interactions. This microarray protein-DNA interaction analysis allowed us to derive a comprehensive view of DNA-binding profiles of AP2/ERF family proteins in Arabidopsis. It also revealed four TFs that bound the EE (evening element) and had the expected phased gene expression under clock-regulation, thus providing a basis for further functional analysis of their roles in clock regulation of gene expression. We also developed procedures for detecting protein interactions using this TF protein microarray and discovered four novel partners that interact with HY5, which can be validated by yeast two-hybrid assays. Thus, plant TF protein microarrays offer an attractive high-throughput alternative to traditional techniques for TF functional characterization on a global scale. PMID:19802365

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis.

PubMed

Luna-Zurita, Luis; Stirnimann, Christian U; Glatt, Sebastian; Kaynak, Bogac L; Thomas, Sean; Baudin, Florence; Samee, Md Abul Hassan; He, Daniel; Small, Eric M; Mileikovsky, Maria; Nagy, Andras; Holloway, Alisha K; Pollard, Katherine S; Müller, Christoph W; Bruneau, Benoit G

2016-02-25

Transcription factors (TFs) are thought to function with partners to achieve specificity and precise quantitative outputs. In the developing heart, heterotypic TF interactions, such as between the T-box TF TBX5 and the homeodomain TF NKX2-5, have been proposed as a mechanism for human congenital heart defects. We report extensive and complex interdependent genomic occupancy of TBX5, NKX2-5, and the zinc finger TF GATA4 coordinately controlling cardiac gene expression, differentiation, and morphogenesis. Interdependent binding serves not only to co-regulate gene expression but also to prevent TFs from distributing to ectopic loci and activate lineage-inappropriate genes. We define preferential motif arrangements for TBX5 and NKX2-5 cooperative binding sites, supported at the atomic level by their co-crystal structure bound to DNA, revealing a direct interaction between the two factors and induced DNA bending. Complex interdependent binding mechanisms reveal tightly regulated TF genomic distribution and define a combinatorial logic for heterotypic TF regulation of differentiation. Copyright © 2016 Elsevier Inc. All rights reserved.

FANCD2 functions as a critical factor downstream of MiTF to maintain the proliferation and survival of melanoma cells.

PubMed

Bourseguin, Julie; Bonet, Caroline; Renaud, Emilie; Pandiani, Charlotte; Boncompagni, Marina; Giuliano, Sandy; Pawlikowska, Patrycja; Karmous-Benailly, Houda; Ballotti, Robert; Rosselli, Filippo; Bertolotto, Corine

2016-11-09

Proteins involved in genetic stability maintenance and safeguarding DNA replication act not only against cancer initiation but could also play a major role in sustaining cancer progression. Here, we report that the FANC pathway is highly expressed in metastatic melanoma harboring the oncogenic microphthalmia-associated transcription factor (MiTF). We show that MiTF downregulation in melanoma cells lowers the expression of several FANC genes and proteins. Moreover, we observe that, similarly to the consequence of MiTF downregulation, FANC pathway silencing alters proliferation, migration and senescence of human melanoma cells. We demonstrate that the FANC pathway acts downstream MiTF and establish the existence of an epistatic relationship between MiTF and the FANC pathway. Our findings point to a central role of the FANC pathway in cellular and chromosomal resistance to both DNA damage and targeted therapies in melanoma cells. Thus, the FANC pathway is a promising new therapeutic target in melanoma treatment.

FANCD2 functions as a critical factor downstream of MiTF to maintain the proliferation and survival of melanoma cells

PubMed Central

Bourseguin, Julie; Bonet, Caroline; Renaud, Emilie; Pandiani, Charlotte; Boncompagni, Marina; Giuliano, Sandy; Pawlikowska, Patrycja; Karmous-Benailly, Houda; Ballotti, Robert; Rosselli, Filippo; Bertolotto, Corine

2016-01-01

Proteins involved in genetic stability maintenance and safeguarding DNA replication act not only against cancer initiation but could also play a major role in sustaining cancer progression. Here, we report that the FANC pathway is highly expressed in metastatic melanoma harboring the oncogenic microphthalmia-associated transcription factor (MiTF). We show that MiTF downregulation in melanoma cells lowers the expression of several FANC genes and proteins. Moreover, we observe that, similarly to the consequence of MiTF downregulation, FANC pathway silencing alters proliferation, migration and senescence of human melanoma cells. We demonstrate that the FANC pathway acts downstream MiTF and establish the existence of an epistatic relationship between MiTF and the FANC pathway. Our findings point to a central role of the FANC pathway in cellular and chromosomal resistance to both DNA damage and targeted therapies in melanoma cells. Thus, the FANC pathway is a promising new therapeutic target in melanoma treatment. PMID:27827420

A Long Terminal Repeat-Containing Retrotransposon of Schizosaccharomyces pombe Expresses a Gag-Like Protein That Assembles into Virus-Like Particles Which Mediate Reverse Transcription

PubMed Central

Teysset, Laure; Dang, Van-Dinh; Kim, Min Kyung; Levin, Henry L.

2003-01-01

The Tf1 element of Schizosaccharomyces pombe is a long terminal repeat-containing retrotransposon that encodes functional protease, reverse transcriptase, and integrase proteins. Although these proteins are known to be necessary for protein processing, reverse transcription, and integration, respectively, the function of the protein thought to be Gag has not been determined. We present here the first electron microscopy of Tf1 particles. We tested whether the putative Gag of Tf1 was required for particle formation, packaging of RNA, and reverse transcription. We generated deletions of 10 amino acids in each of the four hydrophilic domains of the protein and found that all four mutations reduced transposition activity. The N-terminal deletion removed a nuclear localization signal and inhibited nuclear import of the transposon. The two mutations in the center of Gag destabilized the protein and resulted in no virus-like particles. The C-terminal deletion caused a defect in RNA packaging and, as a result, low levels of cDNA. The electron microscopy of cells expressing a truncated Tf1 showed that Gag alone was sufficient for the formation of virus-like particles. Taken together, these results indicate that Tf1 encodes a Gag protein that is a functional equivalent of the Gag proteins of retroviruses. PMID:12692246

Characterization of water-soluble organic aerosol in coastal New England: Implications of variations in size distribution

NASA Astrophysics Data System (ADS)

Ziemba, L. D.; Griffin, R. J.; Whitlow, S.; Talbot, R. W.

2011-12-01

Size distributions up to 10-micron aerosol diameter ( DP) of organic carbon (OC) and water-soluble organic carbon (WSOC) were measured at two sites in coastal New England, slightly inland at Thompson Farm (TF) and offshore at Isles of Shoals (IOS). Significant OC concentrations were measured across the full size distribution at TF and IOS, respectively. The WSOC fraction (WSOC/OC) was largest in the accumulation mode with values of 0.86 and 0.93 and smallest in the coarse mode with values of 0.61 and 0.79 at TF and IOS, respectively. Dicarboxylic acids containing up to five carbon atoms (C 5) were concentrated in droplet and accumulation mode aerosol with only minor contributions in the coarse mode. C 1-C 3 monocarboxylic acids were generally near or below detection limits. Results from proton nuclear magnetic resonance (H +-NMR) spectroscopy analyses showed that the organic functional group characterized by protons in the alpha position to an unsaturated carbon atoms ([H-C-C dbnd ]) was the dominant WSOC functionality at both TF and IOS, constituting 34 and 43% of carbon-weighted H +-NMR signal, respectively. Size distributions of each H +-NMR-resolved organic functionality are presented. Source apportionment using H +-NMR fingerprints is also presented, and results indicate that nearly all of the WSOC at TF and IOS spectroscopically resembled secondary organic aerosol, regardless of DP.

New method for determining free core nutation parameters, considering geophysical effects

NASA Astrophysics Data System (ADS)

Vondrák, J.; Ron, C.

2017-08-01

Context. In addition to the torques exerted by the Moon, Sun, and planets, changes of precession-nutation are known to be caused also by geophysical excitations. Recently studies suggest that geomagnetic jerks (GMJ) might be associated with sudden changes of phase and amplitude of free core nutation. We showed that using atmospheric and oceanic excitations with those by GMJ improves substantially the agreement with observed celestial pole offsets. Aims: Traditionally, the period Tf and quality factor Qf of the free core nutation (FCN) are derived from VLBI-based celestial pole offsets (CPO). Either direct analysis of the observed CPO, or indirect method using resonant effects of nutation terms with frequencies close to FCN, are used. The latter method is usually preferred, since it yields more accurate results. Our aim is to combine both approaches to better derive FCN parameters. Methods: We numerically integrated the part of CPO that is due to geophysical excitations for different combinations of Tf, Qf, using Brzeziński's broadband Liouville equations (Brzeziński 1994, Manuscripta geodaetica, 19, 157), and compared the results with the observed values of CPO. The values yielding the best fit were then estimated. The observed CPO, however, must be corrected for the change of nutation that is caused by the Tf, Qf values different from those used to calculate IAU 2000 model of nutation. To this end, we have used the Mathews-Herring-Buffet transfer function and applied it to the five most affected terms of nutation (with periods 365.26, 182.62, 121.75, 27.55 and 13.66 days). Results: The results, based on the CPO data in the interval 1986.0—2016.0 and excitations with three different models, are presented. We demonstrate that better results are obtained if the influence of additional excitations at GMJ epochs is added to excitations by the atmosphere and oceans. Our preferred values are Tf = 430.28 ± 0.04 mean solar days and Qf = 19 500 ± 200.

Micelle assisted thin-film solid phase microextraction: a new approach for determination of quaternary ammonium compounds in environmental samples.

PubMed

Boyacı, Ezel; Pawliszyn, Janusz

2014-09-16

Determination of quaternary ammonium compounds (QACs) often is considered to be a challenging undertaking owing to secondary interactions of the analytes' permanently charged quaternary ammonium head or hydrophobic tail with the utilized labware. Here, for the first time, a micelle assisted thin-film solid phase microextraction (TF-SPME) using a zwitterionic detergent 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) as a matrix modifier is introduced as a novel approach for in-laboratory sample preparation of the challenging compounds. The proposed micelle assisted TF-SPME method offers suppression/enhancement free electrospray ionization of analytes in mass spectrometric detection, minimal interaction of the micelles with the TF-SPME coating, and chromatographic stationary phase and analysis free of secondary interactions. Moreover, it was found that the matrix modifier has multiple functions; when its concentration is found below the critical micelle concentration (CMC), the matrix modifier primarily acts as a surface deactivator; above its CMC, it acts as a stabilizer for QACs. Additionally, shorter equilibrium extraction times in the presence of the modifier demonstrated that micelles also assist in the transfer of analytes from the bulk of the sample to the surface of the coating. The developed micelle assisted TF-SPME protocol using the 96-blade system requires only 30 min of extraction and 15 min of desorption. Together with a conditioning step (15 min), the entire method is 60 min; considering the advantage of using the 96-blade system, if all the blades in the brush are used, the sample preparation time per sample is 0.63 min. Moreover, the recoveries for all analytes with the developed method were found to range within 80.2-97.3%; as such, this method can be considered an open bed solid phase extraction. The proposed method was successfully validated using real samples.

PRISM offers a comprehensive genomic approach to transcription factor function prediction

PubMed Central

Wenger, Aaron M.; Clarke, Shoa L.; Guturu, Harendra; Chen, Jenny; Schaar, Bruce T.; McLean, Cory Y.; Bejerano, Gill

2013-01-01

The human genome encodes 1500–2000 different transcription factors (TFs). ChIP-seq is revealing the global binding profiles of a fraction of TFs in a fraction of their biological contexts. These data show that the majority of TFs bind directly next to a large number of context-relevant target genes, that most binding is distal, and that binding is context specific. Because of the effort and cost involved, ChIP-seq is seldom used in search of novel TF function. Such exploration is instead done using expression perturbation and genetic screens. Here we propose a comprehensive computational framework for transcription factor function prediction. We curate 332 high-quality nonredundant TF binding motifs that represent all major DNA binding domains, and improve cross-species conserved binding site prediction to obtain 3.3 million conserved, mostly distal, binding site predictions. We combine these with 2.4 million facts about all human and mouse gene functions, in a novel statistical framework, in search of enrichments of particular motifs next to groups of target genes of particular functions. Rigorous parameter tuning and a harsh null are used to minimize false positives. Our novel PRISM (predicting regulatory information from single motifs) approach obtains 2543 TF function predictions in a large variety of contexts, at a false discovery rate of 16%. The predictions are highly enriched for validated TF roles, and 45 of 67 (67%) tested binding site regions in five different contexts act as enhancers in functionally matched cells. PMID:23382538

Identification and expression of the tig gene coding for trigger factor from psychrophilic bacteria with no information of genome sequence available.

PubMed

Lee, Kyunghee; Choi, Hyojung; Im, Hana

2009-08-01

Trigger factor (TF) plays a key role as a molecular chaperone with a peptidyl-prolyl cis-trans isomerase (PPIase) activity by which cells promote folding of newly synthesized proteins coming out of ribosomes. Since psychrophilic bacteria grow at a quite low temperature, between 4 and 15 degrees C, TF from such bacteria was investigated and compared with that of mesophilic bacteria E. coli in order to offer an explanation of cold-adaptation at a molecular level. Using a combination of gradient PCRs with homologous primers and LA PCR in vitro cloning technology, the tig gene was fully identified from Psychromonas arctica, whose genome sequence is not yet available. The resulting amino acid sequence of the TF was compared with other homologous TFs using sequence alignments to search for common domains. In addition, we have developed a protein expression system, by which TF proteins from P. arctica (PaTF) were produced by IPTG induction upon cloning the tig gene on expression vectors, such as pAED4. We have further examined the role of expressed psychrophilic PaTF on survival against cold treatment at 4 degrees C. Finally, we have attempted the in vitro biochemical characterization of TF proteins with His-tags expressed in a pET system, such as the PPIase activity of PaTF protein. Our results demonstrate that the expressed PaTF proteins helped cells survive against cold environments in vivo and the purified PaTF in vitro display the functional PPIase activity in a concentration dependent manner.

Role of initial state and final quench temperature on aging properties in phase-ordering kinetics.

PubMed

Corberi, Federico; Villavicencio-Sanchez, Rodrigo

2016-05-01

We study numerically the two-dimensional Ising model with nonconserved dynamics quenched from an initial equilibrium state at the temperature T_{i}≥T_{c} to a final temperature T_{f} below the critical one. By considering processes initiating both from a disordered state at infinite temperature T_{i}=∞ and from the critical configurations at T_{i}=T_{c} and spanning the range of final temperatures T_{f}∈[0,T_{c}[ we elucidate the role played by T_{i} and T_{f} on the aging properties and, in particular, on the behavior of the autocorrelation C and of the integrated response function χ. Our results show that for any choice of T_{f}, while the autocorrelation function exponent λ_{C} takes a markedly different value for T_{i}=∞ [λ_{C}(T_{i}=∞)≃5/4] or T_{i}=T_{c} [λ_{C}(T_{i}=T_{c})≃1/8] the response function exponents are unchanged. Supported by the outcome of the analytical solution of the solvable spherical model we interpret this fact as due to the different contributions provided to autocorrelation and response by the large-scale properties of the system. As changing T_{f} is considered, although this is expected to play no role in the large-scale and long-time properties of the system, we show important effects on the quantitative behavior of χ. In particular, data for quenches to T_{f}=0 are consistent with a value of the response function exponent λ_{χ}=1/2λ_{C}(T_{i}=∞)=5/8 different from the one [λ_{χ}∈(0.5-0.56)] found in a wealth of previous numerical determinations in quenches to finite final temperatures. This is interpreted as due to important preasymptotic corrections associated to T_{f}>0.

Improved axial point spread function in a two-frequency laser scanning confocal fluorescence microscope

NASA Astrophysics Data System (ADS)

Wu, Jheng-Syong; Chung, Yung-Chin; Chien, Jun-Jei; Chou, Chien

2018-01-01

A two-frequency laser scanning confocal fluorescence microscope (TF-LSCFM) based on intensity modulated fluorescence signal detection was proposed. The specimen-induced spherical aberration and scattering effect were suppressed intrinsically, and high image contrast was presented due to heterodyne interference. An improved axial point spread function in a TF-LSCFM compared with a conventional laser scanning confocal fluorescence microscope was demonstrated and discussed.

"Hit-and-Run" transcription: de novo transcription initiated by a transient bZIP1 "hit" persists after the "run".

PubMed

Doidy, Joan; Li, Ying; Neymotin, Benjamin; Edwards, Molly B; Varala, Kranthi; Gresham, David; Coruzzi, Gloria M

2016-02-03

Dynamic transcriptional regulation is critical for an organism's response to environmental signals and yet remains elusive to capture. Such transcriptional regulation is mediated by master transcription factors (TF) that control large gene regulatory networks. Recently, we described a dynamic mode of TF regulation named "hit-and-run". This model proposes that master TF can interact transiently with a set of targets, but the transcription of these transient targets continues after the TF dissociation from the target promoter. However, experimental evidence validating active transcription of the transient TF-targets is still lacking. Here, we show that active transcription continues after transient TF-target interactions by tracking de novo synthesis of RNAs made in response to TF nuclear import. To do this, we introduced an affinity-labeled 4-thiouracil (4tU) nucleobase to specifically isolate newly synthesized transcripts following conditional TF nuclear import. Thus, we extended the TARGET system (Transient Assay Reporting Genome-wide Effects of Transcription factors) to include 4tU-labeling and named this new technology TARGET-tU. Our proof-of-principle example is the master TF Basic Leucine Zipper 1 (bZIP1), a central integrator of metabolic signaling in plants. Using TARGET-tU, we captured newly synthesized mRNAs made in response to bZIP1 nuclear import at a time when bZIP1 is no longer detectably bound to its target. Thus, the analysis of de novo transcripomics demonstrates that bZIP1 may act as a catalyst TF to initiate a transcriptional complex ("hit"), after which active transcription by RNA polymerase continues without the TF being bound to the gene promoter ("run"). Our findings provide experimental proof for active transcription of transient TF-targets supporting a "hit-and-run" mode of action. This dynamic regulatory model allows a master TF to catalytically propagate rapid and broad transcriptional responses to changes in environment. Thus, the functional read-out of de novo transcripts produced by transient TF-target interactions allowed us to capture new models for genome-wide transcriptional control.

Transferrin Receptor 1 in Chronic Hypoxia-Induced Pulmonary Vascular Remodeling.

PubMed

Naito, Yoshiro; Hosokawa, Manami; Sawada, Hisashi; Oboshi, Makiko; Hirotani, Shinichi; Iwasaku, Toshihiro; Okuhara, Yoshitaka; Morisawa, Daisuke; Eguchi, Akiyo; Nishimura, Koichi; Soyama, Yuko; Fujii, Kenichi; Mano, Toshiaki; Ishihara, Masaharu; Tsujino, Takeshi; Masuyama, Tohru

2016-06-01

Iron is associated with the pathophysiology of several cardiovascular diseases, including pulmonary hypertension (PH). In addition, disrupted pulmonary iron homeostasis has been reported in several chronic lung diseases. Transferrin receptor 1 (TfR1) plays a key role in cellular iron transport. However, the role of TfR1 in the pathophysiology of PH has not been well characterized. In this study, we investigate the role of TfR1 in the development of hypoxia-induced pulmonary vascular remodeling. PH was induced by exposing wild-type (WT) mice and TfR1 hetero knockout mice to hypoxia for 4 weeks and evaluated via assessment of pulmonary vascular remodeling, right ventricular (RV) systolic pressure, and RV hypertrophy. In addition, we assessed the functional role of TfR1 in pulmonary artery smooth muscle cells in vitro. The morphology of pulmonary arteries did not differ between WT mice and TfR1 hetero knockout mice under normoxic conditions. In contrast, TfR1 hetero knockout mice exposed to 4 weeks hypoxia showed attenuated pulmonary vascular remodeling, RV systolic pressure, and RV hypertrophy compared with WT mice. In addition, the depletion of TfR1 by RNA interference attenuated human pulmonary artery smooth muscle cells proliferation induced by platelet-derived growth factor-BB (PDGF-BB) in vitro. These results suggest that TfR1 plays an important role in the development of hypoxia-induced pulmonary vascular remodeling. © American Journal of Hypertension, Ltd 2015. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Effect of toroidal field ripple on plasma rotation in JET

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

De Vries, P.; Salmi, A.; Parail, V.

Dedicated experiments on TF ripple effects on the performance of tokamak plasmas have been carried out at JET. The TF ripple was found to have a profound effect on the plasma rotation. The central Mach number, M, defined as the ratio of the rotation velocity and the thermal velocity, was found to drop as a function of TF ripple amplitude ( ) from an average value of M = 0.40 0.55 for operations at the standard JET ripple of = 0.08% to M = 0.25 0.40 for = 0.5% and M = 0.1 0.3 for = 1%. TF ripple effectsmore » should be considered when estimating the plasma rotation in ITER. With standard co-current injection of neutral beam injection (NBI), plasmas were found to rotate in the co-current direction. However, for higher TF ripple amplitudes ( ~ 1%) an area of counter rotation developed at the edge of the plasma, while the core kept its co-rotation. The edge counter rotation was found to depend, besides on the TF ripple amplitude, on the edge temperature. The observed reduction of toroidal plasma rotation with increasing TF ripple could partly be explained by TF ripple induced losses of energetic ions, injected by NBI. However, the calculated torque due to these losses was insufficient to explain the observed counter rotation and its scaling with edge parameters. It is suggested that additional TF ripple induced losses of thermal ions contribute to this effect.« less

Term frequency - function of document frequency: a new term weighting scheme for enterprise information retrieval

NASA Astrophysics Data System (ADS)

Zhang, Hui; Wang, Deqing; Wu, Wenjun; Hu, Hongping

2012-11-01

In today's business environment, enterprises are increasingly under pressure to process the vast amount of data produced everyday within enterprises. One method is to focus on the business intelligence (BI) applications and increasing the commercial added-value through such business analytics activities. Term weighting scheme, which has been used to convert the documents as vectors in the term space, is a vital task in enterprise Information Retrieval (IR), text categorisation, text analytics, etc. When determining term weight in a document, the traditional TF-IDF scheme sets weight value for the term considering only its occurrence frequency within the document and in the entire set of documents, which leads to some meaningful terms that cannot get the appropriate weight. In this article, we propose a new term weighting scheme called Term Frequency - Function of Document Frequency (TF-FDF) to address this issue. Instead of using monotonically decreasing function such as Inverse Document Frequency, FDF presents a convex function that dynamically adjusts weights according to the significance of the words in a document set. This function can be manually tuned based on the distribution of the most meaningful words which semantically represent the document set. Our experiments show that the TF-FDF can achieve higher value of Normalised Discounted Cumulative Gain in IR than that of TF-IDF and its variants, and improving the accuracy of relevance ranking of the IR results.

[Atelocollagen-mediated small interfering RNA delivery for effective gene silencing in rat vein grafts].

PubMed

Qiu, Xue-feng; Dong, Nian-guo; Sun, Zong-quan; Su, Wei; Shi, Jia-wei

2009-07-01

To evaluate the efficacy of using small interfering RNA targeting TF as a therapy for vein graft failure. External jugular vein to carotid artery interposition vein grafts, which were applied to a low flow condition, were made in 120 Sprague-Dawley rats weighing 260 to 300 g. These rats were randomly divided into 4 groups, 30 rats each group. Group A was atelocollagen-TF Stealth Select RNAi group. Group B was atelocollagen-TF Stealth RNAi group. Group C was atelocollagen group. Group D was control group. Small interfering RNA mixed with atelocollagen was administrated to the external wall of grafted veins. The TF protein expression of vein grafts was analyzed by Western blot at 1, 3, 7, 14, and 28 d postoperatively, and by immunochemistry at 3 d postoperatively. The proliferation index was determined at 14 d postoperatively. Neointimal hyperplasia was evaluated at 28 d postoperatively. BLOCK-iT fluorescent oligo was used to confirm its stability and successful transfer into the vein graft wall at 3 and 7 d postoperatively for another group (n=12). Fluorescence of BLOCK-iT fluorescent oligo could be detected in the graft wall even at 7 d postoperatively. Knockdown of the TF expression was achieved by perivascular application of siRNA using atelocollagen. Compared with control group, the intima thickness at 28 d after grafting was significantly reduced (P < 0.05). This phenomenon was preceded by significant reduction of cell proliferation in siRNA-treated grafts at 14 d postoperatively (P < 0.05). The expression of TF in vein grafts can be effectively inhibited by specific siRNAs using a atelocollagen-based nonviral delivery approach in vivo, so that the neointimal thickening can be prevented. Transplants;

Growth-inhibition patterns and transfer-factor profiles in arsenic-stressed rice (Oryza sativa L.).

PubMed

Jung, Ha-Il; Lee, Jinwook; Chae, Mi-Jin; Kong, Myung-Suk; Lee, Chang-Hoon; Kang, Seong-Soo; Kim, Yoo-Hak

2017-11-16

Arsenic (As) accumulation in rice owing to uptake from the soil is a critical human health issue. Here, we studied the chemical properties of As-treated soils, growth inhibition patterns of As-stressed rice plants, changes in the As content of soil and soil solutions, and the relationship between As accumulation and As transfer factor from the soil to the rice organs. Rice plants were cultivated in a greenhouse under four concentrations of As: 0 (control), 25, 50, and 75 mg kg -1 . A significant positive correlation was found between available P 2 O 5 and exchangeable K and between As concentration and available P 2 O 5 or exchangeable K. The As concentration for 50% shoot growth inhibition was 50 mg kg -1 . As levels in roots and shoots were positively correlated with the growth stages of rice. The transfer factor (TF) root/soil increased with As concentration at the tillering stage but decreased at the heading stage. TF root/soil and TF shoot/soil were higher at the heading stage than at the tillering stage. As accumulation in the 25 mg kg -1 treatment was higher during the heading stage, whereas no difference was found at the tillering stage. As accumulation was related to plant biomass and soil As concentration. We found that As accumulation was greater at As concentrations that allowed for plant growth and development. Thus, species-specific threshold concentrations must be determined based on As phytotoxicity for the phytoremediation of As-contaminated soils. Hence, developing practical approaches for managing safe crop production in farmlands with an As contamination of 25 mg kg -1 or less is necessary.

Protein disulfide isomerase acts as an injury response signal that enhances fibrin generation via tissue factor activation

PubMed Central

Reinhardt, Christoph; von Brühl, Marie-Luise; Manukyan, Davit; Grahl, Lenka; Lorenz, Michael; Altmann, Berid; Dlugai, Silke; Hess, Sonja; Konrad, Ildiko; Orschiedt, Lena; Mackman, Nigel; Ruddock, Lloyd; Massberg, Steffen; Engelmann, Bernd

2008-01-01

The activation of initiator protein tissue factor (TF) is likely to be a crucial step in the blood coagulation process, which leads to fibrin formation. The stimuli responsible for inducing TF activation are largely undefined. Here we show that the oxidoreductase protein disulfide isomerase (PDI) directly promotes TF-dependent fibrin production during thrombus formation in vivo. After endothelial denudation of mouse carotid arteries, PDI was released at the injury site from adherent platelets and disrupted vessel wall cells. Inhibition of PDI decreased TF-triggered fibrin formation in different in vivo murine models of thrombus formation, as determined by intravital fluorescence microscopy. PDI infusion increased — and, under conditions of decreased platelet adhesion, PDI inhibition reduced — fibrin generation at the injury site, indicating that PDI can directly initiate blood coagulation. In vitro, human platelet–secreted PDI contributed to the activation of cryptic TF on microvesicles (microparticles). Mass spectrometry analyses indicated that part of the extracellular cysteine 209 of TF was constitutively glutathionylated. Mixed disulfide formation contributed to maintaining TF in a state of low functionality. We propose that reduced PDI activates TF by isomerization of a mixed disulfide and a free thiol to an intramolecular disulfide. Our findings suggest that disulfide isomerases can act as injury response signals that trigger the activation of fibrin formation following vessel injury. PMID:18274674

Protein disulfide isomerase acts as an injury response signal that enhances fibrin generation via tissue factor activation.

PubMed

Reinhardt, Christoph; von Brühl, Marie-Luise; Manukyan, Davit; Grahl, Lenka; Lorenz, Michael; Altmann, Berid; Dlugai, Silke; Hess, Sonja; Konrad, Ildiko; Orschiedt, Lena; Mackman, Nigel; Ruddock, Lloyd; Massberg, Steffen; Engelmann, Bernd

2008-03-01

The activation of initiator protein tissue factor (TF) is likely to be a crucial step in the blood coagulation process, which leads to fibrin formation. The stimuli responsible for inducing TF activation are largely undefined. Here we show that the oxidoreductase protein disulfide isomerase (PDI) directly promotes TF-dependent fibrin production during thrombus formation in vivo. After endothelial denudation of mouse carotid arteries, PDI was released at the injury site from adherent platelets and disrupted vessel wall cells. Inhibition of PDI decreased TF-triggered fibrin formation in different in vivo murine models of thrombus formation, as determined by intravital fluorescence microscopy. PDI infusion increased - and, under conditions of decreased platelet adhesion, PDI inhibition reduced - fibrin generation at the injury site, indicating that PDI can directly initiate blood coagulation. In vitro, human platelet-secreted PDI contributed to the activation of cryptic TF on microvesicles (microparticles). Mass spectrometry analyses indicated that part of the extracellular cysteine 209 of TF was constitutively glutathionylated. Mixed disulfide formation contributed to maintaining TF in a state of low functionality. We propose that reduced PDI activates TF by isomerization of a mixed disulfide and a free thiol to an intramolecular disulfide. Our findings suggest that disulfide isomerases can act as injury response signals that trigger the activation of fibrin formation following vessel injury.

Adventitious sounds identification and extraction using temporal-spectral dominance-based features.

PubMed

Jin, Feng; Krishnan, Sridhar Sri; Sattar, Farook

2011-11-01

Respiratory sound (RS) signals carry significant information about the underlying functioning of the pulmonary system by the presence of adventitious sounds (ASs). Although many studies have addressed the problem of pathological RS classification, only a limited number of scientific works have focused on the analysis of the evolution of symptom-related signal components in joint time-frequency (TF) plane. This paper proposes a new signal identification and extraction method for various ASs based on instantaneous frequency (IF) analysis. The presented TF decomposition method produces a noise-resistant high definition TF representation of RS signals as compared to the conventional linear TF analysis methods, yet preserving the low computational complexity as compared to those quadratic TF analysis methods. The discarded phase information in conventional spectrogram has been adopted for the estimation of IF and group delay, and a temporal-spectral dominance spectrogram has subsequently been constructed by investigating the TF spreads of the computed time-corrected IF components. The proposed dominance measure enables the extraction of signal components correspond to ASs from noisy RS signal at high noise level. A new set of TF features has also been proposed to quantify the shapes of the obtained TF contours, and therefore strongly, enhances the identification of multicomponents signals such as polyphonic wheezes. An overall accuracy of 92.4±2.9% for the classification of real RS recordings shows the promising performance of the presented method.

Effects of mutations at amino acid 61 in the arm of TF1 on its DNA-binding properties.

PubMed

Sayre, M H; Geiduschek, E P

1990-12-20

Transcription factor 1 (TF1) is the Bacillus subtilis phage SPO1-encoded member of the family of bacterial DNA-binding proteins that includes Escherichia coli HU and integration host factor (IHF). We have initiated a mutational analysis of the TF1 molecule to understand better its unique DNA-binding properties and to investigate its physiological function. We report here the consequences of mutating the putative DNA-binding "arms" of TF1. At position 61 in its primary sequence, TF1 contains a Phe residue in place of the Arg residue found in all other known members of the HU family. Substituting polar, uncharged residues for Phe61 substantially reduced the DNA-binding affinity and site-selectivity of TF1 in vitro, whereas the substitution of Tyr had no effect. Substituting Trp or Arg for Phe61 had little effect on the affinity of TF1 for SPO1 DNA, but altered the electrophoretic mobilities of protein-DNA complexes in non-denaturing gels. The Arg61 substitution increased the affinity of the protein for non-specific sites on thymine-containing DNA, thus reducing the natural preference of TF1 for (5-hydroxymethyluracil)-containing DNA. The Phe61-to-Arg mutation was also correlated with decreased phage yield and aberrant regulation of viral protein synthesis in vivo.

Construction and properties of a temperature-sensitive mutation in the gene for the bacteriophage SPO1 DNA-binding protein TF1.

PubMed

Sayre, M H; Geiduschek, E P

1990-08-01

The Bacillus subtilis bacteriophage SPO1 encodes the DNA-binding protein TF1, a homolog of the ubiquitous type II DNA-binding proteins that are components of bacterial chromatin. The known three-dimensional structure of a related protein was used in devising a scheme of site-directed mutagenesis that led to the creation of a temperature-sensitive mutation in the TF1 gene. At the nonpermissive temperature, this mutation disrupted the temporal regulation of viral protein synthesis and processing, altered the kinetics of accumulation of at least one viral transcript, and prohibited the production of infective progeny phage. We suggest that TF1 function is required to shut off the expression of several early-middle and middle viral genes and that TF1 plays a role in phage head morphogenesis. Spontaneous second-site mutations of the temperature-sensitive mutant TF1 allele that suppressed its associated phenotypes were analyzed. These suppressor mutations conferred greater amino acid sequence homology with the type II DNA-binding protein from the thermophile Bacillus stearothermophilus.

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.

PubMed

Kılıç, Sefa; Sagitova, Dinara M; Wolfish, Shoshannah; Bely, Benoit; Courtot, Mélanie; Ciufo, Stacy; Tatusova, Tatiana; O'Donovan, Claire; Chibucos, Marcus C; Martin, Maria J; Erill, Ivan

2016-01-01

Domain-specific databases are essential resources for the biomedical community, leveraging expert knowledge to curate published literature and provide access to referenced data and knowledge. The limited scope of these databases, however, poses important challenges on their infrastructure, visibility, funding and usefulness to the broader scientific community. CollecTF is a community-oriented database documenting experimentally validated transcription factor (TF)-binding sites in the Bacteria domain. In its quest to become a community resource for the annotation of transcriptional regulatory elements in bacterial genomes, CollecTF aims to move away from the conventional data-repository paradigm of domain-specific databases. Through the adoption of well-established ontologies, identifiers and collaborations, CollecTF has progressively become also a portal for the annotation and submission of information on transcriptional regulatory elements to major biological sequence resources (RefSeq, UniProtKB and the Gene Ontology Consortium). This fundamental change in database conception capitalizes on the domain-specific knowledge of contributing communities to provide high-quality annotations, while leveraging the availability of stable information hubs to promote long-term access and provide high-visibility to the data. As a submission portal, CollecTF generates TF-binding site information through direct annotation of RefSeq genome records, definition of TF-based regulatory networks in UniProtKB entries and submission of functional annotations to the Gene Ontology. As a database, CollecTF provides enhanced search and browsing, targeted data exports, binding motif analysis tools and integration with motif discovery and search platforms. This innovative approach will allow CollecTF to focus its limited resources on the generation of high-quality information and the provision of specialized access to the data.Database URL: http://www.collectf.org/. © The Author(s) 2016. Published by Oxford University Press.

A Follow-Up Study from a Multisite, Randomized Controlled Trial for Traumatized Children Receiving TF-CBT.

PubMed

Jensen, Tine K; Holt, Tonje; Ormhaug, Silje M

2017-11-01

Trauma-focused cognitive behavioral therapy (TF-CBT) is the treatment of choice for traumatized youth, however, follow-up studies are scarce, and treatment effects for co-occurring depression show mixed findings. The aims of this study were to examine whether treatment effects of TF-CBT are maintained at 18 month follow-up and whether degree of co-occurring depression influences treatment effects. As rapid improvement in psychological functioning is warranted for youth, we also investigated whether the symptom trajectory was different for TF-CBT compared to therapy as usual (TAU). The sample consisted of 156 youth (M age = 15.05, 79.50% girls) randomly assigned to TF-CBT or TAU. The youth were assessed for posttraumatic stress symptoms (PTSS), depression, anxiety and general mental health symptoms. Mixed effects analyses followed the symptom courses over 5 time points. Youth receiving TF-CBT maintained their symptom improvement at 18 months follow-up with scores below clinical cut-of on all symptom measures. The most depressed youth had also a significant decline in symptoms that were maintained at follow-up. Symptom trajectories differed as the TF-CBT group reported a more rapid symptom reduction compared to the TAU condition. In the TAU condition, participants received 1.5 times the number of treatment sessions compared to the TF-CBT participants. After 18 months the groups were significantly different on general mental health symptoms only. In conclusion, youth receiving TF-CBT experienced more efficient improvement in trauma related symptoms than youth receiving TAU and these improvements were maintained after 18 months. Also youth experiencing serious co-occurring depression benefitted from TF-CBT.

Physical properties of a resin system for filling the inter-space in the ITER TF coil casing

NASA Astrophysics Data System (ADS)

Evans, D.; Baynahm, E.; Canfer, S.; Foussat, A.

2014-01-01

Each of the eighteen ITER Toroidal Field (TF) coils will consist of seven double pancakes. Each double pancake will have been individually vacuum impregnated and then the seven units assembled together, over-wrapped with glass fabric based insulation and finally vacuum impregnated again to form the TF coil winding pack [1]. The winding pack (WP) will be finally assembled into the coil casing (CC) and to allow for manufacturing tolerances and final geometric definition, a nominal 10 mm gap will exist between the winding pack and the coil case but in practice, this gap may vary between 3 and 15 mm. After assembly, the final step will be to fill the gap with a material that will maintain the final position of the WP and to uniformly transfer load from WP to CC. This paper deals with the selection of materials and techniques to fill the gap and details some of the properties of the chosen material.

Vertebrate LTR retrotransposons of the Tf1/sushi group.

PubMed

Butler, M; Goodwin, T; Simpson, M; Singh, M; Poulter, R

2001-03-01

LTR retrotransposons of the Tf1/sushi group from a diversity of vertebrates, including fish, amphibians, and mammals (humans, mice, and others), are described as full-length or partial elements. These elements are compared, and the mechanisms involved in self-priming of reverse transcriptase and programmed phase shifting are inferred. Evidence is presented that in mammals these elements are still transcriptionally active and are represented as proteins. This suggests that members of the Tf1/sushi group are present as functional elements (or incorporated as partial elements into host genes) in diverse vertebrate lineages.

Restriction of Retrotransposon Mobilization in Schizosaccharomyces pombe by Transcriptional Silencing and Higher-Order Chromatin Organization

PubMed Central

Murton, Heather E.; Grady, Patrick J. R.; Chan, Tsun Ho; Cam, Hugh P.; Whitehall, Simon K.

2016-01-01

Uncontrolled propagation of retrotransposons is potentially detrimental to host genome integrity. Therefore, cells have evolved surveillance mechanisms to restrict the mobility of these elements. In Schizosaccharomyces pombe the Tf2 LTR retrotransposons are transcriptionally silenced and are also clustered in the nucleus into structures termed Tf bodies. Here we describe the impact of silencing and clustering on the mobility of an endogenous Tf2 element. Deletion of genes such as set1+ (histone H3 lysine 4 methyltransferase) or abp1+ (CENP-B homolog) that both alleviate silencing and clustering, result in a corresponding increase in mobilization. Furthermore, expression of constitutively active Sre1, a transcriptional activator of Tf2 elements, also alleviates clustering and induces mobilization. In contrast, clustering is not disrupted by loss of the HIRA histone chaperone, despite high levels of expression, and in this background, mobilization frequency is only marginally increased. Thus, mutations that compromise transcriptional silencing but not Tf bodies are insufficient to drive mobilization. Furthermore, analyses of mutant alleles that separate the transcriptional repression and clustering functions of Set1 are consistent with control of Tf2 propagation via a combination of silencing and spatial organization. Our results indicate that host surveillance mechanisms operate at multiple levels to restrict Tf2 retrotransposon mobilization. PMID:27343236

Tissue factor expression by endothelial cells in sickle cell anemia.

PubMed

Solovey, A; Gui, L; Key, N S; Hebbel, R P

1998-05-01

The role of the vascular endothelium in activation of the coagulation system, a fundamental homeostatic mechanism of mammalian biology, is uncertain because there is little evidence indicating that endothelial cells in vivo express tissue factor (TF), the system's triggering mechanism. As a surrogate for vessel wall endothelium, we examined circulating endothelial cells (CEC) from normals and patients with sickle cell anemia, a disease associated with activation of coagulation. We find that sickle CEC abnormally express TF antigen (expressed as percent CEC that are TF-positive), with 66+/-13% positive in sickle patients in steady-state, 83+/-19% positive in sickle patients presenting with acute vasoocclusive episodes, and only 10+/-13% positive in normal controls. Repeated samplings confirmed this impression that TF expression is greater when sickle patients develop acute vasoocclusive episodes. Sickle CEC are also positive for TF mRNA, with excellent concurrence between antigen and mRNA expression. The TF expressed on the antigen-positive CEC is functional, as demonstrated by a binding assay for Factor VIIa and a chromogenic assay sensitive to generation of Factor Xa. By establishing that endothelial cells in vivo can express TF, these data imply that the vast endothelial surface area does provide an important pathophysiologic trigger for coagulation activation.

Engineering of a membrane-triggered activity switch in coagulation factor VIIa

PubMed Central

Nielsen, Anders L.; Sorensen, Anders B.; Holmberg, Heidi L.; Gandhi, Prafull S.; Karlsson, Johan; Buchardt, Jens; Lamberth, Kasper; Kjelgaard-Hansen, Mads; Ley, Carsten Dan; Sørensen, Brit B.; Ruf, Wolfram; Olsen, Ole H.; Østergaard, Henrik

2017-01-01

Recombinant factor VIIa (FVIIa) variants with increased activity offer the promise to improve the treatment of bleeding episodes in patients with inhibitor-complicated hemophilia. Here, an approach was adopted to enhance the activity of FVIIa by selectively optimizing substrate turnover at the membrane surface. Under physiological conditions, endogenous FVIIa engages its cell-localized cofactor tissue factor (TF), which stimulates activity through membrane-dependent substrate recognition and allosteric effects. To exploit these properties of TF, a covalent complex between FVIIa and the soluble ectodomain of TF (sTF) was engineered by introduction of a nonperturbing cystine bridge (FVIIa Q64C-sTF G109C) in the interface. Upon coexpression, FVIIa Q64C and sTF G109C spontaneously assembled into a covalent complex with functional properties similar to the noncovalent wild-type complex. Additional introduction of a FVIIa-M306D mutation to uncouple the sTF-mediated allosteric stimulation of FVIIa provided a final complex with FVIIa-like activity in solution, while exhibiting a two to three orders-of-magnitude increase in activity relative to FVIIa upon exposure to a procoagulant membrane. In a mouse model of hemophilia A, the complex normalized hemostasis upon vascular injury at a dose of 0.3 nmol/kg compared with 300 nmol/kg for FVIIa. PMID:29109275

Gallium Maltolate Disrupts Tumor Iron Metabolism and Retards the Growth of Glioblastoma by Inhibiting Mitochondrial Function and Ribonucleotide Reductase.

PubMed

Chitambar, Christopher R; Al-Gizawiy, Mona M; Alhajala, Hisham S; Pechman, Kimberly R; Wereley, Janine P; Wujek, Robert; Clark, Paul A; Kuo, John S; Antholine, William E; Schmainda, Kathleen M

2018-06-01

Gallium, a metal with antineoplastic activity, binds transferrin (Tf) and enters tumor cells via Tf receptor1 (TfR1); it disrupts iron homeostasis leading to cell death. We hypothesized that TfR1 on brain microvascular endothelial cells (BMEC) would facilitate Tf-Ga transport into the brain enabling it to target TfR-bearing glioblastoma. We show that U-87 MG and D54 glioblastoma cell lines and multiple glioblastoma stem cell (GSC) lines express TfRs, and that their growth is inhibited by gallium maltolate (GaM) in vitro After 24 hours of incubation with GaM, cells displayed a loss of mitochondrial reserve capacity followed by a dose-dependent decrease in oxygen consumption and a decrease in the activity of the iron-dependent M2 subunit of ribonucleotide reductase (RRM2). IHC staining of rat and human tumor-bearing brains showed that glioblastoma, but not normal glial cells, expressed TfR1 and RRM2, and that glioblastoma expressed greater levels of H- and L-ferritin than normal brain. In an orthotopic U-87 MG glioblastoma xenograft rat model, GaM retarded the growth of brain tumors relative to untreated control ( P = 0.0159) and reduced tumor mitotic figures ( P = 0.045). Tumors in GaM-treated animals displayed an upregulation of TfR1 expression relative to control animals, thus indicating that gallium produced tumor iron deprivation. GaM also inhibited iron uptake and upregulated TfR1 expression in U-87 MG and D54 cells in vitro We conclude that GaM enters the brain via TfR1 on BMECs and targets iron metabolism in glioblastoma in vivo, thus inhibiting tumor growth. Further development of novel gallium compounds for brain tumor treatment is warranted. Mol Cancer Ther; 17(6); 1240-50. ©2018 AACR . ©2018 American Association for Cancer Research.

Soil-to-plant transfer of arsenic and phosphorus along a contamination gradient in the mining-impacted Ogosta River floodplain.

PubMed

Simmler, Michael; Suess, Elke; Christl, Iso; Kotsev, Tsvetan; Kretzschmar, Ruben

2016-12-01

Riverine floodplains downstream of active or former metal sulfide mines are in many cases contaminated with trace metals and metalloids, including arsenic (As). Since decontamination of such floodplains on a large scale is unfeasible, management of contaminated land must focus on providing land use guidelines or even restrictions. This should be based on knowledge about how contaminants enter the food chain. For As, uptake by plants may be an important pathway, but the As soil-to-plant transfer under field conditions is poorly understood. Here, we investigated the soil-to-shoot transfer of As and phosphorus (P) in wild populations of herbaceous species growing along an As contamination gradient across an extensive pasture in the mining-impacted Ogosta River floodplain. The As concentrations in the shoots of Trifolium repens and Holcus lanatus reflected the soil contamination gradient. However, the soil-to-shoot transfer factors (TF) were fairly low, with values mostly below 0.07 (TF=As shoot /As soil ). We found no evidence for interference of As with P uptake by plants, despite extremely high molar As:P ratios (up to 2.6) in Olsen soil extracts of the most contaminated topsoils (0-20cm). Considering the restricted soil-to-shoot transfer, we estimated that for grazing livestock As intake via soil ingestion is likely more important than intake via pasture herbage. Copyright © 2016 Elsevier B.V. All rights reserved.

Effect of SO2 on the transport properties of an imidazolium ionic liquid and its lithium solution.

PubMed

Monteiro, Marcelo J; Ando, Rômulo A; Siqueira, Leonardo J A; Camilo, Fernanda F; Santos, Paulo S; Ribeiro, Mauro C C; Torresi, Roberto M

2011-08-11

Transport coefficients have been measured as a function of the concentration of sulfur dioxide, SO(2), dissolved in 1-butyl-2,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide, [BMMI][Tf(2)N], as well as in its lithium salt solution, Li[Tf(2)N]. The SO(2) reduces viscosity and density and increases conductivity and diffusion coefficients in both the neat [BMMI][Tf(2)N] and the [BMMI][Tf(2)N]-Li[Tf(2)N] solution. The conductivity enhancement is not assigned to a simple viscosity effect; the weakening of ionic interactions upon SO(2) addition also plays a role. Microscopic details of the SO(2) effect were unraveled using Raman spectroscopy and molecular dynamics (MD) simulations. The Raman spectra suggest that the Li(+)-[Tf(2)N] interaction is barely affected by SO(2), and the SO(2)-[Tf(2)N] interaction is weaker than previously observed in an investigation of an ionic liquid containing the bromide anion. Transport coefficients calculated by MD simulations show the same trend as the experimental data with respect to SO(2) content. The MD simulations provide structural information on SO(2) molecules around [Tf(2)N], in particular the interaction of the sulfur atom of SO(2) with oxygen and fluorine atoms of the anion. The SO(2)-[BMMI] interaction is also important because the [BMMI] cations with above-average mobility have a larger number of nearest-neighbor SO(2) molecules. © 2011 American Chemical Society

Trigger Factor can antagonize both SecB and DnaK/DnaJ chaperone functions in Escherichia coli

PubMed Central

Ullers, Ronald S.; Ang, Debbie; Schwager, Françoise; Georgopoulos, Costa; Genevaux, Pierre

2007-01-01

Polypeptides emerging from the ribosome are assisted by a pool of molecular chaperones and targeting factors, which enable them to efficiently partition as cytoplasmic, integral membrane, or exported proteins. In Escherichia coli, the chaperones SecB, Trigger Factor (TF), and DnaK are key players in this process. Here, we report that, as with dnaK or dnaJ mutants, a secB null strain exhibits a strong cold-sensitive (Cs) phenotype. Through suppressor analyses, we found that inactivating mutations in the tig gene encoding TF fully relieve both the Cs phenotype and protein aggregation observed in the absence of SecB. This antagonistic effect of TF depends on its ribosome-binding and chaperone activities but unrelated to its peptidyl-prolyl cis/trans isomerase (PPIase) activity. Furthermore, in contrast to the previously known synergistic action of TF and DnaK/DnaJ above 30°C, a tig null mutation partially suppresses the Cs phenotype exhibited by a compromised DnaK/DnaJ chaperone machine. The antagonistic role of TF is further exemplified by the fact that the secB dnaJ double mutant is viable only in the absence of TF. Finally, we show that, in the absence of TF, more SecA and ribosomes are associated with the inner membrane, suggesting that the presence of TF directly or indirectly interferes with the process of cotranslational protein targeting to the Sec translocon. PMID:17360615

Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus

PubMed Central

Sundaram, Vasavi; Choudhary, Mayank N. K.; Pehrsson, Erica; Xing, Xiaoyun; Fiore, Christopher; Pandey, Manishi; Maricque, Brett; Udawatta, Methma; Ngo, Duc; Chen, Yujie; Paguntalan, Asia; Ray, Tammy; Hughes, Ava; Cohen, Barak A.; Wang, Ting

2017-01-01

Cis-regulatory modules contain multiple transcription factor (TF)-binding sites and integrate the effects of each TF to control gene expression in specific cellular contexts. Transposable elements (TEs) are uniquely equipped to deposit their regulatory sequences across a genome, which could also contain cis-regulatory modules that coordinate the control of multiple genes with the same regulatory logic. We provide the first evidence of mouse-specific TEs that encode a module of TF-binding sites in mouse embryonic stem cells (ESCs). The majority (77%) of the individual TEs tested exhibited enhancer activity in mouse ESCs. By mutating individual TF-binding sites within the TE, we identified a module of TF-binding motifs that cooperatively enhanced gene expression. Interestingly, we also observed the same motif module in the in silico constructed ancestral TE that also acted cooperatively to enhance gene expression. Our results suggest that ancestral TE insertions might have brought in cis-regulatory modules into the mouse genome. PMID:28348391

Time and Frequency Activities at NICT, Japan

DTIC Science & Technology

2009-11-01

consistency and accuracy of our development. 4.2. TWSTFT [11] NICT and major T&F institutes in the Asia-Pacific region, such as NMIA in Australia, NTSC...in China, TL in Taipei, Taiwan, and KRISS in Korea are cooperatively constructing a TWSTFT network in this region. Time transfer is regularly...8 in 2009. A TWSTFT link between NICT and PTB has been established by using IS-4 satellite. The time transfer is performed hourly and the data

PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes

PubMed Central

Bhawna; Bonthala, V.S.; Gajula, MNV Prasad

2016-01-01

The common bean [Phaseolus vulgaris (L.)] is one of the essential proteinaceous vegetables grown in developing countries. However, its production is challenged by low yields caused by numerous biotic and abiotic stress conditions. Regulatory transcription factors (TFs) symbolize a key component of the genome and are the most significant targets for producing stress tolerant crop and hence functional genomic studies of these TFs are important. Therefore, here we have constructed a web-accessible TFs database for P. vulgaris, called PvTFDB, which contains 2370 putative TF gene models in 49 TF families. This database provides a comprehensive information for each of the identified TF that includes sequence data, functional annotation, SSRs with their primer sets, protein physical properties, chromosomal location, phylogeny, tissue-specific gene expression data, orthologues, cis-regulatory elements and gene ontology (GO) assignment. Altogether, this information would be used in expediting the functional genomic studies of a specific TF(s) of interest. The objectives of this database are to understand functional genomics study of common bean TFs and recognize the regulatory mechanisms underlying various stress responses to ease breeding strategy for variety production through a couple of search interfaces including gene ID, functional annotation and browsing interfaces including by family and by chromosome. This database will also serve as a promising central repository for researchers as well as breeders who are working towards crop improvement of legume crops. In addition, this database provide the user unrestricted public access and the user can download entire data present in the database freely. Database URL: http://www.multiomics.in/PvTFDB/ PMID:27465131

Stochastic model of transcription factor-regulated gene expression

NASA Astrophysics Data System (ADS)

Karmakar, Rajesh; Bose, Indrani

2006-09-01

We consider a stochastic model of transcription factor (TF)-regulated gene expression. The model describes two genes, gene A and gene B, which synthesize the TFs and the target gene proteins, respectively. We show through analytic calculations that the TF fluctuations have a significant effect on the distribution of the target gene protein levels when the mean TF level falls in the highest sensitive region of the dose-response curve. We further study the effect of reducing the copy number of gene A from two to one. The enhanced TF fluctuations yield results different from those in the deterministic case. The probability that the target gene protein level exceeds a threshold value is calculated with the knowledge of the probability density functions associated with the TF and target gene protein levels. Numerical simulation results for a more detailed stochastic model are shown to be in agreement with those obtained through analytic calculations. The relevance of these results in the context of the genetic disorder haploinsufficiency is pointed out. Some experimental observations on the haploinsufficiency of the tumour suppressor gene, Nkx 3.1, are explained with the help of the stochastic model of TF-regulated gene expression.

Synthesis and Physicochemical Characterization of D-Tagatose-1-Phosphate: The Substrate of the Tagatose-1-Phosphate Kinase in the Phosphotransferase System-Mediated D-Tagatose Catabolic Pathway of Bacillus licheniformis.

PubMed

Van der Heiden, Edwige; Delmarcelle, Michaël; Simon, Patricia; Counson, Melody; Galleni, Moreno; Freedberg, Darón I; Thompson, John; Joris, Bernard; Battistel, Marcos D

2015-01-01

We report the first enzymatic synthesis of D-tagatose-1-phosphate (Tag-1P) by the multicomponent phosphoenolpyruvate:sugar phosphotransferase system (PEP-PTS) present in tagatose-grown cells of Klebsiella pneumoniae. Physicochemical characterization by (31)P and (1)H nuclear magnetic resonance spectroscopy reveals that, in solution, this derivative is primarily in the pyranose form. Tag-1P was used to characterize the putative tagatose-1-phosphate kinase (TagK) of the Bacillus licheniformis PTS-mediated D-tagatose catabolic pathway (Bli-TagP). For this purpose, a soluble protein fusion was obtained with the 6 His-tagged trigger factor (TF(His6)) of Escherichia coli. The active fusion enzyme was named TagK-TF(His6). Tag-1P and D-fructose-1-phosphate are substrates for the TagK-TF(His6) enzyme, whereas the isomeric derivatives D-tagatose-6-phosphate and D-fructose-6-phosphate are inhibitors. Studies of catalytic efficiency (kcat/Km) reveal that the enzyme specificity is markedly in favor of Tag-1P as the substrate. Importantly, we show in vivo that the transfer of the phosphate moiety from PEP to the B. licheniformis tagatose-specific Enzyme II in E. coli is inefficient. The capability of the PTS general cytoplasmic components of B. subtilis, HPr and Enzyme I to restore the phosphate transfer is demonstrated. © 2015 S. Karger AG, Basel.

Cross-talk between the Tissue Factor/coagulation factor VIIa complex and the tyrosine kinase receptor EphA2 in cancer.

PubMed

Eriksson, Oskar; Thulin, Åsa; Asplund, Anna; Hegde, Geeta; Navani, Sanjay; Siegbahn, Agneta

2016-05-31

Tissue Factor (TF) forms a proteolytically active complex together with coagulation factor VIIa (FVIIa) and functions as the trigger of blood coagulation or alternatively activates cell signaling. We recently described that EphA2 of the Eph tyrosine kinase receptor family is cleaved directly by the TF/FVIIa complex. The aim of the present study was to further characterize the cross-talk between TF/FVIIa and EphA2 using in vitro model systems and human cancer specimens. Cleavage and phosphorylation of EphA2 was studied by Western blot. Subcellular localization of TF and EphA2 was investigated by a proximity ligation assay and confocal microscopy. Phalloidin staining of the actin cytoskeleton was used to study cell rounding and retraction fiber formation. Expression of TF and EphA2 in human colorectal cancer specimens was examined by immunohistochemistry. TF and EphA2 co-localized constitutively in MDA-MB-231 cells, and addition of FVIIa resulted in cleavage of EphA2 by a PAR2-independent mechanism. Overexpression of TF in U251 glioblastoma cells lead to co-localization with EphA2 at the leading edge and FVIIa-dependent cleavage of EphA2. FVIIa potentiated ephrin-A1-induced cell rounding and retraction fiber formation in MDA-MB-231 cells through a RhoA/ROCK-dependent pathway that did not require PAR2-activation. TF and EphA2 were expressed in colorectal cancer specimens, and were significantly correlated. These results suggest that TF/FVIIa-EphA2 cross-talk might potentiate ligand-dependent EphA2 signaling in human cancers, and provide initial evidence that it is possible for this interaction to occur in vivo.

FXIa and platelet polyphosphate as therapeutic targets during human blood clotting on collagen/tissue factor surfaces under flow

PubMed Central

Zhu, Shu; Travers, Richard J.; Morrissey, James H.

2015-01-01

Factor XIIa (FXIIa) and factor XIa (FXIa) contribute to thrombosis in animal models, whereas platelet-derived polyphosphate (polyP) may potentiate contact or thrombin-feedback pathways. The significance of these mediators in human blood under thrombotic flow conditions on tissue factor (TF) –bearing surfaces remains inadequately resolved. Human blood (corn trypsin inhibitor treated [4 μg/mL]) was tested by microfluidic assay for clotting on collagen/TF at TF surface concentration ([TF]wall) from ∼0.1 to 2 molecules per μm2. Anti-FXI antibodies (14E11 and O1A6) or polyP-binding protein (PPXbd) were used to block FXIIa-dependent FXI activation, FXIa-dependent factor IX (FIX) activation, or platelet-derived polyP, respectively. Fibrin formation was sensitive to 14E11 at 0 to 0.1 molecules per µm2 and sensitive to O1A6 at 0 to 0.2 molecules per µm2. However, neither antibody reduced fibrin generation at ∼2 molecules per µm2 when the extrinsic pathway became dominant. Interestingly, PPXbd reduced fibrin generation at low [TF]wall (0.1 molecules per µm2) but not at zero or high [TF]wall, suggesting a role for polyP distinct from FXIIa activation and requiring low extrinsic pathway participation. Regardless of [TF]wall, PPXbd enhanced fibrin sensitivity to tissue plasminogen activator and promoted clot retraction during fibrinolysis concomitant with an observed PPXbd-mediated reduction of fibrin fiber diameter. This is the first detection of endogenous polyP function in human blood under thrombotic flow conditions. When triggered by low [TF]wall, thrombosis may be druggable by contact pathway inhibition, although thrombolytic susceptibility may benefit from polyP antagonism regardless of [TF]wall. PMID:26136249

Vitamin D modulates tissue factor and protease-activated receptor 2 expression in vascular smooth muscle cells.

PubMed

Martinez-Moreno, Julio M; Herencia, Carmen; Montes de Oca, Addy; Muñoz-Castañeda, Juan R; Rodríguez-Ortiz, M Encarnación; Díaz-Tocados, Juan M; Peralbo-Santaella, Esther; Camargo, Antonio; Canalejo, Antonio; Rodriguez, Mariano; Velasco-Gimena, Francisco; Almaden, Yolanda

2016-03-01

Clinical and epidemiologic studies reveal an association between vitamin D deficiency and increased risk of cardiovascular disease. Because vascular smooth muscle cell (VSMC)-derived tissue factor (TF) is suggested to be critical for arterial thrombosis, we investigated whether the vitamin D molecules calcitriol and paricalcitol could reduce the expression of TF induced by the proinflammatory cytokine TNF-α in human aortic VSMCs. We found that, compared with controls, incubation with TNF-α increased TF expression and procoagulant activity in a NF-κB-dependent manner, as deduced from the increased nuclear translocation of nuclear factor κ-light-chain-enhancer of activated B cells protein 65 (p65-NF-κB) and direct interaction of NF-κB to the TF promoter. This was accompanied by the up-regulation of TF signaling mediator protease-activated receptor 2 (PAR-2) expression and by the down-regulation of vitamin D receptor expression in a miR-346-dependent way. However, addition of calcitriol or paricalcitol blunted the TNF-α-induced TF expression and activity (2.01 ± 0.24 and 1.32 ± 0.14 vs. 3.02 ± 0.39 pmol/mg protein, P < 0.05), which was associated with down-regulation of NF-κB signaling and PAR-2 expression, as well as with restored levels of vitamin D receptor and enhanced expression of TF pathway inhibitor. Our data suggest that inflammation promotes a prothrombotic state through the up-regulation of TF function in VSMCs and that the beneficial cardiovascular effects of vitamin D may be partially due to decreases in TF expression and its activity in VSMCs. © FASEB.

Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction

NASA Astrophysics Data System (ADS)

Hansen, Matthew; Everett, Logan; Singh, Larry; Hannenhalli, Sridhar

Functionally related genes tend to be correlated in their expression patterns across multiple conditions and/or tissue-types. Thus co-expression networks are often used to investigate functional groups of genes. In particular, when one of the genes is a transcription factor (TF), the co-expression-based interaction is interpreted, with caution, as a direct regulatory interaction. However, any particular TF, and more importantly, any particular regulatory interaction, is likely to be active only in a subset of experimental conditions. Moreover, the subset of expression samples where the regulatory interaction holds may be marked by presence or absence of a modifier gene, such as an enzyme that post-translationally modifies the TF. Such subtlety of regulatory interactions is overlooked when one computes an overall expression correlation. Here we present a novel mixture modeling approach where a TF-Gene pair is presumed to be significantly correlated (with unknown coefficient) in a (unknown) subset of expression samples. The parameters of the model are estimated using a Maximum Likelihood approach. The estimated mixture of expression samples is then mined to identify genes potentially modulating the TF-Gene interaction. We have validated our approach using synthetic data and on three biological cases in cow and in yeast. While limited in some ways, as discussed, the work represents a novel approach to mine expression data and detect potential modulators of regulatory interactions.

Varying iron release from transferrin and lactoferrin proteins. A laboratory experiment.

PubMed

Carmona, Fernando; González, Ana; Sánchez, Manu; Gálvez, Natividad; Cuesta, Rafael; Capdevila, Mercè; Dominguez-Vera, Jose M

2017-11-01

Iron metabolism is an important subject of study for undergraduate students of chemistry and biochemistry. Relevant laboratory exercises are scarce in the literature but would be very helpful in assisting students grasp key concepts. The experiment described here deals with different iron release mechanisms of two protagonists in iron metabolism: serum transferrin (Tf) and lactoferrin (Lf). Despite having very similar structures and iron-binding sites, Tf releases practically all its iron at pH 5.5 while Lf requires a significantly lower pH of 3. This difference in behavior is directly related to their respective biological functions as Tf blood-borne iron into the cell, while Lf competes with pathogens to sequester iron in biological fluids at more acidic pHs.  During this experiment, the students will carry out iron loading and unloading on both human Lf and Tf and monitor the iron release at different pHs using UV-Vis spectroscopy. With this simple approach, the students will discover the different patterns of iron release of Tf and Lf and how this variance in behavior relates to their biological functions. Furthermore, this laboratory practice can be expanded to allow students to investigate a variety of iron proteins. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):521-527, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

ASXL gain-of-function truncation mutants: defective and dysregulated forms of a natural ribosomal frameshifting product?

PubMed

Dinan, Adam M; Atkins, John F; Firth, Andrew E

2017-10-16

Programmed ribosomal frameshifting (PRF) is a gene expression mechanism which enables the translation of two N-terminally coincident, C-terminally distinct protein products from a single mRNA. Many viruses utilize PRF to control or regulate gene expression, but very few phylogenetically conserved examples are known in vertebrate genes. Additional sex combs-like (ASXL) genes 1 and 2 encode important epigenetic and transcriptional regulatory proteins that control the expression of homeotic genes during key developmental stages. Here we describe an ~150-codon overlapping ORF (termed TF) in ASXL1 and ASXL2 that, with few exceptions, is conserved throughout vertebrates. Conservation of the TF ORF, strong suppression of synonymous site variation in the overlap region, and the completely conserved presence of an EH[N/S]Y motif (a known binding site for Host Cell Factor-1, HCF-1, an epigenetic regulatory factor), all indicate that TF is a protein-coding sequence. A highly conserved UCC_UUU_CGU sequence (identical to the known site of +1 ribosomal frameshifting for influenza virus PA-X expression) occurs at the 5' end of the region of enhanced synonymous site conservation in ASXL1. Similarly, a highly conserved RG_GUC_UCU sequence (identical to a known site of -2 ribosomal frameshifting for arterivirus nsp2TF expression) occurs at the 5' end of the region of enhanced synonymous site conservation in ASXL2. Due to a lack of appropriate splice forms, or initiation sites, the most plausible mechanism for translation of the ASXL1 and 2 TF regions is ribosomal frameshifting, resulting in a transframe fusion of the N-terminal half of ASXL1 or 2 to the TF product, termed ASXL-TF. Truncation or frameshift mutants of ASXL are linked to myeloid malignancies and genetic diseases, such as Bohring-Opitz syndrome, likely at least in part as a result of gain-of-function or dominant-negative effects. Our hypothesis now indicates that these disease-associated mutant forms represent overexpressed defective versions of ASXL-TF. This article was reviewed by Laurence Hurst and Eugene Koonin.

Angiotensin II Type 1 Receptor Antagonism Attenuates Abnormalities in Dynamic Renal Blood Flow Autoregulation in Rats with Endotoxin-Induced Acute Kidney Injury.

PubMed

Nitescu, Nicoletta; DiBona, Gerald F; Grimberg, Elisabeth; Guron, Gregor

2010-01-01

The aim was to examine the role of angiotensin II type 1 receptors in dynamic autoregulation of renal blood flow (RBF) in endotoxemia. Experiments were performed on anesthetized rats 16 h after intraperitoneal lipopolysaccharide (LPS) or vehicle administration. After baseline measurements, groups Sham-Saline, LPS-Saline and LPS-Candesartan received isotonic saline or candesartan (10 μg kg(-1) i.v.). Data were collected during eight consecutive 20-min clearance periods (C1-8). Transfer function (TF) analysis in the frequency domain was used to examine dynamic autoregulation of RBF. Endotoxemic rats showed an approximate 50% reduction in glomerular filtration rate (GFR) and RBF (p < 0.05 vs. Sham-Saline). Candesartan significantly increased RBF (+40 ± 6% vs. baseline; p < 0.05) but did not significantly influence GFR. Endotoxemic animals showed a normal myogenic response but had elevated TF gain values in the frequency range of the tubuloglomerular feedback mechanism (TGF; 0.01-0.03 Hz) reflecting impaired autoregulation (periods C3-4, 2.2 ± 1.6 vs. -2.6 ± 0.6 dB, p < 0.05, and C7-8, -0.4 ± 1.3 vs. -4.0 ± 0.8 dB, p < 0.05; in groups LPS-Saline and Sham-Saline, respectively). Candesartan normalized TF gain in this frequency range (periods C7-8, -6.1 ± 2.3 dB in group LPS-Candesartan, p < 0.05 vs. LPS-Saline). Candesartan ameliorates the adverse effect of endotoxin on the TGF component of dynamic autoregulation of RBF. Copyright © 2010 S. Karger AG, Basel.

Radiocaesium soil-to-wood transfer in commercial willow short rotation coppice on contaminated farm land.

PubMed

Gommers, A; Gäfvert, T; Smolders, E; Merckx, R; Vandenhove, H

2005-01-01

The feasibility of willow short rotation coppice (SRC) for energy production as a revaluation tool for severely radiocaesium-contaminated land was studied. The effects of crop age, clone and soil type on the radiocaesium levels in the wood were assessed following sampling in 14 existing willow SRC fields, planted on radiocaesium-contaminated land in Sweden following Chernobyl deposition. There was only one plot where willow stands of different maturity (R6S2 and R5S4: R, root age and S, shoot age) and clone (Rapp and L78183 both of age category R5S4) were sampled and no significant differences were found. The soils differed among others in clay fraction (3-34%), radiocaesium interception potential (515-6884 meq kg(-1)), soil solution K (0.09-0.95 mM), exchangeable K (0.58-5.77 meq kg(-1)) and cation exchange capacity (31-250 meq kg(-1)). The soil-to-wood transfer factor (TF) of radiocaesium differed significantly between soil types. The TF recorded was generally small (0.00086-0.016 kg kg(-1)), except for willows established on sandy soil (0.19-0.46 kg kg(-1)). Apart from the weak yet significant exponential correlation between the Cs-TF and the solid/liquid distribution coefficient (R2 = 0.54) or the radiocaesium interception potential, RIP (R2 = 0.66), no single significant correlations between soil characteristics and TF were found. The wood-soil solution 137Cs concentration factor (CF) was significantly related to the potassium concentration in the soil solution. A different relation was, however, found between the sandy Trödje soils (CF = 1078.8 x m(K)(-1.83), R2 = 0.99) and the other soils (CF = 35.75 x m(K)(-0.61), R2 =0.61). Differences in the ageing rate of radiocaesium in the soil (hypothesised fraction of bioavailable caesium subjected to fast ageing for Trödje soils only 1% compared to other soils), exchangeable soil K (0.8-1.8 meq kg(-1) for Trödje soils and 1.5-5.8 meq kg(-1) for the other soils) and the ammonium concentration in the soil solution (0.09-0.31 mM NH4+ for the Trödje soils compared to 0.003-0.11 mM NH4+ for the other soils) are put forward as potential factors explaining the higher CF and TF observed for the Trödje soils. Though from the dataset available it was not possible to unequivocally predict the Cs-soil-to-wood-transfer, the generally low TFs observed point to the particular suitability for establishment of SRC on radiocaesium-contaminated land.

Transferrin adsorption onto PLGA nanoparticles governs their interaction with biological systems from blood circulation to brain cancer cells.

PubMed

Chang, Jiang; Paillard, Archibald; Passirani, Catherine; Morille, Marie; Benoit, Jean-Pierre; Betbeder, Didier; Garcion, Emmanuel

2012-06-01

Nanomedicines represent an alternative for the treatment of aggressive glioblastoma tumors. Behaviour of PLGA-nanoparticles (NPs) was here investigated as a function of their protein adsorption characteristics at the different biological interfaces they are expected to face in order to reach brain cancer cells. NPs were studied for size, zeta potential, blood half-life, in vitro endocytic behavior and in vivo accumulation within healthy rat brain and brain tumors. While slightly modifying size (80 to 90 nm) and zeta potential (-44 to -32 mV) protein coating of PLGA-NPs by bovine serum albumin (BSA) or transferrin (Tf) greatly prolonged their blood half-life when intravenously injected in rats and mice. In contrast with THP-1 monocytes, differentiated THP-1 macrophages, F98 glioma cells and astrocytes internalized BSA- and Tf-NPs in vitro. Increase of Tf-NP uptake by F98 cells through caveolae- and clathrin-mediated pathways supports specific interaction between Tf and overexpressed Tf-receptor. Finally, in vivo targeting of healthy brain was found higher with Tf-NPs than with BSA-NPs while both NPs entered massively within brain-developed tumors. Taken together, those data evidence that Tf-NPs represent an interesting nanomedicine to deliver anticancer drugs to glioma cells through systemic or locoregional strategies at early and late tumor stages.

PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

PubMed Central

Jin, Jinpu; Zhang, He; Kong, Lei; Gao, Ge; Luo, Jingchu

2014-01-01

With the aim to provide a resource for functional and evolutionary study of plant transcription factors (TFs), we updated the plant TF database PlantTFDB to version 3.0 (http://planttfdb.cbi.pku.edu.cn). After refining the TF classification pipeline, we systematically identified 129 288 TFs from 83 species, of which 67 species have genome sequences, covering main lineages of green plants. Besides the abundant annotation provided in the previous version, we generated more annotations for identified TFs, including expression, regulation, interaction, conserved elements, phenotype information, expert-curated descriptions derived from UniProt, TAIR and NCBI GeneRIF, as well as references to provide clues for functional studies of TFs. To help identify evolutionary relationship among identified TFs, we assigned 69 450 TFs into 3924 orthologous groups, and constructed 9217 phylogenetic trees for TFs within the same families or same orthologous groups, respectively. In addition, we set up a TF prediction server in this version for users to identify TFs from their own sequences. PMID:24174544

AES/GRG5: more than just a dominant-negative TLE/GRG family member.

PubMed

Beagle, Brandon; Johnson, Gail V W

2010-11-01

The human Transducin-like Enhancer of Split (TLE) and mouse homologue, Groucho gene-related protein (GRG), represent a family of conserved non-DNA binding transcriptional modulatory proteins divided into two subgroups based upon size. The long TLE/GRGs consist of four pentadomain proteins that are dedicated co-repressors for multiple transcription factors (TF). The second TLE/GRG subgroup is composed of the Amino-terminal Enhancer of Split (AES) in humans and its mouse homolog GRG5 (AES/GRG5). In contrast to the dedicated co-repressor function of long TLE/GRGs, AES/GRG5 can both positively or negatively modulate various TF as well as non-TF proteins in a long TLE/GRG-dependent or -independent manner. Therefore, AES/GRG5 is a functionally dynamic protein that is not exclusively defined by its role as a long TLE/GRG antagonist. AES/GRG5 may function in various developmental and pathological processes but the functional characteristics of endogenous AES/GRG5 in a physiologically relevant context remains to be determined. © 2010 Wiley-Liss, Inc.

Fructose induces prothrombotic phenotype in human endothelial cells : A new role for "added sugar" in cardio-metabolic risk.

PubMed

Cirillo, Plinio; Pellegrino, Grazia; Conte, Stefano; Maresca, Fabio; Pacifico, Francesco; Leonardi, Antonio; Trimarco, Bruno

2015-11-01

Intake of large amounts of added sweeteners has been associated with the pathogenesis of cardiometabolic risk. Several studies have shown that fructose increases the cardiovascular risk by modulating endothelial dysfunction and promoting atherosclerosis. Recently, a potential role for fructose in cardiovascular thrombosis has been suggested but with controversial results. Tissue factor (TF) plays a pivotal role in the pathophysiology of cardiovascular thrombosis by triggering the formation of intracoronary thrombi following endothelial injury. This study investigates the effects of fructose, in a concentration range usually observed in the plasma of patients with increased cardiovascular risk, on TF in human umbilical endothelial cells (HUVECs). Cells were stimulated with increasing concentrations of fructose (0.25, 1 and 2.5 mM) and then processed to evaluate TF-mRNA levels by real-time PCR as well as TF expression/activity by FACS analysis and procoagulant activity. Finally, a potential molecular pathway involved in modulating this phenomenon was investigated. We demonstrate that fructose induces transcription of mRNA for TF. In addition, we show that this monosaccharide promotes surface expression of TF that is functionally active. Fructose effects on TF appear modulated by the oxygen free radicals through activation of the transcription factor NF-κB since superoxide dismutase and NF-κB inhibitors suppressed TF expression. Data of the present study, although in vitro, indicate that fructose, besides promoting atherosclerosis, induces a prothrombotic phenotype in HUVECs, thus indicating one the mechanism(s) by which this sweetener might increase cardiometabolic risk.

Dietary exposure to the endocrine disruptor tolylfluanid promotes global metabolic dysfunction in male mice.

PubMed

Regnier, Shane M; Kirkley, Andrew G; Ye, Honggang; El-Hashani, Essam; Zhang, Xiaojie; Neel, Brian A; Kamau, Wakanene; Thomas, Celeste C; Williams, Ayanna K; Hayes, Emily T; Massad, Nicole L; Johnson, Daniel N; Huang, Lei; Zhang, Chunling; Sargis, Robert M

2015-03-01

Environmental endocrine disruptors are implicated as putative contributors to the burgeoning metabolic disease epidemic. Tolylfluanid (TF) is a commonly detected fungicide in Europe, and previous in vitro and ex vivo work has identified it as a potent endocrine disruptor with the capacity to promote adipocyte differentiation and induce adipocytic insulin resistance, effects likely resulting from activation of glucocorticoid receptor signaling. The present study extends these findings to an in vivo mouse model of dietary TF exposure. After 12 weeks of consumption of a normal chow diet supplemented with 100 parts per million TF, mice exhibited increased body weight gain and an increase in total fat mass, with a specific augmentation in visceral adipose depots. This increased adipose accumulation is proposed to occur through a reduction in lipolytic and fatty acid oxidation gene expression. Dietary TF exposure induced glucose intolerance, insulin resistance, and metabolic inflexibility, while also disrupting diurnal rhythms of energy expenditure and food consumption. Adipose tissue endocrine function was also impaired with a reduction in serum adiponectin levels. Moreover, adipocytes from TF-exposed mice exhibited reduced insulin sensitivity, an effect likely mediated through a specific down-regulation of insulin receptor substrate-1 expression, mirroring effects of ex vivo TF exposure. Finally, gene set enrichment analysis revealed an increase in adipose glucocorticoid receptor signaling with TF treatment. Taken together, these findings identify TF as a novel in vivo endocrine disruptor and obesogen in mice, with dietary exposure leading to alterations in energy homeostasis that recapitulate many features of the metabolic syndrome.

Tissue factor expressed by circulating cancer cell-derived microparticles drastically increases the incidence of deep vein thrombosis in mice.

PubMed

Thomas, G M; Brill, A; Mezouar, S; Crescence, L; Gallant, M; Dubois, C; Wagner, D D

2015-07-01

The risk of thrombotic complications such as deep vein thrombosis (DVT) during tumor development is well known. Tumors release into the circulation procoagulant microparticles (MPs) that can participate in thrombus formation following vessel injury. The importance of this MP tissue factor (TF) in the initiation of cancer-associated DVT remains uncertain. To investigate how pancreatic cancer MPs promote DVT in vivo. We combined a DVT mouse model in which thrombosis is induced by flow restriction in the inferior vena cava with one of subcutaneous pancreatic cancer in C57BL/6J mice. We infused high-TF and low-TF tumor MPs to determine the importance of TF in experimental cancer-associated DVT. Both tumor-bearing mice and mice infused with tumor MPs subjected to 3 h of partial flow restriction developed an occlusive thrombus; fewer than one-third of the control mice did. We observed that MPs adhered to neutrophil extracellular traps (NETs), which are functionally important players during DVT, whereas neither P-selectin nor glycoprotein Ib were required for MP recruitment in DVT. The thrombotic phenotype induced by MP infusion was suppressed by hirudin, suggesting the importance of thrombin generation. TF carried by tumor MPs was essential to promote DVT, as mice infused with low-TF tumor MPs had less thrombosis than mice infused with high-TF tumor MPs. TF expressed on tumor MPs contributes to the increased incidence of cancer-associated venous thrombosis in mice in vivo. These MPs may adhere to NETs formed at the site of thrombosis. © 2015 International Society on Thrombosis and Haemostasis.

Hydrogen Maser Clocks in Space for Solid-Earth Research and Time-Transfer Applications: Experiment Overview and Evaluation of Russian Miniature Sapphire Loaded Cavity,

DTIC Science & Technology

cavity, a technique pioneered at VNIIFTRI . Various contacts between West-European parties, headed by ESA, and the Russian parties, headed by RSA, Led...provided by ON and the other by VNIIFTRI . T/F transfer and precise positioning will be performed by both a microwave link, using PRARE equipment, and...sapphire loaded microwave cavity, on Loan from VNIIFTRI , was evaluated in a full-size EFOS hydrogen maser built by ON. The experimental evaluation

Optical Rotation Curves and Linewidths for Tully-Fisher Applications

NASA Astrophysics Data System (ADS)

Courteau, Stephane

1997-12-01

We present optical long-slit rotation curves for 304 northern Sb-Sc UGC galaxies from a sample designed for Tully-Fisher (TF) applications. Matching r-band photometry exists for each galaxy. We describe the procedures of rotation curve (RC) extraction and construction of optical profiles analogous to 21 cm integrated linewidths. More than 20% of the galaxies were observed twice or more, allowing for a proper determination of systematic errors. Various measures of maximum rotational velocity to be used as input in the TF relation are tested on the basis of their repeatability, minimization of TF scatter, and match with 21 cm linewidths. The best measure of TF velocity, V2.2 is given at the location of peak rotational velocity of a pure exponential disk. An alternative measure to V2.2 which makes no assumption about the luminosity profile or shape of the rotation curve is Vhist, the 20% width of the velocity histogram, though the match with 21 cm linewidths is not as good. We show that optical TF calibrations yield internal scatter comparable to, if not smaller than, the best calibrations based on single-dish 21 cm radio linewidths. Even though resolved H I RCs are more extended than their optical counterpart, a tight match between optical and radio linewidths exists since the bulk of the H I surface density is enclosed within the optical radius. We model the 304 RCs presented here plus a sample of 958 curves from Mathewson et al. (1992, APJS, 81, 413) with various fitting functions. An arctan function provides an adequate simple fit (not accounting for non-circular motions and spiral arms). More elaborate, empirical models may yield a better match at the expense of strong covariances. We caution against physical or "universal" parametrizations for TF applications.

Entry of Porphyromonas gingivalis outer membrane vesicles into epithelial cells causes cellular functional impairment.

PubMed

Furuta, Nobumichi; Takeuchi, Hiroki; Amano, Atsuo

2009-11-01

Porphyromonas gingivalis, a periodontal pathogen, secretes outer membrane vesicles (MVs) that contain major virulence factors, including proteases termed gingipains (Arg-gingipain [Rgp] and Lys-gingipain [Kgp]). We recently showed that P. gingivalis MVs swiftly enter host epithelial cells via an endocytosis pathway and are finally sorted to lytic compartments. However, it remains unknown whether MV entry impairs cellular function. Herein, we analyzed cellular functional impairment following entry of P. gingivalis into epithelial cells, including HeLa and immortalized human gingival epithelial (IHGE) cells. After being taken up by endocytic vacuoles, MVs degraded the cellular transferrin receptor (TfR) and integrin-related signaling molecules, such as paxillin and focal adhesion kinase (FAK), which resulted in depletion of intracellular transferrin and inhibition of cellular migration. Few Rgp-null MVs entered the cells, and these negligibly degraded TfR, whereas paxillin and FAK degradation was significant. In contrast, Kgp-null MVs clearly entered the cells and degraded TfR, while they scarcely degraded paxillin and FAK. In addition, both wild-type and Kgp-null MVs significantly impaired cellular migration, whereas the effect of Rgp-null MVs was limited. Our findings suggest that, following entry of P. gingivalis MVs into host cells, MV-associated gingipains degrade cellular functional molecules such as TfR and paxillin/FAK, resulting in cellular impairment, indicating that P. gingivalis MVs are potent vehicles for transmission of virulence factors into host cells and are involved in the etiology of periodontitis.

Entry of Porphyromonas gingivalis Outer Membrane Vesicles into Epithelial Cells Causes Cellular Functional Impairment▿

PubMed Central

Furuta, Nobumichi; Takeuchi, Hiroki; Amano, Atsuo

2009-01-01

Porphyromonas gingivalis, a periodontal pathogen, secretes outer membrane vesicles (MVs) that contain major virulence factors, including proteases termed gingipains (Arg-gingipain [Rgp] and Lys-gingipain [Kgp]). We recently showed that P. gingivalis MVs swiftly enter host epithelial cells via an endocytosis pathway and are finally sorted to lytic compartments. However, it remains unknown whether MV entry impairs cellular function. Herein, we analyzed cellular functional impairment following entry of P. gingivalis into epithelial cells, including HeLa and immortalized human gingival epithelial (IHGE) cells. After being taken up by endocytic vacuoles, MVs degraded the cellular transferrin receptor (TfR) and integrin-related signaling molecules, such as paxillin and focal adhesion kinase (FAK), which resulted in depletion of intracellular transferrin and inhibition of cellular migration. Few Rgp-null MVs entered the cells, and these negligibly degraded TfR, whereas paxillin and FAK degradation was significant. In contrast, Kgp-null MVs clearly entered the cells and degraded TfR, while they scarcely degraded paxillin and FAK. In addition, both wild-type and Kgp-null MVs significantly impaired cellular migration, whereas the effect of Rgp-null MVs was limited. Our findings suggest that, following entry of P. gingivalis MVs into host cells, MV-associated gingipains degrade cellular functional molecules such as TfR and paxillin/FAK, resulting in cellular impairment, indicating that P. gingivalis MVs are potent vehicles for transmission of virulence factors into host cells and are involved in the etiology of periodontitis. PMID:19737899

Mode Shape Estimation Algorithms Under Ambient Conditions: A Comparative Review

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

Dosiek, Luke; Zhou, Ning; Pierre, John W.

Abstract—This paper provides a comparative review of five existing ambient electromechanical mode shape estimation algorithms, i.e., the Transfer Function (TF), Spectral, Frequency Domain Decomposition (FDD), Channel Matching, and Subspace Methods. It is also shown that the TF Method is a general approach to estimating mode shape and that the Spectral, FDD, and Channel Matching Methods are actually special cases of it. Additionally, some of the variations of the Subspace Method are reviewed and the Numerical algorithm for Subspace State Space System IDentification (N4SID) is implemented. The five algorithms are then compared using data simulated from a 17-machine model of themore » Western Electricity Coordinating Council (WECC) under ambient conditions with both low and high damping, as well as during the case where ambient data is disrupted by an oscillatory ringdown. The performance of the algorithms is compared using the statistics from Monte Carlo Simulations and results from measured WECC data, and a discussion of the practical issues surrounding their implementation, including cases where power system probing is an option, is provided. The paper concludes with some recommendations as to the appropriate use of the various techniques. Index Terms—Electromechanical mode shape, small-signal stability, phasor measurement units (PMU), system identification, N4SID, subspace.« less

Pressure Autoregulation Measurement Techniques in Adult Traumatic Brain Injury, Part I: A Scoping Review of Intermittent/Semi-Intermittent Methods.

PubMed

Zeiler, Frederick A; Donnelly, Joseph; Calviello, Leanne; Menon, David K; Smielewski, Peter; Czosnyka, Marek

2017-12-01

The purpose of this study was to perform a systematic, scoping review of commonly described intermittent/semi-intermittent autoregulation measurement techniques in adult traumatic brain injury (TBI). Nine separate systematic reviews were conducted for each intermittent technique: computed tomographic perfusion (CTP)/Xenon-CT (Xe-CT), positron emission tomography (PET), magnetic resonance imaging (MRI), arteriovenous difference in oxygen (AVDO 2 ) technique, thigh cuff deflation technique (TCDT), transient hyperemic response test (THRT), orthostatic hypotension test (OHT), mean flow index (Mx), and transfer function autoregulation index (TF-ARI). MEDLINE ® , BIOSIS, EMBASE, Global Health, Scopus, Cochrane Library (inception to December 2016), and reference lists of relevant articles were searched. A two tier filter of references was conducted. The total number of articles utilizing each of the nine searched techniques for intermittent/semi-intermittent autoregulation techniques in adult TBI were: CTP/Xe-CT (10), PET (6), MRI (0), AVDO 2 (10), ARI-based TCDT (9), THRT (6), OHT (3), Mx (17), and TF-ARI (6). The premise behind all of the intermittent techniques is manipulation of systemic blood pressure/blood volume via either chemical (such as vasopressors) or mechanical (such as thigh cuffs or carotid compression) means. Exceptionally, Mx and TF-ARI are based on spontaneous fluctuations of cerebral perfusion pressure (CPP) or mean arterial pressure (MAP). The method for assessing the cerebral circulation during these manipulations varies, with both imaging-based techniques and TCD utilized. Despite the limited literature for intermittent/semi-intermittent techniques in adult TBI (minus Mx), it is important to acknowledge the availability of such tests. They have provided fundamental insight into human autoregulatory capacity, leading to the development of continuous and more commonly applied techniques in the intensive care unit (ICU). Numerous methods of intermittent/semi-intermittent pressure autoregulation assessment in adult TBI exist, including: CTP/Xe-CT, PET, AVDO 2 technique, TCDT-based ARI, THRT, OHT, Mx, and TF-ARI. MRI-based techniques in adult TBI are yet to be described, with the main focus of MRI techniques on metabolic-based cerebrovascular reactivity (CVR) and not pressure-based autoregulation.

Initial HIV-1 Antigen-Specific CD8+ T Cells in Acute HIV-1 Infection Inhibit Transmitted/Founder Virus Replication

PubMed Central

Freel, Stephanie A.; Picking, Ralph A.; Ferrari, Guido; Ding, Haitao; Ochsenbauer, Christina; Kappes, John C.; Kirchherr, Jennifer L.; Soderberg, Kelly A.; Weinhold, Kent J.; Cunningham, Coleen K.; Denny, Thomas N.; Crump, John A.; Cohen, Myron S.; McMichael, Andrew J.; Haynes, Barton F.

2012-01-01

CD8-mediated virus inhibition can be detected in HIV-1-positive subjects who naturally control virus replication. Characterizing the inhibitory function of CD8+ T cells during acute HIV-1 infection (AHI) can elucidate the nature of the CD8+ responses that can be rapidly elicited and that contribute to virus control. We examined the timing and HIV-1 antigen specificity of antiviral CD8+ T cells during AHI. Autologous and heterologous CD8+ T cell antiviral functions were assessed longitudinally during AHI in five donors from the CHAVI 001 cohort using a CD8+ T cell-mediated virus inhibition assay (CD8 VIA) and transmitted/founder (T/F) viruses. Potent CD8+ antiviral responses against heterologous T/F viruses appeared during AHI at the first time point sampled in each of the 5 donors (Fiebig stages 1/2 to 5). Inhibition of an autologous T/F virus was durable to 48 weeks; however, inhibition of heterologous responses declined concurrent with the resolution of viremia. HIV-1 viruses from 6 months postinfection were more resistant to CD8+-mediated virus inhibition than cognate T/F viruses, demonstrating that the virus escapes early from CD8+ T cell-mediated inhibition of virus replication. CD8+ T cell antigen-specific subsets mediated inhibition of T/F virus replication via soluble components, and these soluble responses were stimulated by peptide pools that include epitopes that were shown to drive HIV-1 escape during AHI. These data provide insights into the mechanisms of CD8-mediated virus inhibition and suggest that functional analyses will be important for determining whether similar antigen-specific virus inhibition can be induced by T cell-directed vaccine strategies. PMID:22514337

Functionalized nano-graphene oxide particles for targeted fluorescence imaging and photothermy of glioma U251 cells.

PubMed

Li, Zhong-Jun; Li, Chao; Zheng, Mei-Guang; Pan, Jia-Dong; Zhang, Li-Ming; Deng, Yue-Fei

2015-01-01

This study was to prepare the functionalized nano-graphene oxide (nano-GO) particles, and observe targeted fluorescence imaging and photothermy of U251 glioma cells under near infrared (NIR) exposure. The functionalized nano-GO-Tf-FITC particles were prepared and then were incubated with U251 glioma cells. Estimation of CCK8 cell activity was adopted for measurement of cytotoxicity. The effect of fluorescein imaging was detected by fluorescence microscope with anti-CD71-FITC as a control. Finally, we detected the killing efficacy with flow cytometry after an 808 nm NIR exposure. Both nano-GO-Tf-FITC group and CD71-FITC group exhibited green-yellow fluorescence, while the control group without the target molecule nano-GO-FITC was negative. The nano-GO-Tf-FITC was incubated with U251 cells at 0.1 mg/ml, 1.0 mg/ml, 3.0 mg/ml and 5.0 mg/ml. After 48 h of incubation, the absorbance was 0.747 ± 0.031, 0.732 ± 0.043, 0.698 ± 0.051 and 0.682 ± 0.039, while the absorbance of control group is 0.759 ± 0.052. There is no significant difference between the nano-GO-FITC groups and control group. In addition, the apoptosis and death index of nano-GO-Tf-FITC group was significantly higher than that of nano-GO-FITC and blank control group (P < 0.05). The nano-GO-Tf-FITC particles with good biological compatibility and low cytotoxicity are successfully made, which have an observed effect of target imaging and photothermal therapy on glioma U251 cells.

PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes.

PubMed

Bhawna; Bonthala, V S; Gajula, Mnv Prasad

2016-01-01

The common bean [Phaseolus vulgaris (L.)] is one of the essential proteinaceous vegetables grown in developing countries. However, its production is challenged by low yields caused by numerous biotic and abiotic stress conditions. Regulatory transcription factors (TFs) symbolize a key component of the genome and are the most significant targets for producing stress tolerant crop and hence functional genomic studies of these TFs are important. Therefore, here we have constructed a web-accessible TFs database for P. vulgaris, called PvTFDB, which contains 2370 putative TF gene models in 49 TF families. This database provides a comprehensive information for each of the identified TF that includes sequence data, functional annotation, SSRs with their primer sets, protein physical properties, chromosomal location, phylogeny, tissue-specific gene expression data, orthologues, cis-regulatory elements and gene ontology (GO) assignment. Altogether, this information would be used in expediting the functional genomic studies of a specific TF(s) of interest. The objectives of this database are to understand functional genomics study of common bean TFs and recognize the regulatory mechanisms underlying various stress responses to ease breeding strategy for variety production through a couple of search interfaces including gene ID, functional annotation and browsing interfaces including by family and by chromosome. This database will also serve as a promising central repository for researchers as well as breeders who are working towards crop improvement of legume crops. In addition, this database provide the user unrestricted public access and the user can download entire data present in the database freely.Database URL: http://www.multiomics.in/PvTFDB/. © The Author(s) 2016. Published by Oxford University Press.

Testing the nonlocal kinetic energy functional of an inhomogeneous, two-dimensional degenerate Fermi gas within the average density approximation

NASA Astrophysics Data System (ADS)

Towers, J.; van Zyl, B. P.; Kirkby, W.

2015-08-01

In a recent paper [B. P. van Zyl et al., Phys. Rev. A 89, 022503 (2014), 10.1103/PhysRevA.89.022503], the average density approximation (ADA) was implemented to develop a parameter-free, nonlocal kinetic energy functional to be used in the orbital-free density functional theory of an inhomogeneous, two-dimensional (2D) Fermi gas. In this work, we provide a detailed comparison of self-consistent calculations within the ADA with the exact results of the Kohn-Sham density functional theory and the elementary Thomas-Fermi (TF) approximation. We demonstrate that the ADA for the 2D kinetic energy functional works very well under a wide variety of confinement potentials, even for relatively small particle numbers. Remarkably, the TF approximation for the kinetic energy functional, without any gradient corrections, also yields good agreement with the exact kinetic energy for all confining potentials considered, although at the expense of the spatial and kinetic energy densities exhibiting poor pointwise agreement, particularly near the TF radius. Our findings illustrate that the ADA kinetic energy functional yields accurate results for both the local and global equilibrium properties of an inhomogeneous 2D Fermi gas, without the need for any fitting parameters.

Analyses of the NAC transcription factor gene family in Gossypium raimondii Ulbr.: chromosomal location, structure, phylogeny, and expression patterns.

PubMed

Shang, Haihong; Li, Wei; Zou, Changsong; Yuan, Youlu

2013-07-01

NAC domain proteins are plant-specific transcription factors known to play diverse roles in various plant developmental processes. In the present study, we performed the first comprehensive study of the NAC gene family in Gossypium raimondii Ulbr., incorporating phylogenetic, chromosomal location, gene structure, conserved motif, and expression profiling analyses. We identified 145 NAC transcription factor (NAC-TF) genes that were phylogenetically clustered into 18 distinct subfamilies. Of these, 127 NAC-TF genes were distributed across the 13 chromosomes, 80 (55%) were preferentially retained duplicates located in both duplicated regions and six were located in triplicated chromosomal regions. The majority of NAC-TF genes showed temporal-, spatial-, and tissue-specific expression patterns based on transcriptomic and qRT-PCR analyses. However, the expression patterns of several duplicate genes were partially redundant, suggesting the occurrence of sub-functionalization during their evolution. Based on their genomic organization, we concluded that genomic duplications contributed significantly to the expansion of the NAC-TF gene family in G. raimondii. Comprehensive analysis of their expression profiles could provide novel insights into the functional divergence among members of the NAC gene family in G. raimondii. © 2013 Institute of Botany, Chinese Academy of Sciences.

Growth and (137)Cs uptake of four Brassica species influenced by inoculation with a plant growth-promoting rhizobacterium Bacillus pumilus in three contaminated farmlands in Fukushima prefecture, Japan.

PubMed

Aung, Han Phyo; Djedidi, Salem; Oo, Aung Zaw; Aye, Yi Swe; Yokoyama, Tadashi; Suzuki, Sohzoh; Sekimoto, Hitoshi; Bellingrath-Kimura, Sonoko Dorothea

2015-07-15

The effectiveness of the plant growth-promoting rhizobacterium Bacillus pumilus regarding growth promotion and radiocesium ((137)Cs) uptake was evaluated in four Brassica species grown on different (137)Cs contaminated farmlands at Fukushima prefecture in Japan from June to August 2012. B. pumilus inoculation did not enhance growth in any of the plants, although it resulted in a significant increase of (137)Cs concentration and higher (137)Cs transfer from the soil to plants. The Brassica species exhibited different (137)Cs uptake abilities in the order Komatsuna>turnip>mustard>radish. TF values of (137)Cs ranged from 0.018 to 0.069 for all vegetables. Komatsuna possessed the largest root surface area and root volume, and showed a higher (137)Cs concentration in plant tissue and higher (137)Cs TF values (0.060) than the other vegetables. Higher (137)Cs transfer to plants was prominent in soil with a high amount of organic matter and an Al-vermiculite clay mineral type. Copyright © 2015 Elsevier B.V. All rights reserved.

Oligomerization of a molecular chaperone modulates its activity

PubMed Central

Kawagoe, Soichiro; Ishimori, Koichiro

2018-01-01

Molecular chaperones alter the folding properties of cellular proteins via mechanisms that are not well understood. Here, we show that Trigger Factor (TF), an ATP-independent chaperone, exerts strikingly contrasting effects on the folding of non-native proteins as it transitions between a monomeric and a dimeric state. We used NMR spectroscopy to determine the atomic resolution structure of the 100 kDa dimeric TF. The structural data show that some of the substrate-binding sites are buried in the dimeric interface, explaining the lower affinity for protein substrates of the dimeric compared to the monomeric TF. Surprisingly, the dimeric TF associates faster with proteins and it exhibits stronger anti-aggregation and holdase activity than the monomeric TF. The structural data show that the dimer assembles in a way that substrate-binding sites in the two subunits form a large contiguous surface inside a cavity, thus accounting for the observed accelerated association with unfolded proteins. Our results demonstrate how the activity of a chaperone can be modulated to provide distinct functional outcomes in the cell. PMID:29714686

Patellofemoral joint contact forces during activities with high knee flexion.

PubMed

Trepczynski, Adam; Kutzner, Ines; Kornaropoulos, Evgenios; Taylor, William R; Duda, Georg N; Bergmann, Georg; Heller, Markus O

2012-03-01

The patellofemoral (PF) joint plays an essential role in knee function, but little is known about the in vivo loading conditions at the joint. We hypothesized that the forces at the PF joint exceed the tibiofemoral (TF) forces during activities with high knee flexion. Motion analysis was performed in two patients with telemetric knee implants during walking, stair climbing, sit-to-stand, and squat. TF and PF forces were calculated using a musculoskeletal model, which was validated against the simultaneously measured in vivo TF forces, with mean errors of 10% and 21% for the two subjects. The in vivo peak TF forces of 2.9-3.4 bodyweight (BW) varied little across activities, while the peak PF forces showed significant variability, ranging from less than 1 BW during walking to more than 3 BW during high flexion activities, exceeding the TF forces. Together with previous in vivo measurements at the hip and knee, the PF forces determined here provide evidence that peak forces across these joints reach values of around 3 BW during high flexion activities, also suggesting that the in vivo loading conditions at the knee can only be fully understood if the forces at the TF and the PF joints are considered together. Copyright © 2011 Orthopaedic Research Society.

Laboratory experiment on the determination of radiostrontium transfer parameter in water - fish compartment system.

PubMed

Tjahaja, Poppy Intan; Sukmabuana, Putu; Siti Salami, Indah Rahmatiah; Muntalif, Barti Setiani

2012-07-01

A laboratory experiment was conducted to investigate the water - fish transfer parameter of radiostrontium that potentially contaminate human body through water - fish - human pathway in the nuclear accident cases. In this experiment, carp fish (Cyprinus carpio), generally produced and consumed by Indonesian people, were cultured in a tank filled with 500 L water contaminated with (85)Sr for two months. The observation of fish growth and radioactivity were conducted every five days by taking up three fish and water samples. The fish were dissected and separated into muscle, bones and internally organ, then destructed using chloric acid. The fish and water samples were then measured using gamma spectrometer with HPGe detector. The transfer parameter of transfer factor (T(f)), uptake rate constant (u), elimination rate constant (k), and the effective half life (T(e)) were analyzed by mathematical equations. The high (85)Sr concentration was observed in the bone by the T(f) value of 67.99 ± 9.68 mL g(-1) wet weight, whereas the concentration in muscle and internal organ were lower with the T(f) of 26.05 ± 4.44 mL g(-1) wet weight and 16.95 ± 2.34 mL g(-1) wet weight, respectively. The values of u obtained from the mathematical calculation were 0.025 day(-1), 0.029 day(-1), and 0.04 day(-1) for bone, muscle, and internal organ, respectively. Those values were higher compared to the k values, i.e. 0.018 day(-1), 0.025 day(-1), and 0.022 day(-1) indicating the accumulation were take place in bone, muscle, and internal organ. The effective half life, which is the sum of physical and biological half life, of (85)Sr in carp was about 30 days. The transfer parameter values determined from this experiment can be used in internal radiation doses assessment through water - fish - human pathways in case of radiostrontium contamination in freshwater environment, so a recommendation can be considered relating to the fish consumption during or after radiostrontium release to the environment. Copyright © 2012 Elsevier Ltd. All rights reserved.

Principles of regulatory information conservation between mouse and human.

PubMed

Cheng, Yong; Ma, Zhihai; Kim, Bong-Hyun; Wu, Weisheng; Cayting, Philip; Boyle, Alan P; Sundaram, Vasavi; Xing, Xiaoyun; Dogan, Nergiz; Li, Jingjing; Euskirchen, Ghia; Lin, Shin; Lin, Yiing; Visel, Axel; Kawli, Trupti; Yang, Xinqiong; Patacsil, Dorrelyn; Keller, Cheryl A; Giardine, Belinda; Kundaje, Anshul; Wang, Ting; Pennacchio, Len A; Weng, Zhiping; Hardison, Ross C; Snyder, Michael P

2014-11-20

To broaden our understanding of the evolution of gene regulation mechanisms, we generated occupancy profiles for 34 orthologous transcription factors (TFs) in human-mouse erythroid progenitor, lymphoblast and embryonic stem-cell lines. By combining the genome-wide transcription factor occupancy repertoires, associated epigenetic signals, and co-association patterns, here we deduce several evolutionary principles of gene regulatory features operating since the mouse and human lineages diverged. The genomic distribution profiles, primary binding motifs, chromatin states, and DNA methylation preferences are well conserved for TF-occupied sequences. However, the extent to which orthologous DNA segments are bound by orthologous TFs varies both among TFs and with genomic location: binding at promoters is more highly conserved than binding at distal elements. Notably, occupancy-conserved TF-occupied sequences tend to be pleiotropic; they function in several tissues and also co-associate with many TFs. Single nucleotide variants at sites with potential regulatory functions are enriched in occupancy-conserved TF-occupied sequences.

Physiological levels of blood coagulation factors IX and X control coagulation kinetics in an in vitro model of circulating tissue factor

NASA Astrophysics Data System (ADS)

Tormoen, Garth W.; Khader, Ayesha; Gruber, András; McCarty, Owen J. T.

2013-06-01

Thrombosis significantly contributes to cancer morbidity and mortality. The mechanism behind thrombosis in cancer may be circulating tissue factor (TF), as levels of circulating TF are associated with thrombosis. However, circulating TF antigen level alone has failed to predict thrombosis in patients with cancer. We hypothesize that coagulation factor levels regulate the kinetics of circulating TF-induced thrombosis. Coagulation kinetics were measured as a function of individual coagulation factor levels and TF particle concentration. Clotting times increased when pooled plasma was mixed at or above a ratio of 4:6 with PBS. Clotting times increased when pooled plasma was mixed at or above a ratio of 8:2 with factor VII-depleted plasma, 7:3 with factor IX- or factor X-depleted plasmas, or 2:8 with factor II-, V- or VIII-depleted plasmas. Addition of coagulation factors VII, X, IX, V and II to depleted plasmas shortened clotting and enzyme initiation times, and increased enzyme generation rates in a concentration-dependent manner. Only additions of factors IX and X from low-normal to high-normal levels shortened clotting times and increased enzyme generation rates. Our results demonstrate that coagulation kinetics for TF particles are controlled by factor IX and X levels within the normal physiological range. We hypothesize that individual patient factor IX and X levels may be prognostic for susceptibility to circulating TF-induced thrombosis.

Preliminary LOCA analysis of the westinghouse small modular reactor using the WCOBRA/TRAC-TF2 thermal-hydraulics code

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

Liao, J.; Kucukboyaci, V. N.; Nguyen, L.

2012-07-01

The Westinghouse Small Modular Reactor (SMR) is an 800 MWt (> 225 MWe) integral pressurized water reactor (iPWR) with all primary components, including the steam generator and the pressurizer located inside the reactor vessel. The reactor core is based on a partial-height 17x17 fuel assembly design used in the AP1000{sup R} reactor core. The Westinghouse SMR utilizes passive safety systems and proven components from the AP1000 plant design with a compact containment that houses the integral reactor vessel and the passive safety systems. A preliminary loss of coolant accident (LOCA) analysis of the Westinghouse SMR has been performed using themore » WCOBRA/TRAC-TF2 code, simulating a transient caused by a double ended guillotine (DEG) break in the direct vessel injection (DVI) line. WCOBRA/TRAC-TF2 is a new generation Westinghouse LOCA thermal-hydraulics code evolving from the US NRC licensed WCOBRA/TRAC code. It is designed to simulate PWR LOCA events from the smallest break size to the largest break size (DEG cold leg). A significant number of fluid dynamics models and heat transfer models were developed or improved in WCOBRA/TRAC-TF2. A large number of separate effects and integral effects tests were performed for a rigorous code assessment and validation. WCOBRA/TRAC-TF2 was introduced into the Westinghouse SMR design phase to assist a quick and robust passive cooling system design and to identify thermal-hydraulic phenomena for the development of the SMR Phenomena Identification Ranking Table (PIRT). The LOCA analysis of the Westinghouse SMR demonstrates that the DEG DVI break LOCA is mitigated by the injection and venting from the Westinghouse SMR passive safety systems without core heat up, achieving long term core cooling. (authors)« less

The Novel Endocrine Disruptor Tolylfluanid Impairs Insulin Signaling in Primary Rodent and Human Adipocytes through a Reduction in Insulin Receptor Substrate-1 Levels

PubMed Central

Sargis, Robert M.; Neel, Brian A.; Brock, Clifton O.; Lin, Yuxi; Hickey, Allison T.; Carlton, Daniel A.; Brady, Matthew J.

2012-01-01

Emerging data suggest that environmental endocrine disrupting chemicals (EDCs) may contribute to the pathophysiology of obesity and diabetes. In prior work, the phenylsulfamide fungicide tolylfluanid (TF) was shown to augment adipocyte differentiation, yet its effects on mature adipocyte metabolism remain unknown. Because of the central role of adipose tissue in global energy regulation, the present study tested the hypothesis that TF modulates insulin action in primary rodent and human adipocytes. Alterations in insulin signaling in primary mammalian adipocytes were determined by the phosphorylation of Akt, a critical insulin signaling intermediate. Treatment of primary murine adipose tissue in vitro with 100 nM TF for 48 h markedly attenuated acute insulin-stimulated Akt phosphorylation in a strain- and species-independent fashion. Perigonadal, perirenal, and mesenteric fat were all sensitive to TF-induced insulin resistance. A similar TF-induced reduction in insulin-stimulated Akt phosphorylation was observed in primary human subcutaneous adipose tissue. TF-treatment led to a potent and specific reduction in insulin receptor substrate-1 (IRS-1) mRNA and protein levels, a key upstream mediator of insulin’s diverse metabolic effects. In contrast, insulin receptor-β, phosphatidylinositol 3-kinase, and Akt expression were unchanged, indicating a specific abrogation of insulin signaling. Additionally, TF-treated adipocytes exhibited altered endocrine function with a reduction in both basal and insulin-stimulated leptin secretion. These studies demonstrate that TF induces cellular insulin resistance in primary murine and human adipocytes through a reduction of IRS-1 expression and protein stability, raising concern about the potential for this fungicide to disrupt metabolism and thereby contribute to the pathogenesis of diabetes. PMID:22387882

Estimation of soil-to-plant transfer factors of radiocesium in 99 wild plant species grown in arable lands 1 year after the Fukushima 1 Nuclear Power Plant accident.

PubMed

Yamashita, Jun; Enomoto, Takashi; Yamada, Masao; Ono, Toshiro; Hanafusa, Tadashi; Nagamatsu, Tomohiro; Sonoda, Shoji; Yamamoto, Yoko

2014-01-01

One year after the deposition of radionuclides from the Fukushima 1 Nuclear Power Plant (A formal name is Fukushima Daiichi Nuclear Power Station) in March 2011, radiocesium (¹³⁴Cs, ¹³⁷Cs) concentrations ([Cs]) were comprehensively investigated in the wild plants of 99 species most of which were annual or summer green perennial herbs and started to grow from April 2012 at the heavily contaminated fields of paddy (three study sites) and upland (one study site) in Fukushima Prefecture. The survey was conducted three times (April, July and October) in the year. In each site, soils (soil cores of 5-cm depth) and plants (aerial shoots) were collected for determination of [Cs] on a dry weight basis, and then the transfer factor (TF) of radiocesium from soil to plant ([Cs]plant/[Cs]soil) was estimated in each species. The [Cs] values of both soils and plants largely varied. However, some species exhibited relatively high TF values (more than 0.4) (e.g., Athyrium yokoscense, Dryopteris tokyoensis, and Cyperus brevifolius), while others exhibited almost negligible values (less than 0.01) (e.g., Salix miyabeana, Humulus scandens, and Elymus tsukushiensis). In addition, judging from the 11 species grown in both paddy and upland fields, TF values were generally higher in the paddy fields. The estimation of phytoextraction efficiency of soil radiocesium by weed communities in the paddy fields suggests that the weed community is not a practical candidate for phytoremediation technique.

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

Salvagnini, Elena; Bosmans, Hilde; Marshall, Nicholas W.

Purpose: The aim of this paper was to illustrate the value of the new metric effective detective quantum efficiency (eDQE) in relation to more established measures in the optimization process of two digital mammography systems. The following metrics were included for comparison against eDQE: detective quantum efficiency (DQE) of the detector, signal difference to noise ratio (SdNR), and detectability index (d′) calculated using a standard nonprewhitened observer with eye filter.Methods: The two systems investigated were the Siemens MAMMOMAT Inspiration and the Hologic Selenia Dimensions. The presampling modulation transfer function (MTF) required for the eDQE was measured using two geometries: amore » geometry containing scattered radiation and a low scatter geometry. The eDQE, SdNR, and d′ were measured for poly(methyl methacrylate) (PMMA) thicknesses of 20, 40, 60, and 70 mm, with and without the antiscatter grid and for a selection of clinically relevant target/filter (T/F) combinations. Figures of merit (FOMs) were then formed from SdNR and d′ using the mean glandular dose as the factor to express detriment. Detector DQE was measured at energies covering the range of typical clinically used spectra.Results: The MTF measured in the presence of scattered radiation showed a large drop at low spatial frequency compared to the low scatter method and led to a corresponding reduction in eDQE. The eDQE for the Siemens system at 1 mm{sup −1} ranged between 0.15 and 0.27, depending on T/F and grid setting. For the Hologic system, eDQE at 1 mm{sup −1} varied from 0.15 to 0.32, again depending on T/F and grid setting. The eDQE results for both systems showed that the grid increased the system efficiency for PMMA thicknesses of 40 mm and above but showed only small sensitivity to T/F setting. While results of the SdNR and d′ based FOMs confirmed the eDQE grid position results, they were also more specific in terms of T/F selection. For the Siemens system at 20 mm PMMA, the FOMs indicated Mo/Mo (grid out) as optimal while W/Rh (grid in) was the optimal configuration at 40, 60, and 70 mm PMMA. For the Hologic, the FOMs pointed to W/Rh (grid in) at 20 and 40 mm of PMMA while W/Ag (grid in) gave the highest FOM at 60 and 70 mm PMMA. Finally, DQE at 1 mm{sup −1} averaged for the four beam qualities studied was 0.44 ± 0.02 and 0.55 ± 0.03 for the Siemens and Hologic detectors, respectively, indicating only a small influence of energy on detector DQE.Conclusions: Both the DQE and eDQE data showed only a small sensitivity to T/F setting for these two systems. The eDQE showed clear preferences in terms of scatter reduction, being highest for the grid-in geometry for PMMA thicknesses of 40 mm and above. The SdNR and d′ based figures of merit, which contain additional weighting for contrast and dose, pointed to specific T/F settings for both systems.« less

FXIa and platelet polyphosphate as therapeutic targets during human blood clotting on collagen/tissue factor surfaces under flow.

PubMed

Zhu, Shu; Travers, Richard J; Morrissey, James H; Diamond, Scott L

2015-09-17

Factor XIIa (FXIIa) and factor XIa (FXIa) contribute to thrombosis in animal models, whereas platelet-derived polyphosphate (polyP) may potentiate contact or thrombin-feedback pathways. The significance of these mediators in human blood under thrombotic flow conditions on tissue factor (TF) -bearing surfaces remains inadequately resolved. Human blood (corn trypsin inhibitor treated [4 μg/mL]) was tested by microfluidic assay for clotting on collagen/TF at TF surface concentration ([TF]wall) from ∼0.1 to 2 molecules per μm(2). Anti-FXI antibodies (14E11 and O1A6) or polyP-binding protein (PPXbd) were used to block FXIIa-dependent FXI activation, FXIa-dependent factor IX (FIX) activation, or platelet-derived polyP, respectively. Fibrin formation was sensitive to 14E11 at 0 to 0.1 molecules per µm(2) and sensitive to O1A6 at 0 to 0.2 molecules per µm(2). However, neither antibody reduced fibrin generation at ∼2 molecules per µm(2) when the extrinsic pathway became dominant. Interestingly, PPXbd reduced fibrin generation at low [TF]wall (0.1 molecules per µm(2)) but not at zero or high [TF]wall, suggesting a role for polyP distinct from FXIIa activation and requiring low extrinsic pathway participation. Regardless of [TF]wall, PPXbd enhanced fibrin sensitivity to tissue plasminogen activator and promoted clot retraction during fibrinolysis concomitant with an observed PPXbd-mediated reduction of fibrin fiber diameter. This is the first detection of endogenous polyP function in human blood under thrombotic flow conditions. When triggered by low [TF]wall, thrombosis may be druggable by contact pathway inhibition, although thrombolytic susceptibility may benefit from polyP antagonism regardless of [TF]wall. © 2015 by The American Society of Hematology.

Overexpression of COUP-TF1 in murine embryonic stem cells reduces retinoic acid-associated growth arrest and increases extraembryonic endoderm gene expression.

PubMed

Zhuang, Yong; Gudas, Lorraine J

2008-09-01

Vitamin A (retinol [Rol]) and its metabolites are essential for embryonic development. The Rol metabolite all-trans retinoic acid (RA) is a biologically active form of Rol. The orphan nuclear receptor chicken ovalbumin upstream promoter-transcription-factors (COUP-TF) proteins have been implicated in the regulation of several important biological processes, such as embryonic development and neuronal cell differentiation. Because there is evidence that COUP-TFs function in the retinoid signaling network during development and differentiation, we generated murine embryonic stem (ES) cell lines which stably and constitutively overexpress COUP-TF1 (NR2F1) and we analyzed RA-induced differentiation. COUP-TF1 overexpression resulted in reduced RA-associated growth arrest. A 2.4+/-0.17-fold higher Nanog mRNA level was seen in COUP-TF1 overexpressing lines, as compared with wild-type (WT) ES cells, after a 72 hr RA treatment. We also showed that COUP-TF1 overexpression enhanced RA-induced extraembryonic endoderm gene expression. Specifically, COUP-TF1 overexpression increased mRNA levels of GATA6 by 3.3+/-0.3-fold, GATA4 by 3.6+/-0.1-fold, laminin B1 (LAMB1) by 3.4+/-0.1-fold, LAMC1 by 3.4+/-0.2-fold, Dab2 by 2.4+0.1-fold, and SOX17 by 2.5-fold at 72 hr after RA treatment plus LIF, as compared with the increases seen in WT ES cells. However, RA-induced neurogenesis was unaffected by COUP-TF1 overexpression, as shown by the equivalent levels of expression of NeuroD1, nestin, GAP43 and other neuronal markers. Our results revealed for the first time that COUP-TF1 is an important signaling molecule during vitamin A (Rol)-mediated very early stage of embryonic development.

Moderators of treatment response to trauma-focused cognitive behavioral therapy among youth in Zambia.

PubMed

Kane, Jeremy C; Murray, Laura K; Cohen, Judith; Dorsey, Shannon; Skavenski van Wyk, Stephanie; Galloway Henderson, Jennica; Imasiku, Mwiya; Mayeya, John; Bolton, Paul

2016-10-01

The effectiveness of mental health interventions such as trauma-focused cognitive behavioral therapy (TF-CBT) may vary by client, caregiver, and intervention-level variables, but few randomized trials in low- and middle-income countries (LMIC) have conducted moderation analyses to investigate these characteristics. This study explores moderating factors to TF-CBT treatment response among a sample of orphans and vulnerable children (OVC) in Zambia. Data were obtained from a completed randomized trial of TF-CBT among 257 OVC in Zambia. Trauma symptoms and functioning were measured at baseline and following the end of treatment. Mixed effects regression models were estimated for each moderator of interest: gender, age, number of trauma types experienced, history of sexual abuse, orphan status, primary caretaker, school status, and parental involvement in treatment. Treatment effectiveness was moderated by history of sexual abuse with greater reductions in both outcomes (trauma, p < .05; functioning, p < .01) for those that experienced sexual abuse. Primary caretaker was also a moderator with greater trauma reductions in those who identified their mother as the primary caretaker (p < .01), and better functioning in those that identified their father as the primary caretaker (p < .05). Nonorphans and single orphans (mother alive) showed greater reduction in functional impairment (p < .01) compared with double orphans. There was no significant moderator effect found by gender, age, number of trauma types, school status, or caregiver participation in treatment. This study suggests that TF-CBT was effective in reducing trauma symptoms and functional impairment among trauma-affected youth overall and that it may be particularly effective for survivors of child sexual abuse and children whose primary caretaker is a biological parent. Scale-up of TF-CBT is warranted given the wide range of effectiveness and prevalence of child sexual abuse. Future randomized trials of interventions in LMIC should power for moderation analyses in the study design phase when feasible. © 2016 Association for Child and Adolescent Mental Health.

Comparison of Clinical Efficacy Between Interlaminar and Transforaminal Epidural Injection in Patients With Axial Pain due to Cervical Disc Herniation.

PubMed

Lee, Jung Hwan; Lee, Sang-Ho

2016-01-01

Transforaminal (TF) approach is preferred by physician to interlaminar (IL) approach because it can deliver injectates directly around nerve root and dorsal root ganglion, which is regarded as main pain sources. Axial neck pain is originated from sinuvertebral nerve located in ventral epidural spaces, which has been described to be related to central or paramedian disc herniation. It is very questionable that TF injection is also more effective than IL injection in the patients with axial neck or interscapular pain. This study was to evaluate clinical efficacy of cervical epidural injection in patients with axial pain due to cervical disc herniation and to compare the clinical outcomes between TF and IL approaches. Fifty-six and 52 patients who underwent IL and TF epidural injections, respectively, for axial neck/interscapular pain due to central or paramedian cervical disc herniation were included. Numeric Rating Scale (NRS) and Neck Disability Index (NDI) were compared between both groups at 2 and 8 weeks after treatment. Successful pain relief was defined if a 50% or more reduction of NRS score was achieved in comparison with pretreatment one. Successful functional improvement was defined if at least a 40% reduction of NDI was obtained. Overall, 79 (73.1%) and 57 (52.8%) among 108 patients showed successful pain relief at 2 and 8 weeks, respectively. Seventy-six (70.4%) and 52 (48.1%) had successful functional improvement at 2 and 8 weeks, respectively. The IL and TF groups showed no significant difference in proportion of successful results of NRS 2 weeks (73.2% vs 67.3%) and 8 weeks (48.2% vs 48.1%). Also, no significant difference was obtained in proportion of successful NDI between 2 groups at 2 weeks (75.0% vs 71.2%) and 8 weeks (53.6% vs 51.9%). Cervical epidural injection showed favorable results in 2 weeks and moderate results in 8 weeks in patients with axial pain due to cervical disc herniation. IL and TF showed no significant difference in clinical efficacy. Considering TF was relevant to more serious side effects, IL was more recommendable in these patients.

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

PubMed Central

2011-01-01

Background Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has been lacking. Results We analyzed in vitro and in vivo TF-DNA binding data reported in previous large-scale studies to generate a comprehensive, curated resource of DNA binding specificity data for all characterized S. cerevisiae TFs. Our collection comprises DNA binding site motifs and comprehensive in vitro DNA binding specificity data for all possible 8-bp sequences. Investigation of the DNA binding specificities within the basic leucine zipper (bZIP) and VHT1 regulator (VHR) TF families revealed unexpected plasticity in TF-DNA recognition: intriguingly, the VHR TFs, newly characterized by protein binding microarrays in this study, recognize bZIP-like DNA motifs, while the bZIP TF Hac1 recognizes a motif highly similar to the canonical E-box motif of basic helix-loop-helix (bHLH) TFs. We identified several TFs with distinct primary and secondary motifs, which might be associated with different regulatory functions. Finally, integrated analysis of in vivo TF binding data with protein binding microarray data lends further support for indirect DNA binding in vivo by sequence-specific TFs. Conclusions The comprehensive data in this curated collection allow for more accurate analyses of regulatory TF-DNA interactions, in-depth structural studies of TF-DNA specificity determinants, and future experimental investigations of the TFs' predicted target genes and regulatory roles. PMID:22189060

p27{sup Kip1} inhibits tissue factor expression

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

Breitenstein, Alexander, E-mail: alexander.breitenstein@usz.ch; Cardiovascular Research, Physiology Institute, University of Zurich; Center for Integrative Human Physiology

2013-10-04

Highlights: •p27{sup Kip1}regulates the expression of tissue factor at the transcriptional level. •This inhibitory effect of p27{sup Kip1} is independently of its cell regulatory action. •The current study provides new insights into a pleiotrophic function of p27{sup Kip1}. -- Abstract: Background: The cyclin-dependent kinase inhibitor (CDKI) p27{sup Kip1} regulates cell proliferation and thus inhibits atherosclerosis and vascular remodeling. Expression of tissue factor (TF), the key initator of the coagulation cascade, is associated with atherosclerosis. Yet, it has not been studied whether p27{sup Kip1} influences the expression of TF. Methods and results: p27{sup Kip1} overexpression in human aortic endothelial cells wasmore » achieved by adenoviral transfection. Cells were rendered quiescent for 24 h in 0.5% fetal-calf serum. After stimulation with TNF-α (5 ng/ml), TF protein expression and activity was significantly reduced (n = 4; P < 0.001) in cells transfected with p27{sup Kip1}. In line with this, p27{sup Kip1} overexpression reduced cytokine-induced TF mRNA expression (n = 4; P < 0.01) and TF promotor activity (n = 4; P < 0.05). In contrast, activation of the MAP kinases p38, ERK and JNK was not affected by p27{sup Kip1} overexpression. Conclusion: This in vitro study suggests that p27{sup Kip1} inhibits TF expression at the transcriptional level. These data indicate an interaction between p27{sup Kip1} and TF in important pathological alterations such as atherosclerosis and vascular remodeling.« less

Tissue factor expressed by circulating cancer cell-derived microparticles drastically increases the incidence of deep vein thrombosis in mice

PubMed Central

Thomas, G. M.; Brill, A.; Mezouar, S.; Crescence, L.; Gallant, M.; Dubois, C.; Wagner, D. D.

2015-01-01

Background The risk of thrombotic complications such as deep vein thrombosis (DVT) during tumor development is well known. Tumors release into circulation procoagulant microparticles (MPs) that can participate in thrombus formation following vessel injury. The importance of this MP tissue factor (TF) in the initiation of cancer-associated DVT remains uncertain. Objective To address how pancreatic cancer MPs promote DVT in vivo. Methods We combined a DVT mouse model where thrombosis is induced by flow restriction of the inferior vena cava with one of subcutaneous pancreatic cancer in C57BL/6J mice. We infused high and low TF tumor MPs to determine the importance of TF in experimental cancer-associated DVT. Results Both tumor-bearing mice and mice infused with tumor MPs submitted to 3 hours of partial flow restriction developed an occlusive thrombus; fewer than a third of the control mice did. We observed that MPs adhered to neutrophil extracellular traps (NETs), functionally important players during DVT, whereas neither P-selectin nor GPIb were required for the MP recruitment in DVT. The thrombotic phenotype induced by MP infusion was suppressed by hirudin suggesting the importance of thrombin generation. TF carried by tumor MPs was essential to promote DVT as mice infused with low TF tumor MPs had less thrombosis than mice infused with high TF tumor MPs. Conclusions TF expressed on tumor MPs contributes to the increased incidence of cancer-associated venous thrombosis in mice in vivo. These MPs may adhere to NETs formed at the site of thrombosis. PMID:25955268

Establishment of the Inducible Tet-On System for the Activation of the Silent Trichosetin Gene Cluster in Fusarium fujikuroi

PubMed Central

Janevska, Slavica; Arndt, Birgit; Baumann, Leonie; Apken, Lisa Helene; Mauriz Marques, Lucas Maciel; Humpf, Hans-Ulrich; Tudzynski, Bettina

2017-01-01

The PKS-NRPS-derived tetramic acid equisetin and its N-desmethyl derivative trichosetin exhibit remarkable biological activities against a variety of organisms, including plants and bacteria, e.g., Staphylococcus aureus. The equisetin biosynthetic gene cluster was first described in Fusarium heterosporum, a species distantly related to the notorious rice pathogen Fusarium fujikuroi. Here we present the activation and characterization of a homologous, but silent, gene cluster in F. fujikuroi. Bioinformatic analysis revealed that this cluster does not contain the equisetin N-methyltransferase gene eqxD and consequently, trichosetin was isolated as final product. The adaption of the inducible, tetracycline-dependent Tet-on promoter system from Aspergillus niger achieved a controlled overproduction of this toxic metabolite and a functional characterization of each cluster gene in F. fujikuroi. Overexpression of one of the two cluster-specific transcription factor (TF) genes, TF22, led to an activation of the three biosynthetic cluster genes, including the PKS-NRPS key gene. In contrast, overexpression of TF23, encoding a second Zn(II)2Cys6 TF, did not activate adjacent cluster genes. Instead, TF23 was induced by the final product trichosetin and was required for expression of the transporter-encoding gene MFS-T. TF23 and MFS-T likely act in consort and contribute to detoxification of trichosetin and therefore, self-protection of the producing fungus. PMID:28379186

Establishment of the Inducible Tet-On System for the Activation of the Silent Trichosetin Gene Cluster in Fusarium fujikuroi.

PubMed

Janevska, Slavica; Arndt, Birgit; Baumann, Leonie; Apken, Lisa Helene; Mauriz Marques, Lucas Maciel; Humpf, Hans-Ulrich; Tudzynski, Bettina

2017-04-05

The PKS-NRPS-derived tetramic acid equisetin and its N -desmethyl derivative trichosetin exhibit remarkable biological activities against a variety of organisms, including plants and bacteria, e.g., Staphylococcus aureus . The equisetin biosynthetic gene cluster was first described in Fusarium heterosporum , a species distantly related to the notorious rice pathogen Fusarium fujikuroi . Here we present the activation and characterization of a homologous, but silent, gene cluster in F. fujikuroi . Bioinformatic analysis revealed that this cluster does not contain the equisetin N -methyltransferase gene eqxD and consequently, trichosetin was isolated as final product. The adaption of the inducible, tetracycline-dependent Tet-on promoter system from Aspergillus niger achieved a controlled overproduction of this toxic metabolite and a functional characterization of each cluster gene in F. fujikuroi . Overexpression of one of the two cluster-specific transcription factor (TF) genes, TF22 , led to an activation of the three biosynthetic cluster genes, including the PKS-NRPS key gene. In contrast, overexpression of TF23 , encoding a second Zn(II)₂Cys₆ TF, did not activate adjacent cluster genes. Instead, TF23 was induced by the final product trichosetin and was required for expression of the transporter-encoding gene MFS-T . TF23 and MFS-T likely act in consort and contribute to detoxification of trichosetin and therefore, self-protection of the producing fungus.

Phase Transitions of Triflate-Based Ionic Liquids under High Pressure.

PubMed

Faria, Luiz F O; Ribeiro, Mauro C C

2015-11-05

Raman spectroscopy has been used to study phase transitions of ionic liquids based on the triflate anion, [TfO](-), as a function of pressure or temperature. Raman spectra of ionic liquids containing the cations 1-butyl-3-methylimidazolium, [C4C1Im](+), 1-octyl-3-methylimidazolium, [C8C1Im](+), 1-butyl-2,3-dimethylimidazolium, [C4C1C1Im](+), and 1-butyl-1-methylpyrrolidinium, [C4C1Pyr](+), were compared. Vibrational frequencies and binding energy of ionic pairs were calculated by quantum chemistry methods. The ionic liquids [C4C1Im][TfO] and [C4C1Pyr][TfO] crystallize at 1.0 GPa when the pressure is increased in steps of ∼ 0.2 GPa from the atmospheric pressure, whereas [C8C1Im][TfO] and [C4C1C1Im][TfO] do not crystallize up to 2.3 GPa of applied pressure. The low-frequency range of the Raman spectrum of [C4C1Im][TfO] indicates that the system undergoes glass transition, rather than crystallization, when the pressure applied on the liquid has been increased above 2.0 GPa in a single step. Strong hysteresis of spectral features (frequency shift and bandwidth) of the high-pressure crystalline phase when the pressure was released stepwise back to the atmospheric pressure has been found .

PpTFDB: A pigeonpea transcription factor database for exploring functional genomics in legumes

PubMed Central

Singh, Akshay; Sharma, Ajay Kumar; Singh, Nagendra Kumar

2017-01-01

Pigeonpea (Cajanus cajan L.), a diploid legume crop, is a member of the tribe Phaseoleae. This tribe is descended from the millettioid (tropical) clade of the subfamily Papilionoideae, which includes many important legume crop species such as soybean (Glycine max), mung bean (Vigna radiata), cowpea (Vigna ungiculata), and common bean (Phaseolus vulgaris). It plays major role in food and nutritional security, being rich source of proteins, minerals and vitamins. We have developed a comprehensive Pigeonpea Transcription Factors Database (PpTFDB) that encompasses information about 1829 putative transcription factors (TFs) and their 55 TF families. PpTFDB provides a comprehensive information about each of the identified TFs that includes chromosomal location, protein physicochemical properties, sequence data, protein functional annotation, simple sequence repeats (SSRs) with primers derived from their motifs, orthology with related legume crops, and gene ontology (GO) assignment to respective TFs. (PpTFDB: http://14.139.229.199/PpTFDB/Home.aspx) is a freely available and user friendly web resource that facilitates users to retrieve the information of individual members of a TF family through a set of query interfaces including TF ID or protein functional annotation. In addition, users can also get the information by browsing interfaces, which include browsing by TF Categories and by, GO Categories. This PpTFDB will serve as a promising central resource for researchers as well as breeders who are working towards crop improvement of legume crops. PMID:28651001

Plasmodium falciparum-infected erythrocytes induce Tissue Factor expression in endothelial cells and support the assembly of multimolecular coagulation complexes

PubMed Central

Francischetti, Ivo MB; Seydel, Karl B; Monteiro, Robson Q; Whitten, Richard O; Erexson, Cindy R; Noronha, Almério LL; Ostera, Graciela R.; Kamiza, Steve B; Molyneux, Malcolm E; Ward, Jerrold M; Taylor, Terrie E

2010-01-01

Summary Background Plasmodium falciparum malaria infects 300–500 million people every year causing 1–2 million deaths annually. Evidence of a coagulation disorder, activation of endothelial cells (EC) and increase in inflammatory cytokines are often present in malaria. Objectives We have asked whether parasitized red blood cells (pRBC) interaction with EC induces Tissue Factor expression in vitro and in vivo. The potential of phosphatidylserine-containing pRBC to support the assembly of blood coagulation complexes was also investigated. Results We demonstrate that mature forms of pRBC induce functional expression of tissue factor (TF) by endothelial cells (EC) in vitro with productive assembly of the extrinsic Xnase complex and initiation of the coagulation cascade. Late stage pRBC also support the prothrombinase and intrinsic Xnase complex formation in vitro, and may function as activated platelets in the amplification phase of the blood coagulation. Notably, postmortem brain sections obtained from P. falciparum-infected children who died from Cerebral Malaria and other causes display a consistent staining for TF in the EC. Conclusions These findings place TF expression by endothelium and the amplification of the coagulation cascade by pRBC and/or activated platelets as potentially critical steps in the pathogenesis of malaria. Furthermore, it may allow investigators to test other therapeutic alternatives targeting TF or modulators of EC function in the treatment of malaria and/or its complications. PMID:17002660

DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells.

PubMed

Alexandrov, Boian S; Fukuyo, Yayoi; Lange, Martin; Horikoshi, Nobuo; Gelev, Vladimir; Rasmussen, Kim Ø; Bishop, Alan R; Usheva, Anny

2012-11-01

The genome-wide mapping of the major gene expression regulators, the transcription factors (TFs) and their DNA binding sites, is of great importance for describing cellular behavior and phenotypic diversity. Presently, the methods for prediction of genomic TF binding produce a large number of false positives, most likely due to insufficient description of the physiochemical mechanisms of protein-DNA binding. Growing evidence suggests that, in the cell, the double-stranded DNA (dsDNA) is subject to local transient strands separations (breathing) that contribute to genomic functions. By using site-specific chromatin immunopecipitations, gel shifts, BIOBASE data, and our model that accurately describes the melting behavior and breathing dynamics of dsDNA we report a specific DNA breathing profile found at YY1 binding sites in cells. We find that the genomic flanking sequence variations and SNPs, may exert long-range effects on DNA dynamics and predetermine YY1 binding. The ubiquitous TF YY1 has a fundamental role in essential biological processes by activating, initiating or repressing transcription depending upon the sequence context it binds. We anticipate that consensus binding sequences together with the related DNA dynamics profile may significantly improve the accuracy of genomic TF binding sites and TF binding-related functional SNPs.

Role of CoFeB thickness in electric field controlled sub-100 nm sized magnetic tunnel junctions

NASA Astrophysics Data System (ADS)

Lourembam, James; Huang, Jiancheng; Lim, Sze Ter; Gerard, Ernult Franck

2018-05-01

We report a comprehensive study on the role of the free layer thickness (tF) in electric-field controlled nanoscale perpendicular magnetic tunnel junctions (MTJs), comprising of free layer structure Ta/Co40Fe40B20/MgO, by using dc magnetoresistance and ultra-short magnetization switching measurements. Focusing on MTJs that exhibits positive effective device anisotropy (Keff), we observe that both the voltage-controlled magnetic anisotropy (ξ) and voltage modulation of coercivity show strong dependence on tF. We found that ξ varies dramatically and unexpectedly from ˜-3 fJ/V-m to ˜-41 fJ/V-m with increasing tF. We discuss the possibilities of electric-field tuning of the effective surface anisotropy term, KS as well as an additional interfacial magnetoelastic anisotropy term, K3 that scales with 1 /tF2. Voltage pulse induced 180° magnetization reversal is also demonstrated in our MTJs. Unipolar switching and oscillatory function of switching probability vs. pulse duration can be observed at higher tF, and agrees well with the two key device parameters — Keff and ξ.

Transfer Hydrogenation and Antiproliferative Activity of Tethered Half-Sandwich Organoruthenium Catalysts

PubMed Central

2018-01-01

We report the synthesis and characterization of four neutral organometallic tethered complexes, [Ru(η6-Ph(CH2)3-ethylenediamine-N-R)Cl], where R = methanesulfonyl (Ms, 1), toluenesulfonyl (Ts, 2), 4-trifluoromethylbenzenesulfonyl (Tf, 3), and 4-nitrobenzenesulfonyl (Nb, 4), including their X-ray crystal structures. These complexes exhibit moderate antiproliferative activity toward human ovarian, lung, hepatocellular, and breast cancer cell lines. Complex 2 in particular exhibits a low cross-resistance with cisplatin. The complexes show potent catalytic activity in the transfer hydrogenation of NAD+ to NADH with formate as hydride donor in aqueous solution (310 K, pH 7). Substituents on the chelated ligand decreased the turnover frequency in the order Nb > Tf > Ts > Ms. An enhancement of antiproliferative activity (up to 22%) was observed on coadministration with nontoxic concentrations of sodium formate (0.5–2 mM). Complex 2 binds to nucleobase guanine (9-EtG), but DNA appears not to be the target, as little binding to calf thymus DNA or bacterial plasmid DNA was observed. In addition, complex 2 reacts rapidly with glutathione (GSH), which might hamper transfer hydrogenation reactions in cells. Complex 2 induced a dose-dependent G1 cell cycle arrest after 24 h exposure in A2780 human ovarian cancer cells while promoting an increase in reactive oxygen species (ROS), which is likely to contribute to its antiproliferative activity.

Mapping genomic features to functional traits through microbial whole genome sequences.

PubMed

Zhang, Wei; Zeng, Erliang; Liu, Dan; Jones, Stuart E; Emrich, Scott

2014-01-01

Recently, the utility of trait-based approaches for microbial communities has been identified. Increasing availability of whole genome sequences provide the opportunity to explore the genetic foundations of a variety of functional traits. We proposed a machine learning framework to quantitatively link the genomic features with functional traits. Genes from bacteria genomes belonging to different functional traits were grouped to Cluster of Orthologs (COGs), and were used as features. Then, TF-IDF technique from the text mining domain was applied to transform the data to accommodate the abundance and importance of each COG. After TF-IDF processing, COGs were ranked using feature selection methods to identify their relevance to the functional trait of interest. Extensive experimental results demonstrated that functional trait related genes can be detected using our method. Further, the method has the potential to provide novel biological insights.

Nonhumidified intermediate temperature fuel cells using protic ionic liquids.

PubMed

Lee, Seung-Yul; Ogawa, Atsushi; Kanno, Michihiro; Nakamoto, Hirofumi; Yasuda, Tomohiro; Watanabe, Masayoshi

2010-07-21

In this paper, the characterization of a protic ionic liquid, diethylmethylammonium trifluoromethanesulfonate ([dema][TfO]), as a proton conductor for a fuel cell and the fabrication of a membrane-type fuel cell system using [dema][TfO] under nonhumidified conditions at intermediate temperatures are described in detail. In terms of physicochemical and electrochemical properties, [dema][TfO] exhibits high activity for fuel cell electrode reactions (i.e., the hydrogen oxidation reaction (HOR) and oxygen reduction reaction (ORR)) at a Pt electrode, and the open circuit voltage (OCV) of a liquid fuel cell is 1.03 V at 150 degrees C, as has reported in ref 27. However, diethylmethylammonium bis(trifluoromethane sulfonyl)amide ([dema][NTf(2)]) has relatively low HOR and ORR activity, and thus, the OCV is ca. 0.7 V, although [dema][NTf(2)] and [dema][TfO] have an identical cation ([dema]) and similar thermal and bulk-transport properties. Proton conduction occurs mainly via the vehicle mechanism in [dema][TfO] and the proton transference number (t(+)) is 0.5-0.6. This relatively low t(+) appears to be more disadvantageous for a proton conductor than for other electrolytes such as hydrated sulfonated polymer electrolyte membranes (t(+) = 1.0). However, fast proton-exchange reactions occur between ammonium cations and amines in a model compound. This indicates that the proton-exchange mechanism contributes to the fuel cell system under operation, where deprotonated amines are continuously generated by the cathodic reaction, and that polarization of the cell is avoided. Six-membered sulfonated polyimides in the diethylmethylammonium form exhibit excellent compatibility with [dema][TfO]. The composite membranes can be obtained up to a [dema][TfO] content of 80 wt % and exhibit good thermal stability, high ionic conductivity, and mechanical strength and gas permeation comparable to those of hydrated Nafion. H(2)/O(2) fuel cells prepared using the composite membranes can successfully operate at temperatures from 30 to 140 degrees C under nonhumidified conditions, and a current density of 250 mA cm(-2) is achieved at 120 degrees C. The protic ionic liquid and its composite membrane are a possible candidate for an electrolyte of a H(2)/O(2) fuel cell that operates under nonhumidified conditions.

A systems biology approach to the global analysis of transcription factors in colorectal cancer.

PubMed

Pradhan, Meeta P; Prasad, Nagendra K A; Palakal, Mathew J

2012-08-01

Biological entities do not perform in isolation, and often, it is the nature and degree of interactions among numerous biological entities which ultimately determines any final outcome. Hence, experimental data on any single biological entity can be of limited value when considered only in isolation. To address this, we propose that augmenting individual entity data with the literature will not only better define the entity's own significance but also uncover relationships with novel biological entities.To test this notion, we developed a comprehensive text mining and computational methodology that focused on discovering new targets of one class of molecular entities, transcription factors (TF), within one particular disease, colorectal cancer (CRC). We used 39 molecular entities known to be associated with CRC along with six colorectal cancer terms as the bait list, or list of search terms, for mining the biomedical literature to identify CRC-specific genes and proteins. Using the literature-mined data, we constructed a global TF interaction network for CRC. We then developed a multi-level, multi-parametric methodology to identify TFs to CRC. The small bait list, when augmented with literature-mined data, identified a large number of biological entities associated with CRC. The relative importance of these TF and their associated modules was identified using functional and topological features. Additional validation of these highly-ranked TF using the literature strengthened our findings. Some of the novel TF that we identified were: SLUG, RUNX1, IRF1, HIF1A, ATF-2, ABL1, ELK-1 and GATA-1. Some of these TFs are associated with functional modules in known pathways of CRC, including the Beta-catenin/development, immune response, transcription, and DNA damage pathways. Our methodology of using text mining data and a multi-level, multi-parameter scoring technique was able to identify both known and novel TF that have roles in CRC. Starting with just one TF (SMAD3) in the bait list, the literature mining process identified an additional 116 CRC-associated TFs. Our network-based analysis showed that these TFs all belonged to any of 13 major functional groups that are known to play important roles in CRC. Among these identified TFs, we obtained a novel six-node module consisting of ATF2-P53-JNK1-ELK1-EPHB2-HIF1A, from which the novel JNK1-ELK1 association could potentially be a significant marker for CRC.

Simultaneous expression of tissue factor and tissue factor pathway inhibitor by human monocytes. A potential mechanism for localized control of blood coagulation

PubMed Central

1994-01-01

Cells of monocytic lineage can initiate extravascular fibrin deposition via expression of blood coagulation mediators. This report is about experiments on three mechanisms with the potential to modulate monocyte- initiated coagulation. Monocyte procoagulant activity was examined as a function of lipid cofactor, protein cofactor, and specific inhibitor expression during short-term culture in vitro. Lipid cofactor activity was measured as the initial rate of factor X activation by intrinsic- pathway components, the assembly of which depends on this cofactor. Lipid cofactor activity levels changed by < 30% during 48-h culture. Protein cofactor, i.e., tissue factor (TF) antigen was measured by enzyme immunoassay. It increased from 461 pg/ml to a maximum value of 3,550 pg/ml at 24 h and remained at 70% of this value. Specific TF activity, measured as factor VII-dependent factor X activation rate, decreased from 54 to 18 nM FXa/min between 24 and 48 h. TF activity did not correlate well with either lipid cofactor or TF protein levels. In contrast, the decrease in TF activity coincided in time with maximal expression of tissue factor pathway inhibitor (TFPI) mRNA, which was determined using reverse transcriptase polymerase chain reaction (RT- PCR), and with maximal TFPI protein levels measured by immunoassay. The number of mRNA copies coding for TFPI and TF in freshly isolated blood monocytes were 46 and 20 copies/cells, respectively. These values increased to 220 and 63 copies/cell during short-term cell culture in the presence of endotoxin. Results demonstrate concomitant expression by monocytes of genes coding for both the essential protein cofactor and the specific inhibitor of the extrinsic coagulation pathway. Together with functional and antigenic analyses, they also imply that the initiation of blood clotting by extravascular monocyte/macrophages can be modulated locally by TFPI independently of plasma sources of the inhibitor. PMID:8195712

Adult perceptions of dental fluorosis and select dental conditions-an Asian perspective.

PubMed

Nair, Rahul; Chuang, Janice Cheah Ping; Lee, Pauline Shih Jia; Leo, Song Jie; Yang, Naomi QiYue; Yee, Robert; Tong, Huei Jinn

2016-04-01

To compare lay people's perceptions with regard to various levels of dental fluorosis and select dental defects versus normal dentition. Adults rated digitally created photographs made showing lips (without retraction) and teeth depicting the following conditions: no apparent aesthetic defects (normal, Thylstrup- Fejerskov score 0 - TF0), 6 levels of fluorosis (TF1-6), carious lesions (two cavitated and one noncavitated), malocclusions (Class II, Class III, anterior open bite and greater spacing), extrinsic staining and an incisal chip. The photographs were displayed on colour-calibrated iPads(™) . Participants used a self-administered questionnaire to rate their perceptions on (Item 1) how normal teeth were, (Item 2) how attractive the teeth were, (Item 3) need to seek correction of teeth, (Item 4) how well the person took care of their teeth and (Item 5) whether the person was born like this. Data from Item 5 were excluded due to low reliability. Ratings for Item 1 showed that TF1-4 was similar or significantly better than TF0. For Item 2, TF1 and TF4 were significantly better than TF0, with TF2 and TF3 being similar. For Item 3, there was significantly lower need to seek correction with TF2 and TF4 versus TF0, whereas TF1 and TF3 were similar to TF0. TF5 and TF6 were rated significantly lower than TF0 for Item 1 and Item 2, and significantly higher rating for Item 3 (need to seek correction). Ratings for Item 4 were similar, with TF1, TF2 and TF4 being rated significantly higher than TF0, and TF5 and TF6 being rated lower. Cavitated caries and staining were generally perceived as being significantly less favourable than TF6, with higher need to seek correction as well. Noncavitated carious lesion and incisal chip were rated similar to TF0. Cavitated carious lesions were rated aesthetically similar or significantly worse than TF0 and TF6. Severe fluorosis (TF5 and 6) was perceived to be less aesthetically pleasing and received higher ratings for need to seek correction than normal teeth. Mild-to-moderate fluorosis (TF1-4) showed similar or better aesthetic perceptions and similar or lower need to seek correction, when compared to normal teeth (TF0). Easily visible cavitated dental caries was rated worse than teeth with severe fluorosis (TF6) and normal teeth (TF0). © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Principles of regulatory information conservation between mouse and human

DOE PAGES

Cheng, Yong; Ma, Zhihai; Kim, Bong-Hyun; ...

2014-11-19

To broaden our understanding of the evolution of gene regulation mechanisms, we generated occupancy profiles for 34 orthologous transcription factors (TFs) in human–mouse erythroid progenitor, lymphoblast and embryonic stem-cell lines. By combining the genome-wide transcription factor occupancy repertoires, associated epigenetic signals, and co-association patterns, here we deduce several evolutionary principles of gene regulatory features operating since the mouse and human lineages diverged. The genomic distribution profiles, primary binding motifs, chromatin states, and DNA methylation preferences are well conserved for TF-occupied sequences. However, the extent to which orthologous DNA segments are bound by orthologous TFs varies both among TFs and withmore » genomic location: binding at promoters is more highly conserved than binding at distal elements. Notably, occupancy-conserved TF-occupied sequences tend to be pleiotropic; they function in several tissues and also co-associate with many TFs. Lastly, single nucleotide variants at sites with potential regulatory functions are enriched in occupancy-conserved TF-occupied sequences.« less

Application of the weighted total field-scattering field technique to 3D-PSTD light scattering model

NASA Astrophysics Data System (ADS)

Hu, Shuai; Gao, Taichang; Liu, Lei; Li, Hao; Chen, Ming; Yang, Bo

2018-04-01

PSTD (Pseudo Spectral Time Domain) is an excellent model for the light scattering simulation of nonspherical aerosol particles. However, due to the particularity of its discretization form of the Maxwell's equations, the traditional Total Field/Scattering Field (TF/SF) technique for FDTD (Finite Differential Time Domain) is not applicable to PSTD, and the time-consuming pure scattering field technique is mainly applied to introduce the incident wave. To this end, the weighted TF/SF technique proposed by X. Gao is generalized and applied to the 3D-PSTD scattering model. Using this technique, the incident light can be effectively introduced by modifying the electromagnetic components in an inserted connecting region between the total field and the scattering field region with incident terms, where the incident terms are obtained by weighting the incident field by a window function. To optimally determine the thickness of connection region and the window function type for PSTD calculations, their influence on the modeling accuracy is firstly analyzed. To further verify the effectiveness and advantages of the weighted TF/SF technique, the improved PSTD model is validated against the PSTD model equipped with pure scattering field technique in both calculation accuracy and efficiency. The results show that, the performance of PSTD seems to be not sensitive to variation of window functions. The number of the connection layer required decreases with the increasing of spatial resolution, where for spatial resolution of 24 grids per wavelength, a 6-layer region is thick enough. The scattering phase matrices and integral scattering parameters obtained by the improved PSTD show an excellent consistency with those well-tested models for spherical and nonspherical particles, illustrating that the weighted TF/SF technique can introduce the incident precisely. The weighted TF/SF technique shows higher computational efficiency than pure scattering technique.

An Improved Time-Frequency Analysis Method in Interference Detection for GNSS Receivers

PubMed Central

Sun, Kewen; Jin, Tian; Yang, Dongkai

2015-01-01

In this paper, an improved joint time-frequency (TF) analysis method based on a reassigned smoothed pseudo Wigner–Ville distribution (RSPWVD) has been proposed in interference detection for Global Navigation Satellite System (GNSS) receivers. In the RSPWVD, the two-dimensional low-pass filtering smoothing function is introduced to eliminate the cross-terms present in the quadratic TF distribution, and at the same time, the reassignment method is adopted to improve the TF concentration properties of the auto-terms of the signal components. This proposed interference detection method is evaluated by experiments on GPS L1 signals in the disturbing scenarios compared to the state-of-the-art interference detection approaches. The analysis results show that the proposed interference detection technique effectively overcomes the cross-terms problem and also preserves good TF localization properties, which has been proven to be effective and valid to enhance the interference detection performance of the GNSS receivers, particularly in the jamming environments. PMID:25905704

Enhanced efficacy of combined temozolomide and bromodomain inhibitor therapy for gliomas using targeted nanoparticles.

PubMed

Lam, Fred C; Morton, Stephen W; Wyckoff, Jeffrey; Vu Han, Tu-Lan; Hwang, Mun Kyung; Maffa, Amanda; Balkanska-Sinclair, Elena; Yaffe, Michael B; Floyd, Scott R; Hammond, Paula T

2018-05-18

Effective treatment for glioblastoma (GBM) is limited by the presence of the blood-brain barrier (BBB) and rapid resistance to single agent therapies. To address these issues, we developed a transferrin-functionalized nanoparticle (Tf-NP) that can deliver dual combination therapies. Using intravital imaging, we show the ability of Tf-NPs to traverse intact BBB in mice as well as achieve direct tumor binding in two intracranial orthotopic models of GBM. Treatment of tumor-bearing mice with Tf-NPs loaded with temozolomide and the bromodomain inhibitor JQ1 leads to increased DNA damage and apoptosis that correlates with a 1.5- to 2-fold decrease in tumor burden and corresponding increase in survival compared to equivalent free-drug dosing. Immunocompetent mice treated with Tf-NP-loaded drugs also show protection from the effects of systemic drug toxicity, demonstrating the preclinical potential of this nanoscale platform to deliver novel combination therapies to gliomas and other central nervous system tumors.

Radical-scavenging abilities and antioxidant properties of theaflavins and their gallate esters in H2O2-mediated oxidative damage system in the HPF-1 cells.

PubMed

Yang, Ziyin; Jie, Guoliang; Dong, Fang; Xu, Yi; Watanabe, Naoharu; Tu, Youying

2008-08-01

The antioxidant properties of theaflavins and their gallate esters, namely theaflavin (TF1), theaflavin-3(3')-gallate (TF2) and theaflavin-3,3'-digallate (TF3) were investigated by comparing with epigallocatechin gallate (EGCG). The order of hydroxyl radicals-scavenging ability was TF3>TF2>TF1>EGCG. The order of 2,2-diphenyl-1-picrylhydrazyl scavenging ability was TF3>TF2>EGCG>TF1. TF1, TF2, and TF3 showed more effective effects than EGCG in protection against H2O2-mediated damage in HPF-1 cells. TF2 was the most potent accelerant of HPF-1 cell proliferation. TF1, TF2 and TF3 suppressed the accumulation of intracellular reactive species in H2O2-mediated damage HPF-1 cells. Pre-treated for 2h and eliminated from the cells, TF1 and TF3 still showed protective effects against H2O2-mediated damage in HPF-1 cells. This suggests that the protective effects of TF1 and TF3 on oxidative damage HPF-1 cells may be responsible for other mechanisms, rather than only scavenging the already formed reactive species. It remains to be determined whether TF1 and TF3 improved the normal HPF-1 cell resistive abilities toward radical-damage in pre-treatment. Further studies of the effects of theaflavins on some enzymes or signal transduction in the normal HPF-1 cells are underway.

Navigating the Functional Landscape of Transcription Factors via Non-Negative Tensor Factorization Analysis of MEDLINE Abstracts

PubMed Central

Roy, Sujoy; Yun, Daqing; Madahian, Behrouz; Berry, Michael W.; Deng, Lih-Yuan; Goldowitz, Daniel; Homayouni, Ramin

2017-01-01

In this study, we developed and evaluated a novel text-mining approach, using non-negative tensor factorization (NTF), to simultaneously extract and functionally annotate transcriptional modules consisting of sets of genes, transcription factors (TFs), and terms from MEDLINE abstracts. A sparse 3-mode term × gene × TF tensor was constructed that contained weighted frequencies of 106,895 terms in 26,781 abstracts shared among 7,695 genes and 994 TFs. The tensor was decomposed into sub-tensors using non-negative tensor factorization (NTF) across 16 different approximation ranks. Dominant entries of each of 2,861 sub-tensors were extracted to form term–gene–TF annotated transcriptional modules (ATMs). More than 94% of the ATMs were found to be enriched in at least one KEGG pathway or GO category, suggesting that the ATMs are functionally relevant. One advantage of this method is that it can discover potentially new gene–TF associations from the literature. Using a set of microarray and ChIP-Seq datasets as gold standard, we show that the precision of our method for predicting gene–TF associations is significantly higher than chance. In addition, we demonstrate that the terms in each ATM can be used to suggest new GO classifications to genes and TFs. Taken together, our results indicate that NTF is useful for simultaneous extraction and functional annotation of transcriptional regulatory networks from unstructured text, as well as for literature based discovery. A web tool called Transcriptional Regulatory Modules Extracted from Literature (TREMEL), available at http://binf1.memphis.edu/tremel, was built to enable browsing and searching of ATMs. PMID:28894735

Modulation of transferrin receptor mRNA by transferrin-gallium in human myeloid HL60 and lymphoid CCRF-CEM leukaemic cells.

PubMed Central

Ul-Haq, R; Chitambar, C R

1993-01-01

Gallium binds to the iron transport protein transferrin (Tf), is incorporated into cells through transferrin receptors (TfR) and inhibits iron-dependent DNA synthesis. Since cellular TfR expression is tightly regulated by the availability of iron, we investigated the effects of transferrin-gallium (Tf-Ga) on TfR mRNA levels in myeloid HL60 and lymphoid CCRF-CEM cells. In HL60 cells, Tf-Ga increased TfR mRNA levels in a dose-dependent fashion. This increase in TfR mRNA was blocked by Tf-Fe and by cycloheximide. Analysis of the rate of mRNA decay in the presence of actinomycin D revealed that the half-life of TfR mRNA was increased in HL60 cells incubated with Tf-Ga. The rate of transcription of TfR mRNA was not increased by Tf-Ga. In contrast with HL60 cells, CCRF-CEM cells displayed a decrease in the level of TfR mRNA after incubation with Tf-Ga. Tf-Ga inhibited iron uptake in both HL60 and CCRF-CEM cells but increased the level of TfR mRNA only in HL60 cells, suggesting that the Tf-Ga induction of TfR mRNA was not solely due to inhibition of cellular iron uptake. At growth-inhibitory concentrations, Tf-Ga increased the TfR mRNA level in HL60 cells but decreased it in CCRF-CEM cells. Our studies suggest that in HL60 cells, gallium regulates TfR expression at the post-transcriptional level by mechanisms which require de novo protein synthesis and involve interaction with iron. The divergent effects of Tf-Ga on TfR mRNA in myeloid HL60 and lymphoid CCRF-CEM cells suggest that differences exist in the regulation of TfR expression between these two cell types. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 PMID:8379943

The Effects of Hydrogen-Like Impurity and Temperature on State Energies and Transition Frequency of Strong-Coupling Bound Polaron in an Asymmetric Gaussian Potential Quantum Well

NASA Astrophysics Data System (ADS)

Xiao, Jing-lin

2018-02-01

In the present work, we study the ground state energy, the first excited state energy and the transition frequency (TF) between the two states of the strong-coupling impurity bound polaron in an asymmetric Gaussian potential quantum well (AGPQW) by using the variational method of the Pekar type. By employing quantum statistics theory, the temperature effect on the state energies (SEs) and the TF are also calculated with a hydrogen-like impurity at the coordinate origin of the AGPQW. According to the obtained results, we found that the SEs and the TF are increasing functions of the temperature, whereas they are decreasing ones of the Coulombic impurity potential.

Transport properties of bilayer graphene due to charged impurity scattering: Temperature-dependent screening and substrate effects

NASA Astrophysics Data System (ADS)

Linh, Dang Khanh; Khanh, Nguyen Quoc

2018-03-01

We calculate the zero-temperature conductivity of bilayer graphene (BLG) impacted by Coulomb impurity scattering using four different screening models: unscreened, Thomas-Fermi (TF), overscreened and random phase approximation (RPA). We also calculate the conductivity and thermal conductance of BLG using TF, zero- and finite-temperature RPA screening functions. We find large differences between the results of the models and show that TF and finite-temperature RPA give similar results for diffusion thermopower Sd. Using the finite-temperature RPA, we calculate temperature and density dependence of Sd in BLG on SiO2, HfO2 substrates and suspended BLG for different values of interlayer distance c and distance between the first layer and the substrate d.

Distinct Modes of Regulation of Transcription of Hepatitis B Virus by the Nuclear Receptors HNF4α and COUP-TF1

PubMed Central

Yu, Xianming; Mertz, Janet E.

2003-01-01

To study the effects of the nuclear receptors (NRs) HNF4α and COUP-TF1 on the life cycle of hepatitis B virus (HBV), the human hepatoma cell line Huh7 was transiently cotransfected with plasmids containing the HBV genome and encoding these two NRs. Overexpression of HNF4α and COUP-TF1 led to a 9-fold increase and a 7- to 10-fold decrease, respectively, in viral DNA synthesis. These two NRs also exhibited distinct modes of regulation of viral transcription. Overexpression of HNF4α led to a more-than-10-fold increase in synthesis of the pregenomic RNA but to only a 2- to 3-fold increase in synthesis of the pre-C and S RNAs. Moreover, the NR response element within the pre-C promoter, NRREpreC, played the major role in activation of pregenomic RNA synthesis by HNF4α. On the other hand, overexpression of COUP-TF1 led to an over-10-fold repression of synthesis of both pre-C and pregenomic RNAs mediated through either NRREpreC or NRREenhI. HNF4α and COUP-TF1 antagonized each other's effects on synthesis of pregenomic RNA and viral DNA when they were co-overexpressed. A naturally occurring HBV variant which allows for binding by HNF4α but not COUP-TF1 in its NRREpreC exhibited significantly higher levels of synthesis of pregenomic RNA and viral DNA than wild-type HBV in coexpression experiments. Last, deletion analysis revealed that non-NRRE sequences located within both the C and pre-S1 regions are also essential for maximum activation of the pregenomic promoter by HNF4α but not for repression by COUP-TF1. Thus, HNF4α and COUP-TF1 function through different mechanisms to regulate expression of the HBV genes. PMID:12551987

Distinct modes of regulation of transcription of hepatitis B virus by the nuclear receptors HNF4alpha and COUP-TF1.

PubMed

Yu, Xianming; Mertz, Janet E

2003-02-01

To study the effects of the nuclear receptors (NRs) HNF4alpha and COUP-TF1 on the life cycle of hepatitis B virus (HBV), the human hepatoma cell line Huh7 was transiently cotransfected with plasmids containing the HBV genome and encoding these two NRs. Overexpression of HNF4alpha and COUP-TF1 led to a 9-fold increase and a 7- to 10-fold decrease, respectively, in viral DNA synthesis. These two NRs also exhibited distinct modes of regulation of viral transcription. Overexpression of HNF4alpha led to a more-than-10-fold increase in synthesis of the pregenomic RNA but to only a 2- to 3-fold increase in synthesis of the pre-C and S RNAs. Moreover, the NR response element within the pre-C promoter, NRRE(preC,) played the major role in activation of pregenomic RNA synthesis by HNF4alpha. On the other hand, overexpression of COUP-TF1 led to an over-10-fold repression of synthesis of both pre-C and pregenomic RNAs mediated through either NRRE(preC) or NRRE(enhI). HNF4alpha and COUP-TF1 antagonized each other's effects on synthesis of pregenomic RNA and viral DNA when they were co-overexpressed. A naturally occurring HBV variant which allows for binding by HNF4alpha but not COUP-TF1 in its NRRE(preC) exhibited significantly higher levels of synthesis of pregenomic RNA and viral DNA than wild-type HBV in coexpression experiments. Last, deletion analysis revealed that non-NRRE sequences located within both the C and pre-S1 regions are also essential for maximum activation of the pregenomic promoter by HNF4alpha but not for repression by COUP-TF1. Thus, HNF4alpha and COUP-TF1 function through different mechanisms to regulate expression of the HBV genes.

Carbohydrates and activity of natural and recombinant tissue factor.

PubMed

Krudysz-Amblo, Jolanta; Jennings, Mark E; Mann, Kenneth G; Butenas, Saulius

2010-01-29

The effect of glycosylation on tissue factor (TF) activity was evaluated, and site-specific glycosylation of full-length recombinant TF (rTF) and that of natural TF from human placenta (pTF) were studied by liquid chromatography-tandem mass spectrometry. The amidolytic activity of the TF.factor VIIa (FVIIa) complex toward a fluorogenic substrate showed that the catalytic efficiency (V(max)) of the complex increased in the order rTF(1-243) (Escherichia coli) < rTF(1-263) (Sf9 insect cells) < pTF for the glycosylated and deglycosylated forms. Substrate hydrolysis was unaltered by deglycosylation. In FXase, the K(m) of FX for rTF(1-263)-FVIIa remained unchanged after deglycosylation, whereas the k(cat) decreased slightly. A pronounced decrease, 4-fold, in k(cat) was observed for pTF.FVIIa upon deglycosylation, whereas the K(m) was minimally altered. The parameters of FX activation by both rTF(1-263D)-FVIIa and pTF(D)-FVIIa were identical and similar to those for rTF(1-243)-FVIIa. In conclusion, carbohydrates significantly influence the activity of TF proteins. Carbohydrate analysis revealed glycosylation on asparagines 11, 124, and 137 in both rTF(1-263) and pTF. The carbohydrates of rTF(1-263) contain high mannose, hybrid, and fucosylated glycans. Natural pTF contains no high mannose glycans but is modified with hybrid, highly fucosylated, and sialylated sugars.

Evidence for two transferrin loci in the Salmo trutta genome.

PubMed

Rozman, T; Dovc, P; Marić, S; Kokalj-Vokac, N; Erjavec-Skerget, A; Rab, P; Snoj, A

2008-12-01

To determine the organization of transferrin (TF) locus in the Salmo trutta genome, partial DNA and cDNA sequencing, fluorescent in situ hybridization (FISH) and Salmo salar BAC analysis were performed. TF expression levels and copy number prediction were assessed using real-time PCR. In addition to two previously reported DNA TF variant sequences of S. trutta and Salmo marmoratus (TF1), two novel variant sequences (TF2) were revealed in both species. Variant-specific sequence tags, characterizing two variants for each TF type (TF1 and TF2), were identified in genomic clones from each of the F1 hybrids between S. trutta and S. marmoratus. These clearly documented double heterozygote status at the TF loci. The real-time PCR data showed that each of the two TF types (TF1 and TF2) existed in one copy only and that the transcription of TF2 was considerably lower compared with TF1. Using FISH, hybridization signals were observed on two medium-sized acrocentric chromosomes of S. trutta karyotype. A TF type-specific PCR followed by a restriction analysis revealed the presence of two TF loci in the majority of analysed BAC clones. It was concluded that the TF gene is duplicated in the genome of S. trutta, and that the two TF loci are located adjacent to one another on the same chromosome. The differing transcription levels of TF1 and TF2 appear to depend on the corresponding promoter activity, which at least for TF2 seems to vary between different Salmo congeners.

Early coagulation events induce acute lung injury in a rat model of blunt traumatic brain injury.

PubMed

Yasui, Hideki; Donahue, Deborah L; Walsh, Mark; Castellino, Francis J; Ploplis, Victoria A

2016-07-01

Acute lung injury (ALI) and systemic coagulopathy are serious complications of traumatic brain injury (TBI) that frequently lead to poor clinical outcomes. Although the release of tissue factor (TF), a potent initiator of the extrinsic pathway of coagulation, from the injured brain is thought to play a key role in coagulopathy after TBI, its function in ALI following TBI remains unclear. In this study, we investigated whether the systemic appearance of TF correlated with the ensuing coagulopathy that follows TBI in ALI using an anesthetized rat blunt trauma TBI model. Blood and lung samples were obtained after TBI. Compared with controls, pulmonary edema and increased pulmonary permeability were observed as early as 5 min after TBI without evidence of norepinephrine involvement. Systemic TF increased at 5 min and then diminished 60 min after TBI. Lung injury and alveolar hemorrhaging were also observed as early as 5 min after TBI. A biphasic elevation of TF was observed in the lungs after TBI, and TF-positive microparticles (MPs) were detected in the alveolar spaces. Fibrin(ogen) deposition was also observed in the lungs within 60 min after TBI. Additionally, preadministration of a direct thrombin inhibitor, Refludan, attenuated lung injuries, thus implicating thrombin as a direct participant in ALI after TBI. The results from this study demonstrated that enhanced systemic TF may be an initiator of coagulation activation that contributes to ALI after TBI. Copyright © 2016 the American Physiological Society.

System analysis identifies distinct and common functional networks governed by transcription factor ASCL1, in glioma and small cell lung cancer.

PubMed

Donakonda, Sainitin; Sinha, Swati; Dighe, Shrinivas Nivrutti; Rao, Manchanahalli R Satyanarayana

2017-07-25

ASCL1 is a basic Helix-Loop-Helix transcription factor (TF), which is involved in various cellular processes like neuronal development and signaling pathways. Transcriptome profiling has shown that ASCL1 overexpression plays an important role in the development of glioma and Small Cell Lung Carcinoma (SCLC), but distinct and common molecular mechanisms regulated by ASCL1 in these cancers are unknown. In order to understand how it drives the cellular functional network in these two tumors, we generated a gene expression profile in a glioma cell line (U87MG) to identify ASCL1 gene targets by an si RNA silencing approach and then compared this with a publicly available dataset of similarly silenced SCLC (NCI-H1618 cells). We constructed TF-TF and gene-gene interactions, as well as protein interaction networks of ASCL1 regulated genes in glioma and SCLC cells. Detailed network analysis uncovered various biological processes governed by ASCL1 target genes in these two tumor cell lines. We find that novel ASCL1 functions related to mitosis and signaling pathways influencing development and tumor growth are affected in both glioma and SCLC cells. In addition, we also observed ASCL1 governed functional networks that are distinct to glioma and SCLC.

Revised Thomas-Fermi approximation for singular potentials

NASA Astrophysics Data System (ADS)

Dufty, James W.; Trickey, S. B.

2016-08-01

Approximations for the many-fermion free-energy density functional that include the Thomas-Fermi (TF) form for the noninteracting part lead to singular densities for singular external potentials (e.g., attractive Coulomb). This limitation of the TF approximation is addressed here by a formal map of the exact Euler equation for the density onto an equivalent TF form characterized by a modified Kohn-Sham potential. It is shown to be a "regularized" version of the Kohn-Sham potential, tempered by convolution with a finite-temperature response function. The resulting density is nonsingular, with the equilibrium properties obtained from the total free-energy functional evaluated at this density. This new representation is formally exact. Approximate expressions for the regularized potential are given to leading order in a nonlocality parameter, and the limiting behavior at high and low temperatures is described. The noninteracting part of the free energy in this approximation is the usual Thomas-Fermi functional. These results generalize and extend to finite temperatures the ground-state regularization by R. G. Parr and S. Ghosh [Proc. Natl. Acad. Sci. U.S.A. 83, 3577 (1986), 10.1073/pnas.83.11.3577] and by L. R. Pratt, G. G. Hoffman, and R. A. Harris [J. Chem. Phys. 88, 1818 (1988), 10.1063/1.454105] and formally systematize the finite-temperature regularization given by the latter authors.

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

PubMed Central

Marbach, Daniel; Roy, Sushmita; Ay, Ferhat; Meyer, Patrick E.; Candeias, Rogerio; Kahveci, Tamer; Bristow, Christopher A.; Kellis, Manolis

2012-01-01

Gaining insights on gene regulation from large-scale functional data sets is a grand challenge in systems biology. In this article, we develop and apply methods for transcriptional regulatory network inference from diverse functional genomics data sets and demonstrate their value for gene function and gene expression prediction. We formulate the network inference problem in a machine-learning framework and use both supervised and unsupervised methods to predict regulatory edges by integrating transcription factor (TF) binding, evolutionarily conserved sequence motifs, gene expression, and chromatin modification data sets as input features. Applying these methods to Drosophila melanogaster, we predict ∼300,000 regulatory edges in a network of ∼600 TFs and 12,000 target genes. We validate our predictions using known regulatory interactions, gene functional annotations, tissue-specific expression, protein–protein interactions, and three-dimensional maps of chromosome conformation. We use the inferred network to identify putative functions for hundreds of previously uncharacterized genes, including many in nervous system development, which are independently confirmed based on their tissue-specific expression patterns. Last, we use the regulatory network to predict target gene expression levels as a function of TF expression, and find significantly higher predictive power for integrative networks than for motif or ChIP-based networks. Our work reveals the complementarity between physical evidence of regulatory interactions (TF binding, motif conservation) and functional evidence (coordinated expression or chromatin patterns) and demonstrates the power of data integration for network inference and studies of gene regulation at the systems level. PMID:22456606

Detection of eQTL modules mediated by activity levels of transcription factors.

PubMed

Sun, Wei; Yu, Tianwei; Li, Ker-Chau

2007-09-01

Studies of gene expression quantitative trait loci (eQTL) in different organisms have shown the existence of eQTL hot spots: each being a small segment of DNA sequence that harbors the eQTL of a large number of genes. Two questions of great interest about eQTL hot spots arise: (1) which gene within the hot spot is responsible for the linkages, i.e. which gene is the quantitative trait gene (QTG)? (2) How does a QTG affect the expression levels of many genes linked to it? Answers to the first question can be offered by available biological evidence or by statistical methods. The second question is harder to address. One simple situation is that the QTG encodes a transcription factor (TF), which regulates the expression of genes linked to it. However, previous results have shown that TFs are not overrepresented in the eQTL hot spots. In this article, we consider the scenario that the propagation of genetic perturbation from a QTG to other linked genes is mediated by the TF activity. We develop a procedure to detect the eQTL modules (eQTL hot spots together with linked genes) that are compatible with this scenario. We first detect 27 eQTL modules from a yeast eQTL data, and estimate TF activity profiles using the method of Yu and Li (2005). Then likelihood ratio tests (LRTs) are conducted to find 760 relationships supporting the scenario of TF activity mediation: (DNA polymorphism --> cis-linked gene --> TF activity --> downstream linked gene). They are organized into 4 eQTL modules: an amino acid synthesis module featuring a cis-linked gene LEU2 and the mediating TF Leu3; a pheromone response module featuring a cis-linked gene GPA1 and the mediating TF Ste12; an energy-source control module featuring two cis-linked genes, GSY2 and HAP1, and the mediating TF Hap1; a mitotic exit module featuring four cis-linked genes, AMN1, CSH1, DEM1 and TOS1, and the mediating TF complex Ace2/Swi5. Gene Ontology is utilized to reveal interesting functional groups of the downstream genes in each module. Our methods are implemented in an R package: eqtl.TF, which includes source codes and relevant data. It can be freely downloaded at http://www.stat.ucla.edu/~sunwei/software.htm. http://www.stat.ucla.edu/~sunwei/yeast_eQTL_TF/supplementary.pdf.

Improved preoperative iron status assessment by soluble transferrin receptor in elderly patients undergoing knee and hip replacement.

PubMed

Basora, M; Deulofeu, R; Salazar, F; Quinto, L; Gomar, C

2006-12-01

A poor preoperative haemoglobin (Hb) status is frequently encountered among adult patients scheduled for corrective surgery of the locomotive system, representing the main risk factor for blood transfusion. The soluble transferrin receptor (sTfR) has become a highly specific parameter for the detection of iron deficits as it can differentiate between iron deficiency anaemia and anaemia of chronic disease, because of the lack of effect by associated inflammation, unlike ferritin. The objectives of this study were to evaluate patients with the prevalence of risk for transfusion, the effect of inflammation on ferritin (F) values and functional iron deficiency in elderly patients with advanced degenerative arthropathy scheduled for hip or knee replacement. This observational, prospective study included patients over 50 years, operated for hip or knee replacements between April and June 2004. Of 218 patients studied, 87 (39%) presented with Hb levels between 10 and 13 g/dl. The prevalence of functional iron deficit was 27% (sTfR > 1.76 mg/l), while only 8.6% of patients displayed F levels below normal. As expected, C-reactive protein levels were elevated in 24.8% of patients and erythrocyte sedimentation rate was elevated in 50%. These inflammatory markers did not correlate with levels of either F or sTfR. Multiple factors can affect F levels, such as the inflammatory status of osteoarthritis in the elderly, obesity, nonsteroidal anti-inflammatory drugs therapy and low physical performance. As sTfR is not affected by inflammation, it has emerged as a primary parameter for the evaluation of iron status during preoperative assessment among patients scheduled for arthroplasty surgery. Our data strongly suggest that sTfR measurement contributes to improve patient management.

Evaluation of a dense seismic array for acquisition of high quality data in the ACROSS observation

NASA Astrophysics Data System (ADS)

Tsuruga, K.; Kunitomo, T.; Hasada, Y.; Kumazawa, M.; Shigeta, N.; Kasahara, J.

2004-12-01

ACROSS is an active monitoring methodology to detect any subtle temporal change of physical properties in the Earth's interior. We demonstrate the potentiality of the ACROSS observation with a dense sensor array. We have conducted a dense seismic array observation at the distance of 1 km from the ACROSS source since 2003. The array is composed of 36 three-component velocity seismometers buried at 1.8 m deep in an area 25 m square. All the data are recorded accurately referring to a GPS clock. We derived and analyzed a transfer function (TF) from the source to a receiver by the following steps: (1) evaluating a force vector as source characteristics, (2) converting the observed data to the displacement vectors by incorporating all the corrections of the instruments, (3) stacking the observed data for an enough time to suppress the temporal noise, (4) extracting ACROSS signal and evaluating noise level, (5) representing TF in a tensor form with the estimated errors, (6) slant-stacking with variable ray parameters, (7) estimating the travel times and amplitudes of the wave arrivals by Sompi Event Analysis (Hasada et al., 2001) and representing the result by a pulse sequence, and (8) deriving the polarization vector for each arrival to identify all the wave modes. We analyzed TF of SH-wave component from 16 to 20 Hz as an example. We obtained good quality TF with S/N ratio up to 104 by stacking for 12 days at the step (3). The spatial noise originated from the local heterogeneity around the array was eliminated by the step (6). Several arrivals were recognized within the time windows from 0.6 to 1.8 s. The maximum amplitude of event traces was detected at the travel time of 1.064 s with a ray parameter of 7.9x10-4 s/m. We also found the scattered waves probably generated by the heterogeneities around the array. The ACROSS dense array observation would provide a lot of information on the underground heterogeneities. Consequently, we have the important and challenging subjects: (1) optimum designing of ACROSS array to acquire the better data and (2) development of new theoretical method to deal with the variable types of the wave.

Intrauterine exposure to tobacco and executive functioning in high school.

PubMed

Rose-Jacobs, Ruth; Richardson, Mark A; Buchanan-Howland, Kathryn; Chen, Clara A; Cabral, Howard; Heeren, Timothy C; Liebschutz, Jane; Forman, Leah; Frank, Deborah A

2017-07-01

Executive functioning (EF), an umbrella construct encompassing gradual maturation of cognitive organization/management processes, is important to success in multiple settings including high school. Intrauterine tobacco exposure (IUTE) correlates with negative cognitive/behavioral outcomes, but little is known about its association with adolescent EF and information from real-life contexts is sparse. We evaluated the impact of IUTE on teacher-reported observations of EF in urban high school students controlling for covariates including other intrauterine and adolescent substance exposures. A prospective low-income birth cohort (51% male; 89% African American/Caribbean) was followed through late adolescence (16-18 years old). At birth, intrauterine exposures to cocaine and other substances (52% cocaine, 52% tobacco, 26% marijuana, 26% alcohol) were identified by meconium and/or urine assays, and/or maternal self-report. High school teachers knowledgeable about the student and unaware of study aims were asked to complete the Behavior Rating Inventory of Executive Functioning-Teacher Form (BRIEF-TF) annually. Teachers completed at least one BRIEF-TF for 131 adolescents. Multivariable analyses included controls for: demographics; intrauterine cocaine, marijuana, and alcohol exposures; early childhood exposures to lead; and violence exposure from school-age to adolescence. IUTE was associated with less optimal BRIEF-TF Behavioral Regulation scores (p <0.05). Other intrauterine substance exposures did not predict less optimal BRIEF-TF scores, nor did exposures to violence, lead, nor adolescents' own substance use. IUTE is associated with offspring's less optimal EF. Prenatal counseling should emphasize abstinence from tobacco, as well as alcohol and illegal substances. Copyright © 2017 Elsevier B.V. All rights reserved.

SU-D-12A-06: A Comprehensive Parameter Analysis for Low Dose Cone-Beam CT Reconstruction

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

Lu, W; Southern Medical University, Guangzhou; Yan, H

Purpose: There is always a parameter in compressive sensing based iterative reconstruction (IR) methods low dose cone-beam CT (CBCT), which controls the weight of regularization relative to data fidelity. A clear understanding of the relationship between image quality and parameter values is important. The purpose of this study is to investigate this subject based on experimental data and a representative advanced IR algorithm using Tight-frame (TF) regularization. Methods: Three data sets of a Catphan phantom acquired at low, regular and high dose levels are used. For each tests, 90 projections covering a 200-degree scan range are used for reconstruction. Threemore » different regions-of-interest (ROIs) of different contrasts are used to calculate contrast-to-noise ratios (CNR) for contrast evaluation. A single point structure is used to measure modulation transfer function (MTF) for spatial-resolution evaluation. Finally, we analyze CNRs and MTFs to study the relationship between image quality and parameter selections. Results: It was found that: 1) there is no universal optimal parameter. The optimal parameter value depends on specific task and dose level. 2) There is a clear trade-off between CNR and resolution. The parameter for the best CNR is always smaller than that for the best resolution. 3) Optimal parameters are also dose-specific. Data acquired under a high dose protocol require less regularization, yielding smaller optimal parameter values. 4) Comparing with conventional FDK images, TF-based CBCT images are better under a certain optimally selected parameters. The advantages are more obvious for low dose data. Conclusion: We have investigated the relationship between image quality and parameter values in the TF-based IR algorithm. Preliminary results indicate optimal parameters are specific to both the task types and dose levels, providing guidance for selecting parameters in advanced IR algorithms. This work is supported in part by NIH (1R01CA154747-01)« less

Increasing Signal Specificity of the TOL Network of Pseudomonas putida mt-2 by Rewiring the Connectivity of the Master Regulator XylR

PubMed Central

de las Heras, Aitor; Fraile, Sofia; de Lorenzo, Victor

2012-01-01

Prokaryotic transcription factors (TFs) that bind small xenobiotic molecules (e.g., TFs that drive genes that respond to environmental pollutants) often display a promiscuous effector profile for analogs of the bona fide chemical signals. XylR, the master TF for expression of the m-xylene biodegradation operons encoded in the TOL plasmid pWW0 of Pseudomonas putida, responds not only to the aromatic compound but also, albeit to a lesser extent, to many other aromatic compounds, such as 3-methylbenzylalcohol (3MBA). We have examined whether such a relaxed regulatory scenario can be reshaped into a high-capacity/high-specificity regime by changing the connectivity of this effector-sensing TF within the rest of the circuit rather than modifying XylR structure itself. To this end, the natural negative feedback loop that operates on xylR transcription was modified with a translational attenuator that brings down the response to 3MBA while maintaining the transcriptional output induced by m-xylene (as measured with a luxCDABE reporter system). XylR expression was then subject to a positive feedback loop in which the TF was transcribed from its own target promoters, each known to hold different input/output transfer functions. In the first case (xylR under the strong promoter of the upper TOL operon, Pu), the reporter system displayed an increased transcriptional capacity in the resulting network for both the optimal and the suboptimal XylR effectors. In contrast, when xylR was expressed under the weaker Ps promoter, the resulting circuit unmistakably discriminated m-xylene from 3MBA. The non-natural connectivity engineered in the network resulted both in a higher promoter activity and also in a much-increased signal-to-background ratio. These results indicate that the working regimes of given genetic circuits can be dramatically altered through simple changes in the way upstream transcription factors are self-regulated by positive or negative feedback loops. PMID:23071444

Effect of cigarette smoke on monocyte procoagulant activity: Focus on platelet-derived brain-derived neurotrophic factor (BDNF).

PubMed

Amadio, Patrizia; Baldassarre, Damiano; Sandrini, Leonardo; Weksler, Babette B; Tremoli, Elena; Barbieri, Silvia S

2017-01-01

Cigarette smoke (CS) activates platelets, promotes vascular dysfunction, and enhances Tissue Factor (TF) expression in blood monocytes favoring pro-thrombotic states. Brain-derived neurotrophic factor (BDNF), a member of the family of neurotrophins involved in survival, growth, and maturation of neurons, is released by activated platelets (APLTs) and plays a role in the cardiovascular system. The effect of CS on circulating levels of BDNF is controversial and the function of circulating BDNF in atherothrombosis is not fully understood. Here, we have shown that human platelets, treated with an aqueous extract of CS (CSE), released BDNF in a dose-dependent manner. In addition, incubation of human monocytes with BDNF or with the supernatant of platelets activated with CSE increased TF activity by a Tropomyosin receptor kinase B (TrkB)-dependent mechanism. Finally, comparing serum and plasma samples of 12 male never smokers (NS) and 29 male active smokers (AS) we observed a significant increase in microparticle-associated TF activity (MP-TF) as well as BDNF in AS, while in serum, BDNF behaved oppositely. Taken together these findings suggest that platelet-derived BDNF is involved in the regulation of TF activity and that CS plays a role in this pathway by favoring a pro-atherothrombotic state.

Sepsis-Induced Coagulation in the Baboon Lung Is Associated with Decreased Tissue Factor Pathway Inhibitor

PubMed Central

Tang, Haiwang; Ivanciu, Lacramioara; Popescu, Narcis; Peer, Glenn; Hack, Erik; Lupu, Cristina; Taylor, Fletcher B.; Lupu, Florea

2007-01-01

Increased tissue factor (TF)-dependent procoagulant activity in sepsis may be partly due to decreased expression or function of tissue factor pathway inhibitor (TFPI). To test this hypothesis, baboons were infused with live Escherichia coli and sacrificed after 2, 8, or 24 hours. Confocal and electron microscopy revealed increased leukocyte infiltration and fibrin deposition in the intravascular and interstitial compartments. Large amounts of TF were detected by immunostaining in leukocytes and platelet-rich microthrombi. TF induction was documented by quantitative reverse transcriptase-polymerase chain reaction, enzyme-linked immunosorbent assay, and coagulation assays. Lung-associated TFPI antigen and mRNA decreased during sepsis, and TFPI activity diminished abruptly at 2 hours. Blocking antibodies against TFPI increased fibrin deposition in septic baboon lungs, suggesting that TF-dependent coagulation might be aggravated by reduced endothelial TFPI. Decreased TFPI activity coincided with the release of tissue plasminogen activator and the peak of plasmin generation, suggesting that TFPI could undergo proteolytic inactivation by plasmin. Enhanced plasmin produced in septic baboons by infusion of blocking antibodies against plasminogen activator inhibitor-1 led to decreased lung-associated TFPI and unforeseen massive fibrin deposition. We conclude that activation of TF-driven coagulation not adequately countered by TFPI may underlie the widespread thrombotic complications of sepsis. PMID:17640967

Time-dependent changes in the growth of ultrathin ionic liquid films on Ag(111).

PubMed

Lexow, Matthias; Talwar, Timo; Heller, Bettina S J; May, Benjamin; Bhuin, Radha G; Maier, Florian; Steinrück, Hans-Peter

2018-05-09

Various amounts of the ionic liquids (ILs) [C1C1Im][Tf2N] and [C8C1Im][Tf2N] were deposited in vacuo by physical vapour deposition (PVD) on single crystalline Ag(111) at room temperature and subsequently monitored by angle-resolved X-ray photoelectron spectroscopy (ARXPS) as a function of time. For very low coverages of up to one closed molecular layer, an initial wetting layer was rapidly formed for both ILs. Deposition of higher amounts of [C1C1Im][Tf2N] revealed an initial three-dimensional film morphology. On the time scale of hours, characteristic changes of the XPS signals were observed. These are interpreted as island spreading and a transformation towards a nearly two dimensional [C1C1Im][Tf2N] film as the final state. In contrast, a film morphology close to 2D was found from the very beginning for [C8C1Im][Tf2N] deposited on Ag(111) demonstrating the influence of the alkyl chain length on the growth kinetics. These studies also highlight the suitability of time-resolved ARXPS for the investigation of IL/solid interfaces, which play a crucial role in IL thin film applications such as in catalysis, sensor, lubrication, and coating technologies.

Density functional theory study on the ionization potentials and electron affinities of thymine-formamide complexes

NASA Astrophysics Data System (ADS)

Sun, Haitao; Tang, Ke; Li, Yanmin; Su, Chunfang; Zhou, Zhengyu; Wang, Zhizhong

The effect of hydrogen bond interactions on ionization potentials (IPs) and electron affinities (EAs) of thymine-formamide complexes (T-F) have been investigated employing the density functional theory B3LYP at 6-311++G(d, p) basis set level. All complexes experience a geometrical change on either electron detachment or attachment, and the change might be facilitated or hindered according to the strength of the hydrogen-bonding interaction involved. The strength of hydrogen bonds presents an opposite changing trend on the two processes. A more important role that H-bonding interaction plays in the process of electron attachment than in the process of electron detachment can be seen by a comparison of the IPs and EAs of complexes with that of isolated thymine. Futhermore, the EAs of isolated thymine are in good agreement with the experimental values (AEA is 0.79 eV, VEA is -0.29 eV [Wetmore et al., Chem Phys Lett 2000, 322, 129]). The calculated total NPA charge distributions reveal that nearly all the negative charges locate on thymine monomer in the anions and even in the cationic states, there are a few negative charges on thymine monomer. An analysis of dissociation energies predicts the processes T-F+→ T++ F and T-F- → T- + F to be the most energetically favorable for T-F+ and T-F-, respectively. Content:text/plain; charset="UTF-8"

Angiotensin II inhibits uptake of transferrin-bound iron but not non-transferrin-bound iron by cultured astrocytes.

PubMed

Huang, Suna; Du, Fang; Li, Lan; Liu, Yong; Liu, Yuhong; Zhang, Chao; Qian, Zhong Ming

2014-06-01

The existence of all components of the renin-angiotensin system (RAS) and the iron metabolism system, and the recent findings on the functions of angiotensin II (ANGII) in peripheral iron metabolism imply that ANGII might play a role in iron homeostasis by regulating expression of iron transport proteins in the brain. Here, we investigated effects of ANGII on uptake and release of iron as well as expression of cell iron transport proteins in cultured astrocytes. We demonstrated that ANGII could significantly inhibit transferrin-bound iron (Tf-Fe) uptake and iron release as well as the expression of transferrin receptor 1 (TfR1) and the iron exporter ferroportin 1 (Fpn1) in cultured astrocytes. This indicated that the inhibitory role of ANGII on Tf-Fe uptake and iron release is mediated by its negative effect on the expression of TfR1 and Fpn1. We also provided evidence that ANGII had no effect on divalent metal transporter 1 (DMT1) expression as well as non-transferrin-bound iron (NTBI) uptake in the cells. Our findings showed that ANGII has a role to affect expression of iron transport proteins in astrocytes in vitro and also suggested that ANGII might have a physiological function in brain iron homeostasis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Metals in agricultural produce associated with acid-mine drainage in Mount Morgan (Queensland, Australia).

PubMed

Vicente-Beckett, Victoria A; McCauley, Gaylene J Taylor; Duivenvoorden, Leo J

2016-01-01

Acid-mine drainage (AMD) into the Dee River from the historic gold and copper mine in Mount Morgan, Queensland (Australia) has been of concern to farmers in the area since 1925. This study sought to determine the levels of AMD-related metals and sulfur in agricultural produce grown near the mine-impacted Dee River, compare these with similar produce grown in reference fields (which had no known AMD influence), and assess any potential health risk using relevant Australian or US guidelines. Analyses of lucerne (Medicago sativa; also known as alfalfa) from five Dee fields showed the following average concentrations (mg/kg dry basis): Cd < 1, Cu 11, Fe 106, Mn 52, Pb < 5, Zn 25 and S 3934; similar levels were found in lucerne hay (used as cattle feed) from two Dee fields. All lucerne and lucerne hay data were generally comparable with levels found in the lucerne reference fields, suggesting no AMD influence; the levels were within the US National Research Council (US NRC) guidelines for maximum tolerable cattle dietary intake. Pasture grass (also cattle feed) from two fields in the Dee River floodplains gave mean concentrations (mg/kg dry) of Cd 0.14, Cu 12, Fe 313, Mn 111, Pb 1.4, Zn 86 and S 2450. All metal levels from the Dee and from reference sites were below the US NRC guidelines for maximum tolerable cattle dietary intake; however, the average Cd, Cu and Fe levels in Dee samples were significantly greater than the corresponding levels in the pasture grass reference sites, suggesting AMD influence in the Dee samples. The average levels in the edible portions of mandarin oranges (Citrus reticulata) from Dee sites (mg/kg wet weight) were Cd 0.011, Cu 0.59, Fe 2.2, Mn 0.56, Pb 0.18, S 91 and Zn 0.96. Cd and Zn were less than or close to, average Fe and Mn levels were at most twice, Cd 1.8 or 6.5 times, and Pb 8.5 or 72 times the maximum levels in raw oranges reported in the US total diet study (TDS) or the Australian TDS, respectively. Average Cd, Fe, Mn, Pb and Zn levels in the citrus reference samples were found to exceed the maximum reported in one or both TDS surveys. Cu, Fe, Mn, Pb and Zn plant-soil transfer factor (TF) values were < 1 for all agricultural samples from both Dee and reference sites, suggesting relatively poor transfer of these metals from soil to plant. In the case of Cd, TF values for Dee pasture grass and citrus fruit samples were 0.14 and 0.73, respectively; lucerne and lucerne hay from both Dee and reference sites gave TF = 10, suggesting some potential risk to cattle, although this conclusion is tentative because Cd levels were close to or less than the detection limit. TF values for S in lucerne, lucerne hay, pasture grass and mandarin oranges from Dee sites were 18, 14, 3 and 3.6, respectively, indicating that S in soil was readily available to plant or fruit. Sulfur in pasture grass and citrus fruit (TF = 11 for both) was apparently more bioavailable at the reference sites than at the Dee sites (TF = 3.0 for pasture grass; TF = 3.6 for citrus fruit).

Identification and expression of the WRKY transcription factors of Carica papaya in response to abiotic and biotic stresses.

PubMed

Pan, Lin-Jie; Jiang, Ling

2014-03-01

The WRKY transcription factor (TF) plays a very important role in the response of plants to various abiotic and biotic stresses. A local papaya database was built according to the GenBank expressed sequence tag database using the BioEdit software. Fifty-two coding sequences of Carica papaya WRKY TFs were predicted using the tBLASTn tool. The phylogenetic tree of the WRKY proteins was classified. The expression profiles of 13 selected C. papaya WRKY TF genes under stress induction were constructed by quantitative real-time polymerase chain reaction. The expression levels of these WRKY genes in response to 3 abiotic and 2 biotic stresses were evaluated. TF807.3 and TF72.14 are upregulated by low temperature; TF807.3, TF43.76, TF12.199 and TF12.62 are involved in the response to drought stress; TF9.35, TF18.51, TF72.14 and TF12.199 is involved in response to wound; TF12.199, TF807.3, TF21.156 and TF18.51 was induced by PRSV pathogen; TF72.14 and TF43.76 are upregulated by SA. The regulated expression levels of above eight genes normalized against housekeeping gene actin were significant at probability of 0.01 levels. These WRKY TFs could be related to corresponding stress resistance and selected as the candidate genes, especially, the two genes TF807.3 and TF12.199, which were regulated notably by four stresses respectively. This study may provide useful information and candidate genes for the development of transgenic stress tolerant papaya varieties.

Genetic modification of bone-marrow mesenchymal stem cells and hematopoietic cells with human coagulation factor IX-expressing plasmids.

PubMed

Sam, Mohammad Reza; Azadbakhsh, Azadeh Sadat; Farokhi, Farrah; Rezazadeh, Kobra; Sam, Sohrab; Zomorodipour, Alireza; Haddad-Mashadrizeh, Aliakbar; Delirezh, Nowruz; Mokarizadeh, Aram

2016-05-01

Ex-vivo gene therapy of hemophilias requires suitable bioreactors for secretion of hFIX into the circulation and stem cells hold great potentials in this regard. Viral vectors are widely manipulated and used to transfer hFIX gene into stem cells. However, little attention has been paid to the manipulation of hFIX transgene itself. Concurrently, the efficacy of such a therapeutic approach depends on determination of which vectors give maximal transgene expression. With this in mind, TF-1 (primary hematopoietic lineage) and rat-bone marrow mesenchymal stem cells (BMSCs) were transfected with five hFIX-expressing plasmids containing different combinations of two human β-globin (hBG) introns inside the hFIX-cDNA and Kozak element and hFIX expression was evaluated by different methods. In BMSCs and TF-1 cells, the highest hFIX level was obtained from the intron-less and hBG intron-I,II containing plasmids respectively. The highest hFIX activity was obtained from the cells that carrying the hBG intron-I,II containing plasmids. BMSCs were able to produce higher hFIX by 1.4 to 4.7-fold increase with activity by 2.4 to 4.4-fold increase compared to TF-1 cells transfected with the same constructs. BMSCs and TF-1 cells could be effectively bioengineered without the use of viral vectors and hFIX minigene containing hBG introns could represent a particular interest in stem cell-based gene therapy of hemophilias. Copyright © 2016 International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

[Endothelial microparticles (EMP) in physiology and pathology].

PubMed

Sierko, Ewa; Sokół, Monika; Wojtukiewicz, Marek Z

2015-08-18

Endothelial microparticles (EMP) are released from endothelial cells (ECs) in the process of activation and/or apoptosis. They harbor adhesive molecules, enzymes, receptors and cytoplasmic structures and express a wide range of various constitutive antigens, typical for ECs, at their surface. Under physiological conditions the concentration of EMP in the blood is clinically insignificant. However, it was reported that under pathological conditions EMP concentration in the blood might slightly increase and contribute to blood coagulation, angiogenesis and inflammation. It has been shown that EMP directly and indirectly contribute to the activation of blood coagulation. Endothelial microparticles directly participate in blood coagulation through their surface tissue factor (TF) - a major initiator of blood coagulation. Furthermore, EMP exhibit procoagulant potential via expression of negatively charged phospholipids at their surface, which may promote assembly of coagulation enzymes (TF/VII, tenases and prothrombinase complexes), leading to thrombus formation. In addition, they provide a binding surface for coagulation factors: IXa, VIII, Va and IIa. Moreover, it is possible that EMP transfer TF from TF-bearing EMP to activated platelets and monocytes by binding them through adhesion molecules. Also, EMP express von Willebrand factor, which may facilitate platelet aggregation. Apart from their procoagulant properties, it was demonstrated that EMP may express adhesive molecules and metalloproteinases (MMP-2, MMP-9) at their surface and release growth factors, which may contribute to angiogenesis. Additionally, surface presence of C3 and C4 - components of the classical pathway - suggests pro-inflammatory properties of these structures. This article contains a summary of available data on the biology and pathophysiology of endothelial microparticles and their potential role in blood coagulation, angiogenesis and inflammation.

The effects of small interfering RNA–targeting tissue factor on an in vitro model of neovascularization

PubMed Central

Peng, Wenyan; Yu, Ying; Li, Tiejun; Zhu, Yuanyuan

2013-01-01

Purpose Tissue factor (TF) plays an important role in neovascularization (NV). This study aimed to determine whether small interfering RNA–targeting TF (TF-siRNA) could knock down TF expression and inhibit cell proliferation, cell migration, and tube formation in an in vitro model of NV. Methods Lipopolysaccharide (LPS) was used to stimulate human umbilical vein endothelial cell (HUVEC) lines to express TF and mimic certain phenotypes of NV in vitro. HUVECs were transfected with TF-siRNAs and control siRNAs using LipofectamineTM 2000. The inhibitory effect of the siRNAs on the expression of TF mRNA and protein was evaluated by quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and western blot analysis. The effects on the cell viability, migration, and tube formation of siRNA-treated cells were examined by MTT assay, wound-healing assay, and Matrigel-induced capillary tube formation. Results Lipopolysaccharide treatment increased the expression of TF. TF-siRNAs effectively knocked down TF expression, with the most efficient TF-siRNA reducing 78.9% of TF expression. TF protein was also notably curtailed by TF-siRNA. The MTT and wound-healing assays showed that the TF-siRNA substantially inhibited the proliferation and migration of HUVECs. Tube formation was decreased by 47.4% and 59.4% in cells treated with the TF-siRNA and vascular endothelial growth factor–siRNA, respectively, compared with the blank control. Conclusions TF-siRNA can knockdown TF expression and inhibit cell proliferation, migration, and tube formation in vitro. TF-siRNA may provide a novel therapeutic candidate for NV-related diseases. PMID:23805036

Tissue Factor promotes breast cancer stem cell activity in vitro.

PubMed

Shaker, Hudhaifah; Harrison, Hannah; Clarke, Robert; Landberg, Goran; Bundred, Nigel J; Versteeg, Henri H; Kirwan, Cliona C

2017-04-18

Cancer stem cells (CSCs) are a subpopulation of cells that can self-renew and initiate tumours. The clotting-initiating protein Tissue Factor (TF) promotes metastasis and may be overexpressed in cancer cells with increased CSC activity. We sought to determine whether TF promotes breast CSC activity in vitro using human breast cancer cell lines. TF expression was compared in anoikis-resistant (CSC-enriched) and unselected cells. In cells sorted into of TF-expressing and TF-negative (FACS), and in cells transfected to knockdown TF (siRNA) and overexpress TF (cDNA), CSC activity was compared by (i) mammosphere forming efficiency (MFE) (ii) holoclone colony formation (Hc) and (iii) ALDH1 activity. TF expression was increased in anoikis-resistant and high ALDH1-activity T47D cells compared to unselected cells. FACS sorted TF-expressing T47Ds and TF-overexpressing MCF7s had increased CSC activity compared to TF-low cells. TF siRNA cells (MDAMB231,T47D) had reduced CSC activity compared to control cells. FVIIa increased MFE and ALDH1 in a dose-dependent manner (MDAMB231, T47D). The effects of FVIIa on MFE were abrogated by TF siRNA (T47D). Breast CSCs (in vitro) demonstrate increased activity when selected for high TF expression, when induced to overexpress TF, and when stimulated (with FVIIa). Targeting the TF pathway in vivo may abrogate CSC activity.

Effects of tissue factor, PAR-2 and MMP-9 expression on human breast cancer cell line MCF-7 invasion.

PubMed

Lin, Zeng-Mao; Zhao, Jian-Xin; Duan, Xue-Ning; Zhang, Lan-Bo; Ye, Jing-Ming; Xu, Ling; Liu, Yin-Hua

2014-01-01

This study aimed to explore the expression of tissue factor (TF), protease activated receptor-2 (PAR-2), and matrix metalloproteinase-9 (MMP-9) in the MCF-7 breast cancer cell line and influence on invasiveness. Stable MCF-7 cells transfected with TF cDNA and with TF ShRNA were established. TF, PAR-2, and MMP-9 protein expression was analyzed using indirect immunofluorescence and invasiveness was evaluated using a cell invasion test. Effects of an exogenous PAR-2 agonist were also examined. TF protein expression significantly differed between the TF cDNA and TF ShRNA groups. MMP-9 protein expression was significantly correlated with TF protein expression, but PAR-2 protein expression was unaffected. The PAR- 2 agonist significantly enhanced MMP-9 expression and slightly increased TF and PAR-2 expression in the TF ShRNA group, but did not significantly affect protein expression in MCF-7 cells transfected with TF cDNA. TF and MMP-9 expression was positively correlated with the invasiveness of tumor cells. TF, PAR-2, and MMP-9 affect invasiveness of MCF-7 cells. TF may increase MMP-9 expression by activating PAR-2.

High Throughput ELISAs to Measure a Unique Glycan on Transferrin in Cerebrospinal Fluid: A Possible Extension toward Alzheimer's Disease Biomarker Development

PubMed Central

Shirotani, Keiro; Futakawa, Satoshi; Nara, Kiyomitsu; Hoshi, Kyoka; Saito, Toshie; Tohyama, Yuriko; Kitazume, Shinobu; Yuasa, Tatsuhiko; Miyajima, Masakazu; Arai, Hajime; Kuno, Atsushi; Narimatsu, Hisashi; Hashimoto, Yasuhiro

2011-01-01

We have established high-throughput lectin-antibody ELISAs to measure different glycans on transferrin (Tf) in cerebrospinal fluid (CSF) using lectins and an anti-transferrin antibody (TfAb). Lectin blot and precipitation analysis of CSF revealed that PVL (Psathyrella velutina lectin) bound an unique N-acetylglucosamine-terminated N-glycans on “CSF-type” Tf whereas SSA (Sambucus sieboldiana agglutinin) bound α2,6-N-acetylneuraminic acid-terminated N-glycans on “serum-type” Tf. PVL-TfAb ELISA of 0.5 μL CSF samples detected “CSF-type” Tf but not “serum-type” Tf whereas SSA-TfAb ELISA detected “serum-type” Tf but not “CSF-type” Tf, demonstrating the specificity of the lectin-TfAb ELISAs. In idiopathic normal pressure hydrocephalus (iNPH), a senile dementia associated with ventriculomegaly, amounts of the SSA-reactive Tf were significantly higher than in non-iNPH patients, indicating that Tf glycan analysis by the high-throughput lectin-TfAb ELISAs could become practical diagnostic tools for iNPH. The lectin-antibody ELISAs of CSF proteins might be useful for diagnosis of the other neurological diseases. PMID:21876827

High Throughput ELISAs to Measure a Unique Glycan on Transferrin in Cerebrospinal Fluid: A Possible Extension toward Alzheimer's Disease Biomarker Development.

PubMed

Shirotani, Keiro; Futakawa, Satoshi; Nara, Kiyomitsu; Hoshi, Kyoka; Saito, Toshie; Tohyama, Yuriko; Kitazume, Shinobu; Yuasa, Tatsuhiko; Miyajima, Masakazu; Arai, Hajime; Kuno, Atsushi; Narimatsu, Hisashi; Hashimoto, Yasuhiro

2011-01-01

We have established high-throughput lectin-antibody ELISAs to measure different glycans on transferrin (Tf) in cerebrospinal fluid (CSF) using lectins and an anti-transferrin antibody (TfAb). Lectin blot and precipitation analysis of CSF revealed that PVL (Psathyrella velutina lectin) bound an unique N-acetylglucosamine-terminated N-glycans on "CSF-type" Tf whereas SSA (Sambucus sieboldiana agglutinin) bound α2,6-N-acetylneuraminic acid-terminated N-glycans on "serum-type" Tf. PVL-TfAb ELISA of 0.5 μL CSF samples detected "CSF-type" Tf but not "serum-type" Tf whereas SSA-TfAb ELISA detected "serum-type" Tf but not "CSF-type" Tf, demonstrating the specificity of the lectin-TfAb ELISAs. In idiopathic normal pressure hydrocephalus (iNPH), a senile dementia associated with ventriculomegaly, amounts of the SSA-reactive Tf were significantly higher than in non-iNPH patients, indicating that Tf glycan analysis by the high-throughput lectin-TfAb ELISAs could become practical diagnostic tools for iNPH. The lectin-antibody ELISAs of CSF proteins might be useful for diagnosis of the other neurological diseases.

Predicting the binding preference of transcription factors to individual DNA k-mers.

PubMed

Alleyne, Trevis M; Peña-Castillo, Lourdes; Badis, Gwenael; Talukder, Shaheynoor; Berger, Michael F; Gehrke, Andrew R; Philippakis, Anthony A; Bulyk, Martha L; Morris, Quaid D; Hughes, Timothy R

2009-04-15

Recognition of specific DNA sequences is a central mechanism by which transcription factors (TFs) control gene expression. Many TF-binding preferences, however, are unknown or poorly characterized, in part due to the difficulty associated with determining their specificity experimentally, and an incomplete understanding of the mechanisms governing sequence specificity. New techniques that estimate the affinity of TFs to all possible k-mers provide a new opportunity to study DNA-protein interaction mechanisms, and may facilitate inference of binding preferences for members of a given TF family when such information is available for other family members. We employed a new dataset consisting of the relative preferences of mouse homeodomains for all eight-base DNA sequences in order to ask how well we can predict the binding profiles of homeodomains when only their protein sequences are given. We evaluated a panel of standard statistical inference techniques, as well as variations of the protein features considered. Nearest neighbour among functionally important residues emerged among the most effective methods. Our results underscore the complexity of TF-DNA recognition, and suggest a rational approach for future analyses of TF families.

The fast-recycling receptor Megalin defines the apical recycling pathway of epithelial cells

PubMed Central

Perez Bay, Andres E.; Schreiner, Ryan; Benedicto, Ignacio; Paz Marzolo, Maria; Banfelder, Jason; Weinstein, Alan M.; Rodriguez-Boulan, Enrique J.

2016-01-01

The basolateral recycling and transcytotic pathways of epithelial cells were previously defined using markers such as transferrin (TfR) and polymeric IgA (pIgR) receptors. In contrast, our knowledge of the apical recycling pathway remains fragmentary. Here we utilize quantitative live-imaging and mathematical modelling to outline the recycling pathway of Megalin (LRP-2), an apical receptor with key developmental and renal functions, in MDCK cells. We show that, like TfR, Megalin is a long-lived and fast-recycling receptor. Megalin enters polarized MDCK cells through segregated apical sorting endosomes and subsequently intersects the TfR and pIgR pathways at a perinuclear Rab11-negative compartment termed common recycling endosomes (CRE). Whereas TfR recycles to the basolateral membrane from CRE, Megalin, like pIgR, traffics to subapical Rab11-positive apical recycling endosomes (ARE) and reaches the apical membrane in a microtubule- and Rab11-dependent manner. Hence, Megalin defines the apical recycling pathway of epithelia, with CRE as its apical sorting station. PMID:27180806

Matriptase activation connects tissue factor-dependent coagulation initiation to epithelial proteolysis and signaling.

PubMed

Le Gall, Sylvain M; Szabo, Roman; Lee, Melody; Kirchhofer, Daniel; Craik, Charles S; Bugge, Thomas H; Camerer, Eric

2016-06-23

The coagulation cascade is designed to sense tissue injury by physical separation of the membrane-anchored cofactor tissue factor (TF) from inactive precursors of coagulation proteases circulating in plasma. Once TF on epithelial and other extravascular cells is exposed to plasma, sequential activation of coagulation proteases coordinates hemostasis and contributes to host defense and tissue repair. Membrane-anchored serine proteases (MASPs) play critical roles in the development and homeostasis of epithelial barrier tissues; how MASPs are activated in mature epithelia is unknown. We here report that proteases of the extrinsic pathway of blood coagulation transactivate the MASP matriptase, thus connecting coagulation initiation to epithelial proteolysis and signaling. Exposure of TF-expressing cells to factors (F) VIIa and Xa triggered the conversion of latent pro-matriptase to an active protease, which in turn cleaved the pericellular substrates protease-activated receptor-2 (PAR2) and pro-urokinase. An activation pathway-selective PAR2 mutant resistant to direct cleavage by TF:FVIIa and FXa was activated by these proteases when cells co-expressed pro-matriptase, and matriptase transactivation was necessary for efficient cleavage and activation of wild-type PAR2 by physiological concentrations of TF:FVIIa and FXa. The coagulation initiation complex induced rapid and prolonged enhancement of the barrier function of epithelial monolayers that was dependent on matriptase transactivation and PAR2 signaling. These observations suggest that the coagulation cascade engages matriptase to help coordinate epithelial defense and repair programs after injury or infection, and that matriptase may contribute to TF-driven pathogenesis in cancer and inflammation.

Multiple conserved domains of the nucleoporin Nup124p and its orthologs Nup1p and Nup153 are critical for nuclear import and activity of the fission yeast Tf1 retrotransposon.

PubMed

Sistla, Srivani; Pang, Junxiong Vincent; Wang, Cui Xia; Balasundaram, David

2007-09-01

The nucleoporin Nup124p is a host protein required for the nuclear import of both, retrotransposon Tf1-Gag as well as the retroviral HIV-1 Vpr in fission yeast. The human nucleoporin Nup153 and the Saccharomyces cerevisiae Nup1p were identified as orthologs of Nup124p. In this study, we show that all three nucleoporins share a large FG/FXFG-repeat domain and a C-terminal peptide sequence, GRKIxxxxxRRKx, that are absolutely essential for Tf1 retrotransposition. Though the FXFG domain was essential, the FXFG repeats themselves could be eliminated without loss of retrotransposon activity, suggesting the existence of a common element unrelated to FG/FXFG motifs. The Nup124p C-terminal peptide, GRKIAVPRSRRKR, was extremely sensitive to certain single amino acid changes within stretches of the basic residues. On the basis of our comparative study of Nup124p, Nup1p, and Nup153 domains, we have developed peptides that specifically knockdown retrotransposon activity by disengaging the Tf1-Gag from its host nuclear transport machinery without any harmful consequence to the host itself. Our results imply that those domains challenged a specific pathway affecting Tf1 transposition. Although full-length Nup1p or Nup153 does not complement Nup124p, the functionality of their conserved domains with reference to Tf1 activity suggests that these three proteins evolved from a common ancestor.

The long terminal repeat-containing retrotransposon Tf1 possesses amino acids in gag that regulate nuclear localization and particle formation.

PubMed

Kim, Min-Kyung; Claiborn, Kathryn C; Levin, Henry L

2005-08-01

Tf1 is a long terminal repeat-containing retrotransposon of Schizosaccharomyces pombe that is studied to further our understanding of retrovirus propagation. One important application is to examine Tf1 as a model for how human immunodeficiency virus type 1 proteins enter the nucleus. The accumulation of Tf1 Gag in the nucleus requires an N-terminal nuclear localization signal (NLS) and the nuclear pore factor Nup124p. Here, we report that NLS activity is regulated by adjacent residues. Five mutant transposons were made, each with sequential tracts of four amino acids in Gag replaced by alanines. All five versions of Tf1 transposed with frequencies that were significantly lower than that of the wild type. Although all five made normal amounts of Gag, two of the mutations did not make cDNA, indicating that Gag contributed to reverse transcription. The localization of the Gag in the nucleus was significantly reduced by mutations A1, A2, and A3. These results identified residues in Gag that contribute to the function of the NLS. The Gags of A4 and A5 localized within the nucleus but exhibited severe defects in the formation of virus-like particles. Of particular interest was that the mutations in Gag-A4 and Gag-A5 caused their nuclear localization to become independent of Nup124p. These results suggested that Nup124p was only required for import of Tf1 Gag because of its extensive multimerization.

Multiple Conserved Domains of the Nucleoporin Nup124p and Its Orthologs Nup1p and Nup153 Are Critical for Nuclear Import and Activity of the Fission Yeast Tf1 Retrotransposon

PubMed Central

Sistla, Srivani; Pang, Junxiong Vincent; Wang, Cui Xia

2007-01-01

The nucleoporin Nup124p is a host protein required for the nuclear import of both, retrotransposon Tf1-Gag as well as the retroviral HIV-1 Vpr in fission yeast. The human nucleoporin Nup153 and the Saccharomyces cerevisiae Nup1p were identified as orthologs of Nup124p. In this study, we show that all three nucleoporins share a large FG/FXFG-repeat domain and a C-terminal peptide sequence, GRKIxxxxxRRKx, that are absolutely essential for Tf1 retrotransposition. Though the FXFG domain was essential, the FXFG repeats themselves could be eliminated without loss of retrotransposon activity, suggesting the existence of a common element unrelated to FG/FXFG motifs. The Nup124p C-terminal peptide, GRKIAVPRSRRKR, was extremely sensitive to certain single amino acid changes within stretches of the basic residues. On the basis of our comparative study of Nup124p, Nup1p, and Nup153 domains, we have developed peptides that specifically knockdown retrotransposon activity by disengaging the Tf1-Gag from its host nuclear transport machinery without any harmful consequence to the host itself. Our results imply that those domains challenged a specific pathway affecting Tf1 transposition. Although full-length Nup1p or Nup153 does not complement Nup124p, the functionality of their conserved domains with reference to Tf1 activity suggests that these three proteins evolved from a common ancestor. PMID:17615301

Inflammatory monocytes expressing tissue factor drive SIV and HIV coagulopathy

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

Schechter, Melissa E.; Andrade, Bruno B.; He, Tianyu

In HIV infection, persistent inflammation despite effective antiretroviral therapy is linked to increased risk of noninfectious chronic complications such as cardiovascular and thromboembolic disease. Thus, a better understanding of inflammatory and coagulation pathways in HIV infection is needed to optimize clinical care. Markers of monocyte activation and coagulation independently predict morbidity and mortality associated with non-AIDS events. We identified a specific subset of monocytes that express tissue factor (TF), persist after virological suppression, and trigger the coagulation cascade by activating factor X. This subset of monocytes expressing TF had a distinct gene signature with up-regulated innate immune markers and evidencemore » of robust production of multiple proinflammatory cytokines, including interleukin-1β (IL-1β), tumor necrosis factor–α (TNF-α), and IL-6, ex vivo and in vitro upon lipopolysaccharide stimulation. We validated our findings in a nonhuman primate model, showing that TF-expressing inflammatory monocytes were associated with simian immunodeficiency virus (SIV)–related coagulopathy in the progressive [pigtail macaques (PTMs)] but not in the nonpathogenic (African green monkeys) SIV infection model. Last, Ixolaris, an anticoagulant that inhibits the TF pathway, was tested and potently blocked functional TF activity in vitro in HIV and SIV infection without affecting monocyte responses to Toll-like receptor stimulation. Strikingly, in vivo treatment of SIV-infected PTMs with Ixolaris was associated with significant decreases in D-dimer and immune activation. These data suggest that TF-expressing monocytes are at the epicenter of inflammation and coagulation in chronic HIV and SIV infection and may represent a potential therapeutic target.« less

Inflammatory monocytes expressing tissue factor drive SIV and HIV coagulopathy

DOE PAGES

Schechter, Melissa E.; Andrade, Bruno B.; He, Tianyu; ...

2017-08-30

In HIV infection, persistent inflammation despite effective antiretroviral therapy is linked to increased risk of noninfectious chronic complications such as cardiovascular and thromboembolic disease. Thus, a better understanding of inflammatory and coagulation pathways in HIV infection is needed to optimize clinical care. Markers of monocyte activation and coagulation independently predict morbidity and mortality associated with non-AIDS events. We identified a specific subset of monocytes that express tissue factor (TF), persist after virological suppression, and trigger the coagulation cascade by activating factor X. This subset of monocytes expressing TF had a distinct gene signature with up-regulated innate immune markers and evidencemore » of robust production of multiple proinflammatory cytokines, including interleukin-1β (IL-1β), tumor necrosis factor–α (TNF-α), and IL-6, ex vivo and in vitro upon lipopolysaccharide stimulation. We validated our findings in a nonhuman primate model, showing that TF-expressing inflammatory monocytes were associated with simian immunodeficiency virus (SIV)–related coagulopathy in the progressive [pigtail macaques (PTMs)] but not in the nonpathogenic (African green monkeys) SIV infection model. Last, Ixolaris, an anticoagulant that inhibits the TF pathway, was tested and potently blocked functional TF activity in vitro in HIV and SIV infection without affecting monocyte responses to Toll-like receptor stimulation. Strikingly, in vivo treatment of SIV-infected PTMs with Ixolaris was associated with significant decreases in D-dimer and immune activation. These data suggest that TF-expressing monocytes are at the epicenter of inflammation and coagulation in chronic HIV and SIV infection and may represent a potential therapeutic target.« less

The use of Eupatorium Odoratum as bio-monitor for radionuclides determination in Manjung, Perak

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

Zainal, Fetri, E-mail: fetrizainal@yahoo.com; Hamzah, Zaini; Wood, Khalik

2015-04-29

The accumulation of radionuclides in plants can be used as bio-monitoring in the environment. This technique is a cost-effective as the plants used to uptake deposited radionuclides from soil, commonly as soil-to-plant transfer factor (TF), which is widely used for calculating radiological risk. Radionuclides deposited in the soil carry by the air as particles or gases lead to the accumulation in soil. Eupatorium odoratum, known as pokok kapal terbang in Malaysia was chosen as sample for their abundances and properties to measure surface soil contamination. The plants were collected in three different directions (North, North-East and South-East) from Manjung district.more » The plants were collected in same size and then separated in to three parts (roots, stems and leaves) to determine the transfer factor from soil to each part. The concentrations of thorium (Th) and uranium (U) were analyzed using Energy Disperse X-Ray Fluorescence (EDXRF) and found in the range of 1.20-3.50 mg/kg and 1.20-3.90 mg/kg in roots, 1.40-3.90 mg/kg and 1.50-5.90 mg/kg in stems and 1.50-2.50 mg/kg and 2.00-6.00 mg/kg in leaves, respectively. Transfer factor (TF) was calculated through concentrations as reported in this article and show that the plants have transferred and accumulated radionuclides in significant values. From radionuclides concentrations in topsoil, the radiological risk was calculated and the present result show that external hazard index (H{sub ex}) is below than unity indicate low radiological risk at that area.« less

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

PubMed Central

Fang, Bin; Everett, Logan J.; Jager, Jennifer; Briggs, Erika; Armour, Sean M.; Feng, Dan; Roy, Ankur; Gerhart-Hines, Zachary; Sun, Zheng; Lazar, Mitchell A.

2014-01-01

SUMMARY Mammalian transcriptomes display complex circadian rhythms with multiple phases of gene expression that cannot be accounted for by current models of the molecular clock. We have determined the underlying mechanisms by measuring nascent RNA transcription around the clock in mouse liver. Unbiased examination of eRNAs that cluster in specific circadian phases identified functional enhancers driven by distinct transcription factors (TFs). We further identify on a global scale the components of the TF cistromes that function to orchestrate circadian gene expression. Integrated genomic analyses also revealed novel mechanisms by which a single circadian factor controls opposing transcriptional phases. These findings shed new light on the diversity and specificity of TF function in the generation of multiple phases of circadian gene transcription in a mammalian organ. PMID:25416951

Circadian enhancers coordinate multiple phases of rhythmic gene transcription in vivo.

PubMed

Fang, Bin; Everett, Logan J; Jager, Jennifer; Briggs, Erika; Armour, Sean M; Feng, Dan; Roy, Ankur; Gerhart-Hines, Zachary; Sun, Zheng; Lazar, Mitchell A

2014-11-20

Mammalian transcriptomes display complex circadian rhythms with multiple phases of gene expression that cannot be accounted for by current models of the molecular clock. We have determined the underlying mechanisms by measuring nascent RNA transcription around the clock in mouse liver. Unbiased examination of enhancer RNAs (eRNAs) that cluster in specific circadian phases identified functional enhancers driven by distinct transcription factors (TFs). We further identify on a global scale the components of the TF cistromes that function to orchestrate circadian gene expression. Integrated genomic analyses also revealed mechanisms by which a single circadian factor controls opposing transcriptional phases. These findings shed light on the diversity and specificity of TF function in the generation of multiple phases of circadian gene transcription in a mammalian organ.

Isomeric organic semiconductors containing fused-thiophene cores: molecular packing and charge transport.

PubMed

Dang, Dongfeng; Zhou, Pei; Wu, Yong; Xu, Yanzi; Zhi, Ying; Zhu, Weiguo

2018-05-16

Isomeric TF1 and TF2 with highly fused thiophene cores were designed and synthesized here, in which a highly planar molecular structure was obtained for TF1 with the face-to-face sulfur atoms in the lateral region and a twisted molecular backbone was observed for TF2 with the back-to-back sulfur atoms. It is worth noting that different intermolecular interactions dominated in TF1 and TF2 caused by their isomeric thiophene cores, in which strong π-π stacking was achieved for TF1, whereas sulphur-involved nonbonding intermolecular interactions dominated in TF2, leading to the different fluorescence behaviors and also the altered liquid crystalline phases. Finally, typical P-type charge transport behaviors were achieved in both TF1- and TF2-based solution-processed OFETs. Also owing to the much ordered molecular packing in TF1, a higher charge carrier mobility of 3.7 × 10-3 cm2 V-1 s-1 was achieved for TF1-based OFETs compared to TF2-based OFETs.

Spectroscopic studies of the interaction mechanisms between mono-caffeoylquinic acids and transferrin

NASA Astrophysics Data System (ADS)

Guan, Yanqing; Dong, Jing; Chen, Shizhong; Liu, Meixian; Wang, Daidong; Zhang, Xiaotian; Wang, Hong; Lin, Zongtao

2017-06-01

Transferrin (Tf) is an important protein responsible for circulating and transporting iron into cytoplasm. Tf can be taken into cells through endocytosis mediated by Tf receptor, which usually overexpresses in cancer cells. The Tf-Tf receptor pathway opens a possible avenue for novel targeted cancer therapy by utilizing Tf-binding active compounds. Among which, anti-cancer active caffeoylquinic acids (CQAs) were recently found to be promising Tf-binders by our group. For better understanding the anti-cancer activities of CQAs, it is important to unveil the binding mechanisms between CQAs and Tf. In this study, the fluorescence quenching, surface plasmon resonance (SPR), circular dichroism (CD) and molecular docking were used to investigate the interactions between CQA and Tf. The results showed that the calculated apparent association constants of interactions between 1-, 3-, 4- and 5-CQA and Tf at 298 K were 7.97 × 105 M- 1, 4.36 × 107 M- 1, 6.58 × 105 M- 1 and 4.42 × 106 M- 1, respectively. The thermodynamic parameters indicated that the interaction between 1-, 3-, 5-CQA and Tf is due to H-bonding, and electrostatic interactions were likely involved in the binding of 4-CQA and Tf. The CD results indicated that bindings of 1-CQA, 4-CQA and 5-CQA with Tf resulted in more stretched β-turn and random coil translated from β-sheet. In contrast, 3-CQA led to more stable a-helix conformation. Molecular docking studies of CQAs with Tf further displayed that CQAs were able to interact with residues near Fe3 + binding site. The spectroscopic studies revealed the action mechanisms, thermodynamics and interacting forces between CQAs and Tf, and thus are helpful for future design and discovery of Tf-binders for targeted cancer therapy applying Tf-Tf receptor pathway.

PlantTFDB: a comprehensive plant transcription factor database

PubMed Central

Guo, An-Yuan; Chen, Xin; Gao, Ge; Zhang, He; Zhu, Qi-Hui; Liu, Xiao-Chuan; Zhong, Ying-Fu; Gu, Xiaocheng; He, Kun; Luo, Jingchu

2008-01-01

Transcription factors (TFs) play key roles in controlling gene expression. Systematic identification and annotation of TFs, followed by construction of TF databases may serve as useful resources for studying the function and evolution of transcription factors. We developed a comprehensive plant transcription factor database PlantTFDB (http://planttfdb.cbi.pku.edu.cn), which contains 26 402 TFs predicted from 22 species, including five model organisms with available whole genome sequence and 17 plants with available EST sequences. To provide comprehensive information for those putative TFs, we made extensive annotation at both family and gene levels. A brief introduction and key references were presented for each family. Functional domain information and cross-references to various well-known public databases were available for each identified TF. In addition, we predicted putative orthologs of those TFs among the 22 species. PlantTFDB has a simple interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis. PMID:17933783

Analytical gradients for subsystem density functional theory within the slater-function-based amsterdam density functional program.

PubMed

Schlüns, Danny; Franchini, Mirko; Götz, Andreas W; Neugebauer, Johannes; Jacob, Christoph R; Visscher, Lucas

2017-02-05

We present a new implementation of analytical gradients for subsystem density-functional theory (sDFT) and frozen-density embedding (FDE) into the Amsterdam Density Functional program (ADF). The underlying theory and necessary expressions for the implementation are derived and discussed in detail for various FDE and sDFT setups. The parallel implementation is numerically verified and geometry optimizations with different functional combinations (LDA/TF and PW91/PW91K) are conducted and compared to reference data. Our results confirm that sDFT-LDA/TF yields good equilibrium distances for the systems studied here (mean absolute deviation: 0.09 Å) compared to reference wave-function theory results. However, sDFT-PW91/PW91k quite consistently yields smaller equilibrium distances (mean absolute deviation: 0.23 Å). The flexibility of our new implementation is demonstrated for an HCN-trimer test system, for which several different setups are applied. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Soluble tissue factor has unique angiogenic activities that selectively promote migration and differentiation but not proliferation of endothelial cells

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

He Yingbo; Chang Guodong; Zhan Shunli

2008-06-06

The level of circulating tissue factor (TF) is up-regulated in human angiogenesis-related malignancies. However, whether circulating TF has angiogenic activities has not been determined. Soluble TF (sTF) is the main domain of circulating TF. Here, using cell migration, wound healing, and tubule formation assays, human recombinant sTF was found to significantly promote the migration and differentiation of endothelial cells. The stress fiber formation and rearrangement induced by sTF observed through immunofluorescence microscope may be responsible for the stimulatory migration effect of sTF. Nevertheless, sTF had no effects on endothelial cell proliferation. Interestingly, sTF can be internalized by endothelial cells, whichmore » implies a novel mechanism for sTF in angiogenesis. These results suggest that sTF has unique angiogenic activities and may serve as a potential therapeutic target to treat diseases associated with angiogenesis such as cancer and rheumatoid arthritis.« less

Hematopoietic Colony Formation from Human Growth Factor-Dependent TF1 Cells and Human Cord Blood Myeloid Progenitor Cells Depends on SHP2 Phosphatase Function

PubMed Central

Etienne-Julan, Maryse; Gotoh, Akihiko; Braun, Stephen E.; Lu, Li; Cooper, Scott; Feng, Gen-Sheng; Li, Xing Jun

2013-01-01

The protein tyrosine phosphatase, SHP2, is widely expressed; however, previous studies demonstrated that hematopoietic cell development more stringently requires Shp2 expression compared to other tissues. Furthermore, somatic gain-of-function SHP2 mutants are commonly found in human myeloid leukemias. Given that pharmacologic inhibitors to SHP2 phosphatase activity are currently in development as putative antileukemic agents, we conducted a series of experiments examining the necessity of SHP2 phosphatase activity for human hematopoiesis. Anti-sense oligonucleotides to human SHP2 coding sequences reduced human cord blood- and human cell line, TF1-derived colony formation. Expression of truncated SHP2 bearing its Src homology 2 (SH2) domains, but lacking the phosphatase domain similarly reduced human cord blood- and TF1-derived colony formation. Mechanistically, expression of truncated SHP2 reduced the interaction between endogenous, full-length SHP2 with the adapter protein, Grb2. To verify the role of SHP2 phosphatase function in human hematopoietic cell development, human cord blood CD34+ cells were transduced with a leukemia-associated phosphatase gain-of-function SHP2 mutant or with a phosphatase dead SHP2 mutant, which indicated that increased phosphatase function enhanced, while decreased SHP2 phosphatase function reduced, human cord blood-derived colonies. Collectively, these findings indicate that SHP2 phosphatase function regulates human hematopoietic cell development and imply that the phosphatase component of SHP2 may serve as a pharmacologic target in human leukemias bearing increased SHP2 phosphatase activity. PMID:23082805

Hematopoietic colony formation from human growth factor-dependent TF1 cells and human cord blood myeloid progenitor cells depends on SHP2 phosphatase function.

PubMed

Broxmeyer, Hal E; Etienne-Julan, Maryse; Gotoh, Akihiko; Braun, Stephen E; Lu, Li; Cooper, Scott; Feng, Gen-Sheng; Li, Xing Jun; Chan, Rebecca J

2013-03-15

The protein tyrosine phosphatase, SHP2, is widely expressed; however, previous studies demonstrated that hematopoietic cell development more stringently requires Shp2 expression compared to other tissues. Furthermore, somatic gain-of-function SHP2 mutants are commonly found in human myeloid leukemias. Given that pharmacologic inhibitors to SHP2 phosphatase activity are currently in development as putative antileukemic agents, we conducted a series of experiments examining the necessity of SHP2 phosphatase activity for human hematopoiesis. Anti-sense oligonucleotides to human SHP2 coding sequences reduced human cord blood- and human cell line, TF1-derived colony formation. Expression of truncated SHP2 bearing its Src homology 2 (SH2) domains, but lacking the phosphatase domain similarly reduced human cord blood- and TF1-derived colony formation. Mechanistically, expression of truncated SHP2 reduced the interaction between endogenous, full-length SHP2 with the adapter protein, Grb2. To verify the role of SHP2 phosphatase function in human hematopoietic cell development, human cord blood CD34+ cells were transduced with a leukemia-associated phosphatase gain-of-function SHP2 mutant or with a phosphatase dead SHP2 mutant, which indicated that increased phosphatase function enhanced, while decreased SHP2 phosphatase function reduced, human cord blood-derived colonies. Collectively, these findings indicate that SHP2 phosphatase function regulates human hematopoietic cell development and imply that the phosphatase component of SHP2 may serve as a pharmacologic target in human leukemias bearing increased SHP2 phosphatase activity.

Dispersion characteristics of anisotropic unmagnetized ultra-relativistic transverse plasma wave with arbitrary electron degeneracy

NASA Astrophysics Data System (ADS)

Sarfraz, M.; Farooq, H.; Abbas, G.; Noureen, S.; Iqbal, Z.; Rasheed, A.

2018-03-01

Thermal momentum space anisotropy is ubiquitous in many astrophysical and laboratory plasma environments. Using Vlasov-Maxwell's model equations, a generalized polarization tensor for a collisionless ultra-relativistic unmagnetized electron plasma is derived. In particular, the tensor is obtained by considering anisotropy in the momentum space. The integral of moments of Fermi-Dirac distribution function in terms of Polylog functions is used for describing the border line plasma systems (T/e TF e ≈1 ) comprising arbitrary electron degeneracy, where Te and TF e, are thermal and Fermi temperatures, respectively. Furthermore, the effects of variation in thermal momentum space anisotropy on the electron equilibrium number density and the spectrum of electromagnetic waves are analyzed.

Ultrafast vibrational spectroscopy (2D-IR) of CO{sub 2} in ionic liquids: Carbon capture from carbon dioxide’s point of view

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

Brinzer, Thomas; Berquist, Eric J.; Ren, Zhe

2015-06-07

The CO{sub 2}ν{sub 3} asymmetric stretching mode is established as a vibrational chromophore for ultrafast two-dimensional infrared (2D-IR) spectroscopic studies of local structure and dynamics in ionic liquids, which are of interest for carbon capture applications. CO{sub 2} is dissolved in a series of 1-butyl-3-methylimidazolium-based ionic liquids ([C{sub 4}C{sub 1}im][X], where [X]{sup −} is the anion from the series hexafluorophosphate (PF{sub 6}{sup −}), tetrafluoroborate (BF{sub 4}{sup −}), bis-(trifluoromethyl)sulfonylimide (Tf{sub 2}N{sup −}), triflate (TfO{sup −}), trifluoroacetate (TFA{sup −}), dicyanamide (DCA{sup −}), and thiocyanate (SCN{sup −})). In the ionic liquids studied, the ν{sub 3} center frequency is sensitive to the local solvationmore » environment and reports on the timescales for local structural relaxation. Density functional theory calculations predict charge transfer from the anion to the CO{sub 2} and from CO{sub 2} to the cation. The charge transfer drives geometrical distortion of CO{sub 2}, which in turn changes the ν{sub 3} frequency. The observed structural relaxation timescales vary by up to an order of magnitude between ionic liquids. Shoulders in the 2D-IR spectra arise from anharmonic coupling of the ν{sub 2} and ν{sub 3} normal modes of CO{sub 2}. Thermal fluctuations in the ν{sub 2} population stochastically modulate the ν{sub 3} frequency and generate dynamic cross-peaks. These timescales are attributed to the breakup of ion cages that create a well-defined local environment for CO{sub 2}. The results suggest that the picosecond dynamics of CO{sub 2} are gated by local diffusion of anions and cations.« less

A new sample treatment for asialo-Tf determination with capillary electrophoresis: an added value to the analysis of CDT.

PubMed

Porpiglia, Nadia Maria; De Palo, Elio Franco; Savchuk, Sergey Alexandrovich; Appolonova, Svetlana Alexandrovna; Bortolotti, Federica; Tagliaro, Franco

2018-05-10

The non-glycosylated glycoform of transferrin (Tf), known as asialo-Tf, was not selected (in favor of disialo-Tf) as the measurand for the standardization of carbohydrate deficient transferrin (CDT) determination because of a lower diagnostic sensitivity provided with the currently available analytical procedures for sera. However, asialo-Tf could provide an additional value to disialo-Tf in the CDT analysis employed in forensic toxicology contexts. The present work aimed at developing an easy sample preparation based on PEG precipitation in order to improve the detectability of asialo-Tf in capillary electrophoresis (CE). Equal volumes (35 μL) of serum and of 30% PEG-8000 were mixed and briefly vortexed. After centrifugation, the supernatant was iron saturated with a ferric solution (1:1, v/v). The mixture was analyzed in CE for asialo-Tf and disialo-Tf determination. PEG-8000 precipitation allowed the improvement of the baseline in the electropherograms in terms of interferences reduction particularly in the asialo-Tf migration region. The detection of asialo-Tf was possible in 89% of samples with disialo-Tf above the cut-off limit, whereas only 16% of them showed asialo-Tf by employing the traditional sample preteatment. Asialo-Tf represents an additional value to disialo-Tf as a biomarker of alcohol abuse in forensic toxicology. Copyright © 2018. Published by Elsevier B.V.

Improved differential diagnosis of anemia of chronic disease and iron deficiency anemia: a prospective multicenter evaluation of soluble transferrin receptor and the sTfR/log ferritin index.

PubMed

Skikne, Barry S; Punnonen, Kari; Caldron, Paul H; Bennett, Michael T; Rehu, Mari; Gasior, Gail H; Chamberlin, Janna S; Sullivan, Linda A; Bray, Kurtis R; Southwick, Paula C

2011-11-01

Anemia of chronic disease (ACD) and iron deficiency anemia (IDA) are the most prevalent forms of anemia and often occur concurrently. Standard tests of iron status used in differential diagnosis are affected by inflammation, hindering clinical interpretation. In contrast, soluble transferrin receptor (sTfR) indicates iron deficiency and is unaffected by inflammation. Objectives of this prospective multicenter clinical trial were to evaluate and compare the diagnostic accuracy of sTfR and the sTfR/log ferritin index (sTfR Index) for differential diagnosis using the automated Access(®) sTfR assay (Beckman Coulter) and sTfR Index. We consecutively enrolled 145 anemic patients with common disorders associated with IDA and ACD. Subjects with IDA or ACD + IDA had significantly higher sTfR and sTfR Index values than subjects with ACD (P < 0.0001). ROC curves produced the following cutoffs for sTfR: 21 nmol/L (or 1.55 mg/L), and the sTfR Index: 14 (using nmol/L) (or 1.03 using mg/L). The sTfR Index was superior to sTfR (AUC 0.87 vs. 0.74, P < 0.0001). Use of all three parameters in combination more than doubled the detection of IDA, from 41% (ferritin alone) to 92% (ferritin, sTfR, sTfR Index). Use of sTfR and the sTfR Index improves detection of IDA, particularly in situations where routine markers provide equivocal results. Findings demonstrate a significant advantage in the simultaneous determination of ferritin, sTfR and sTfR Index. Obtaining a ferritin level alone may delay diagnosis of combined IDA and ACD. Copyright © 2011 Wiley-Liss, Inc.

Matching synchrosqueezing transform: A useful tool for characterizing signals with fast varying instantaneous frequency and application to machine fault diagnosis

NASA Astrophysics Data System (ADS)

Wang, Shibin; Chen, Xuefeng; Selesnick, Ivan W.; Guo, Yanjie; Tong, Chaowei; Zhang, Xingwu

2018-02-01

Synchrosqueezing transform (SST) can effectively improve the readability of the time-frequency (TF) representation (TFR) of nonstationary signals composed of multiple components with slow varying instantaneous frequency (IF). However, for signals composed of multiple components with fast varying IF, SST still suffers from TF blurs. In this paper, we introduce a time-frequency analysis (TFA) method called matching synchrosqueezing transform (MSST) that achieves a highly concentrated TF representation comparable to the standard TF reassignment methods (STFRM), even for signals with fast varying IF, and furthermore, MSST retains the reconstruction benefit of SST. MSST captures the philosophy of STFRM to simultaneously consider time and frequency variables, and incorporates three estimators (i.e., the IF estimator, the group delay estimator, and a chirp-rate estimator) into a comprehensive and accurate IF estimator. In this paper, we first introduce the motivation of MSST with three heuristic examples. Then we introduce a precise mathematical definition of a class of chirp-like intrinsic-mode-type functions that locally can be viewed as a sum of a reasonably small number of approximate chirp signals, and we prove that MSST does indeed succeed in estimating chirp-rate and IF of arbitrary functions in this class and succeed in decomposing these functions. Furthermore, we describe an efficient numerical algorithm for the practical implementation of the MSST, and we provide an adaptive IF extraction method for MSST reconstruction. Finally, we verify the effectiveness of the MSST in practical applications for machine fault diagnosis, including gearbox fault diagnosis for a wind turbine in variable speed conditions and rotor rub-impact fault diagnosis for a dual-rotor turbofan engine.

Characterizing regulatory and functional differentiation between maize mesophyll and bundle sheath cells by transcriptomic analysis.

PubMed

Chang, Yao-Ming; Liu, Wen-Yu; Shih, Arthur Chun-Chieh; Shen, Meng-Ni; Lu, Chen-Hua; Lu, Mei-Yeh Jade; Yang, Hui-Wen; Wang, Tzi-Yuan; Chen, Sean C-C; Chen, Stella Maris; Li, Wen-Hsiung; Ku, Maurice S B

2012-09-01

To study the regulatory and functional differentiation between the mesophyll (M) and bundle sheath (BS) cells of maize (Zea mays), we isolated large quantities of highly homogeneous M and BS cells from newly matured second leaves for transcriptome profiling by RNA sequencing. A total of 52,421 annotated genes with at least one read were found in the two transcriptomes. Defining a gene with more than one read per kilobase per million mapped reads as expressed, we identified 18,482 expressed genes; 14,972 were expressed in M cells, including 53 M-enriched transcription factor (TF) genes, whereas 17,269 were expressed in BS cells, including 214 BS-enriched TF genes. Interestingly, many TF gene families show a conspicuous BS preference in expression. Pathway analyses reveal differentiation between the two cell types in various functional categories, with the M cells playing more important roles in light reaction, protein synthesis and folding, tetrapyrrole synthesis, and RNA binding, while the BS cells specialize in transport, signaling, protein degradation and posttranslational modification, major carbon, hydrogen, and oxygen metabolism, cell division and organization, and development. Genes coding for several transporters involved in the shuttle of C(4) metabolites and BS cell wall development have been identified, to our knowledge, for the first time. This comprehensive data set will be useful for studying M/BS differentiation in regulation and function.

Theaflavins in black tea and catechins in green tea are equally effective antioxidants.

PubMed

Leung, L K; Su, Y; Chen, R; Zhang, Z; Huang, Y; Chen, Z Y

2001-09-01

Green tea catechins, including (-)-epicatechin (EC), (-)-epicatechin gallate (ECG), (-)-epigallocatechin (EGC) and (-)-epigallocatechin gallate (EGCG), are oxidized and dimerized during the manufacture of black tea and oolong tea to form orange-red pigments, theaflavins (TF), a mixture of theaflavin (TF1), theaflavin-3-gallate (TF2A), theaflavin-3'-gallate (TF2B) and theaflavin-3,3'-digallate (TF3). The present study was designed to compare the antioxidant activities of individual TF with that of each catechin using human LDL oxidation as a model. All catechins and TF tested inhibited Cu(+2)-mediated LDL oxidation. Analysis of the thiobarbituric acid-reactive substances (TBARS) and conjugated dienes produced during LDL oxidation revealed that the antioxidant activity was in the order: TF3 > ECG > EGCG > or = TF2B > or = TF2A > TF1 > or = EC > EGC. Four TF derivatives also demonstrated a dose-dependent antioxidant activity in Cu(+2)-mediated LDL oxidation at concentrations of 5-40 micromol/L. These results demonstrate that the TF present in black tea possess at least the same antioxidant potency as catechins present in green tea, and that the conversion of catechins to TF during fermentation in making black tea does not alter significantly their free radical-scavenging activity.

Detection of cerebrospinal fluid leakage by specific measurement of transferrin glycoforms.

PubMed

Kwon, Seok-Joon; Zhang, Fuming; Dordick, Jonathan S; Sonstein, William J; Linhardt, Robert J

2015-10-01

A simple and rapid detection of cerebrospinal fluid (CSF) leakage would benefit spine surgeons making critical postoperative decisions on patient care. We have assessed novel approaches to selectively determine CSF β2-transferrin (β2TF), an asialo-transferrin (aTF) biomarker, without interference from serum sialo-transferrin (sTF) in test samples. First, we performed mild periodate oxidation to selectively generate aldehyde groups in sTF for capture with magnetic hydrazide microparticles, and selective removal with a magnetic separator. Using this protocol sTF was selectively removed from mixtures of CSF and serum containing CSF aTF (β2TF) and serum sTF, respectively. Second, a two-step enzymatic method was developed with neuraminidase and galactose oxidase for generating aldehyde groups in sTF present in CSF and serum mixtures for magnetic hydrazide microparticle capture. After selectively removing sTF from mixtures of CSF and serum, ELISA could detect significant TF signal only in CSF, while the TF signal in serum was negligible. The new approach for selective removal of only sTF in test samples will be promising for the required intervention by a spine surgeon. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

COUP-TF (chicken ovalbumin upstream promoter transcription factor)-interacting protein 1 (CTIP1) is a sequence-specific DNA binding protein.

PubMed Central

Avram, Dorina; Fields, Andrew; Senawong, Thanaset; Topark-Ngarm, Acharawan; Leid, Mark

2002-01-01

Chicken ovalbumin upstream promoter transcription factor (COUP-TF)-interacting proteins 1 and 2 [CTIP1/Evi9/B cell leukaemia (Bcl) l1a and CTIP2/Bcl11b respectively] are highly related C(2)H(2) zinc finger proteins that are abundantly expressed in brain and the immune system, and are associated with immune system malignancies. A selection procedure was employed to isolate high-affinity DNA binding sites for CTIP1. The core binding site on DNA identified in these studies, 5'-GGCCGG-3' (upper strand), is highly related to the canonical GC box and was bound by a CTIP1 oligomeric complex(es) in vitro. Furthermore, both CTIP1 and CTIP2 repressed transcription of a reporter gene harbouring a multimerized CTIP binding site, and this repression was neither reversed by trichostatin A (an inhibitor of known class I and II histone deacetylases) nor stimulated by co-transfection of a COUP-TF family member. These results demonstrate that CTIP1 is a sequence-specific DNA binding protein and a bona fide transcriptional repressor that is capable of functioning independently of COUP-TF family members. These findings may be relevant to the physiological and/or pathological action(s) of CTIPs in cells that do not express COUP-TF family members, such as cells of the haematopoietic and immune systems. PMID:12196208

Stable nanoconjugates of transferrin with alloyed quaternary nanocrystals Ag-In-Zn-S as a biological entity for tumor recognition.

PubMed

Matysiak-Brynda, Edyta; Bujak, Piotr; Augustin, Ewa; Kowalczyk, Agata; Mazerska, Zofia; Pron, Adam; Nowicka, Anna M

2018-01-18

One way to limit the negative effects of anti-tumor drugs on healthy cells is targeted therapy employing functionalized drug carriers. Here we present a biocompatible and stable nanoconjugate of transferrin anchored to Ag-In-Zn-S quantum dots modified with 11-mercaptoundecanoic acid (Tf-QD) as a drug carrier versus typical anticancer drug, doxorubicin. Detailed investigations of Tf-QD nanoconjugates without and with doxorubicin by fluorescence studies and cytotoxic measurements showed that the biological activity of both the transferrin and doxorubicin was fully retained in the nanoconjugate. In particular, the intercalation capabilities of free doxorubicin versus ctDNA remained essentially intact upon its binding to the nanoconjugate. In order to evaluate these capabilities, we studied the binding constant of doxorubicin attached to Tf-QDs with ctDNA as well as the binding site size on the ctDNA molecule. The binding constant slightly decreased compared to that of free doxorubicin while the binding site size, describing the number of consecutive DNA lattice residues involved in the binding, increased. It was also demonstrated that the QDs alone and in the form of a nanoconjugate with Tf were not cytotoxic towards human non-small cell lung carcinoma (H460 cell line) and the tumor cell sensitivity of the DOX-Tf-QD nanoconjugate was comparable to that of doxorubicin alone.

Mathematical modeling of mutant transferrin-CRM107 molecular conjugates for cancer therapy.

PubMed

Yoon, Dennis J; Chen, Kevin Y; Lopes, André M; Pan, April A; Shiloach, Joseph; Mason, Anne B; Kamei, Daniel T

2017-03-07

The transferrin (Tf) trafficking pathway is a promising mechanism for use in targeted cancer therapy due to the overexpression of transferrin receptors (TfRs) on cancerous cells. We have previously developed a mathematical model of the Tf/TfR trafficking pathway to improve the efficiency of Tf as a drug carrier. By using diphtheria toxin (DT) as a model toxin, we found that mutating the Tf protein to change its iron release rate improves cellular association and efficacy of the drug. Though this is an improvement upon using wild-type Tf as the targeting ligand, conjugated toxins like DT are unfortunately still highly cytotoxic at off-target sites. In this work, we address this hurdle in cancer research by developing a mathematical model to predict the efficacy and selectivity of Tf conjugates that use an alternative toxin. For this purpose, we have chosen to study a mutant of DT, cross-reacting material 107 (CRM107). First, we developed a mathematical model of the Tf-DT trafficking pathway by extending our Tf/TfR model to include intracellular trafficking via DT and DT receptors. Using this mathematical model, we subsequently investigated the efficacy of several conjugates in cancer cells: DT and CRM107 conjugated to wild-type Tf, as well as to our engineered mutant Tf proteins (K206E/R632A Tf and K206E/R534A Tf). We also investigated the selectivity of mutant Tf-CRM107 against non-neoplastic cells. Through the use of our mathematical model, we predicted that (i) mutant Tf-CRM107 exhibits a greater cytotoxicity than wild-type Tf-CRM107 against cancerous cells, (ii) this improvement was more drastic with CRM107 conjugates than with DT conjugates, and (iii) mutant Tf-CRM107 conjugates were selective against non-neoplastic cells. These predictions were validated with in vitro cytotoxicity experiments, demonstrating that mutant Tf-CRM107 conjugates is indeed a more suitable therapeutic agent. Validation from in vitro experiments also confirmed that such whole-cell kinetic models can be useful in cancer therapeutic design. Copyright © 2017 Elsevier Ltd. All rights reserved.

Preliminary Kalman Filter Design to Improve Air Combat Maneuvering Target Estimation for the F-4E/G Fire Control System.

DTIC Science & Technology

1985-12-01

ADDED TN~*************************** COMMON/AIR/RATE,PHI ,PHIDIT,PP-HI ,PITCH,PITCHD,PPITCHTRATE, 1 TURN,TURND,FPTURNTR1 ,TR2,TR3,TR4, TF1 ,TF2...READ(2,*)ALPHAE’ETA *C READ(2,*)TR1, TF1 !FORWARD ROLL START,STOP TIMES READ(2,*)TR1 , TF1 C READ(2,*)TR2,TF2 !REVERSE ROLL START,STOP TIMES READ(2... TF1 ,TR2, 1 TF2,TR3,TF3,TR4,TF4,HORT1 ,1ORT2,HORTGEIELTA C C INITIALIZE AIRCRAFT MODEL C IA IR=0 CALL AIR C C INITIALIZE RADAR MODEL -- C I RADAR=O CALL

Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF.

PubMed

Cong, Yingnan; Chan, Yao-Ban; Phillips, Charles A; Langston, Michael A; Ragan, Mark A

2017-01-01

Bacteria and archaea can exchange genetic material across lineages through processes of lateral genetic transfer (LGT). Collectively, these exchange relationships can be modeled as a network and analyzed using concepts from graph theory. In particular, densely connected regions within an LGT network have been defined as genetic exchange communities (GECs). However, it has been problematic to construct networks in which edges solely represent LGT. Here we apply term frequency-inverse document frequency (TF-IDF), an alignment-free method originating from document analysis, to infer regions of lateral origin in bacterial genomes. We examine four empirical datasets of different size (number of genomes) and phyletic breadth, varying a key parameter (word length k ) within bounds established in previous work. We map the inferred lateral regions to genes in recipient genomes, and construct networks in which the nodes are groups of genomes, and the edges natively represent LGT. We then extract maximum and maximal cliques (i.e., GECs) from these graphs, and identify nodes that belong to GECs across a wide range of k . Most surviving lateral transfer has happened within these GECs. Using Gene Ontology enrichment tests we demonstrate that biological processes associated with metabolism, regulation and transport are often over-represented among the genes affected by LGT within these communities. These enrichments are largely robust to change of k .

Transcription Factor Networks Directing the Development, Function, and Evolution of Innate Lymphoid Effectors

PubMed Central

Kang, Joonsoo; Malhotra, Nidhi

2015-01-01

Mammalian lymphoid immunity is mediated by fast and slow responders to pathogens. Fast innate lymphocytes are active within hours after infections in mucosal tissues. Slow adaptive lymphocytes are conventional T and B cells with clonal antigen receptors that function days after pathogen exposure. A transcription factor (TF) regulatory network guiding early T cell development is at the core of effector function diversification in all innate lymphocytes, and the kinetics of immune responses is set by developmental programming. Operational units within the innate lymphoid system are not classified by the types of pathogen-sensing machineries but rather by discrete effector functions programmed by regulatory TF networks. Based on the evolutionary history of TFs of the regulatory networks, fast effectors likely arose earlier in the evolution of animals to fortify body barriers, and in mammals they often develop in fetal ontogeny prior to the establishment of fully competent adaptive immunity. PMID:25650177

Amniotic fluid: Source of trophic factors for the developing intestine

PubMed Central

Dasgupta, Soham; Arya, Shreyas; Choudhary, Sanjeev; Jain, Sunil K

2016-01-01

The gastrointestinal tract (GIT) is a complex system, which changes in response to requirements of the body. GIT represents a barrier to the external environment. To achieve this, epithelial cells must renew rapidly. This renewal of epithelial cells starts in the fetal life under the influence of many GIT peptides by swallowing amniotic fluid (AF). Development and maturation of GIT is a very complex cascade that begins long before birth and continues during infancy and childhood by breast-feeding. Many factors like genetic preprogramming, local and systemic endocrine secretions and many trophic factors (TF) from swallowed AF contribute and modulate the development and growth of the GIT. GIT morphogenesis, differentiation and functional development depend on the activity of various TF in the AF. This manuscript will review the role of AF borne TF in the development of GIT. PMID:26909227

Supervised dictionary learning for inferring concurrent brain networks.

PubMed

Zhao, Shijie; Han, Junwei; Lv, Jinglei; Jiang, Xi; Hu, Xintao; Zhao, Yu; Ge, Bao; Guo, Lei; Liu, Tianming

2015-10-01

Task-based fMRI (tfMRI) has been widely used to explore functional brain networks via predefined stimulus paradigm in the fMRI scan. Traditionally, the general linear model (GLM) has been a dominant approach to detect task-evoked networks. However, GLM focuses on task-evoked or event-evoked brain responses and possibly ignores the intrinsic brain functions. In comparison, dictionary learning and sparse coding methods have attracted much attention recently, and these methods have shown the promise of automatically and systematically decomposing fMRI signals into meaningful task-evoked and intrinsic concurrent networks. Nevertheless, two notable limitations of current data-driven dictionary learning method are that the prior knowledge of task paradigm is not sufficiently utilized and that the establishment of correspondences among dictionary atoms in different brains have been challenging. In this paper, we propose a novel supervised dictionary learning and sparse coding method for inferring functional networks from tfMRI data, which takes both of the advantages of model-driven method and data-driven method. The basic idea is to fix the task stimulus curves as predefined model-driven dictionary atoms and only optimize the other portion of data-driven dictionary atoms. Application of this novel methodology on the publicly available human connectome project (HCP) tfMRI datasets has achieved promising results.

[Nutrient Characteristics and Nitrogen Forms of Rhizosphere Soils Under Four Typical Plants in the Littoral Zone of TGR].

PubMed

Wang, Xiao-feng; Yuan, Xing-zhong; Liu, Hong; Zhang, Lei; Yu, Jian-jun; Yue, Jun-sheng

2015-10-01

The Three Gorges Reservoir (TGR), which is the largest water conservancy project ever built in tne world, produced a drawdown area of about 348.93 km2 because of water level control. The biological geochemical cycle of the soil in the drawdown zone has been changed as the result of long-term winter flooding and summer drought and vegetation covering. The loss of soil nitrogen in the drawdown zone poses a threat to the water environmental in TGR. Pengxi river, is an important anabranch, which has the largest drawdown area has been selected in the present study. The four typical vegetation, contained Cynodon dactylon, Cyperus rotundus, Anthium sibiricum and Zea mays L. as the control, were studied to measure nutrient characteristics and nitrogen forms of rhizosphere and non-rhizosphere soils in three distribution areas with different soil types (paddy soil, purple soil and fluvo-aquic soils). The variables measured included organic matter (OM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), hydrolysis N, available P and available K, pH, ion-exchangeable N (IEE-N), weak acid extractable N (CF-N) , iron-manganese oxides N (IMOF-N), organic matter sulfide N (OSF-N), added up four N forms for total transferable N (TF-N) and TN minus TF-N for non-transferable N (NTF-N). The results showed: (1) pH of rhizosphere soil was generally lower than that of non-rhizosphere soil under different vegetation in different type soils because the possible organic acid and H+ released form plant roots and cation absorption differences, and the OM, TP, TN and hydrolysis N of rhizosphere soil were generally higher than those of non-rhizosphere soil, and that the enrichment ratio (ER) of all the four nutrient indicators showed Cyperus rotundus > Cynodon dactylon > Zea mays L. > Anthium sibiricum. Available P showed enrichment in the rhizosphere of three natural vegetations but lose under corn, and available K, TK showed different ER in different conditions. (2) IEF-N CF-N, IMOF-N, OSF-N and TF-N of rhizosphere soil were generally higher than those of non-rhizosphere soil, but the TF-N to TN ratio in rhizosphere of Cyperus rotundus and Cynodon dactylon were lower than those of non-rhizosphere soil, and in rhizosphere of Anthium sibiricum and Zea mays L. were higher, the rhizosphere effect of different vegetations on the N cycle was significant difference. (3) the correlation between nutrient characteristics and nitrogen forms was evaluated to explore the influence factor for the N forms changing. There was a significant correlation between soil OM and four N forms, TP was significantly correlated with CF-N, OSF-N, TF-N, and soil available P content was significantly negatively correlated with IMOF-N, OSF-N, TF-N and TN. Our research could provide that the drawdown zone covered with Cyperus rotundus and Cynodon dactylon was better than Anthium sibiricum and Zea mays L. to improve soil N holding and fixation. The vegetation recovery in the drawdown zone should consider the rhizosphere effect of different vegetations on N cycle.

Antigen targeting to antigen-presenting cells enhances presentation to class II-restricted T lymphocytes.

PubMed Central

Scardino, A; Paroli, M; De Petrillo, G; Michel, M L; Barnaba, V

1994-01-01

Receptor-mediated uptake increases by several orders of magnitude the efficiency of APC to internalize Ag, and is stringently required for the Ag-presenting function of T lymphocytes due to their inability to take up Ag non-specifically. We have previously reported that hepatitis B envelope antigen (HBenvAg) can be internalized by T cells via transferrin receptor (TfR). To evaluate if Ag targeting to receptors expressed on APC could be an effective tool for promoting Ag uptake and presentation, we tested the capacity of activated T cells not expressing TfR to induce HBenvAg-specific T-cell responses when pulsed with a hybrid particle containing HBenvAg coupled to gp120 of human immunodeficiency virus (HIV), exploiting the ability of gp120 to bind to CD4 receptor. We found that CD4+/TfR- T cells pulsed either with the hybrid particle or peptide (S193-207) but not with S, L Ag, a recombinant form of HBenvAg, induced a specific proliferative response of a T-cell clone recognizing peptide (S193-207) of HBenvAg. The finding that the addition of anti-CD4 monoclonal antibody (mAb) before the pulsing of CD4+/TfR- T cells with the hybrid particle drastically blocked the specific T-cell response, together with the finding that CD8+/TfR- T cells were unable to serve as APC even if pulsed with this molecule, demonstrated that CD4 receptor was crucial for the HBenvAg internalization. On the other hand, HBenvAg presentation by CD4+/TfR+ T cells pulsed with the hybrid particle was inhibited only when both anti-CD4 and anti-TfR were added before the pulsing. These results suggest that Ag targeting to APC receptors may be usefully exploited to improve Ag-presentation efficiency in potential immunotherapeutic approaches. PMID:7907575

Hemoglobin enhances tissue factor expression on human malignant cells.

PubMed

Siddiqui, F A; Amirkhosravi, A; Amaya, M; Meyer, T; Biggerstaff, J; Desai, H; Francis, J L

2001-04-01

Tissue Factor (TF) is a transmembrane glycoprotein that complexes with factor VII/activated factor VII to initiate blood coagulation. TF may be expressed on the surface of various cells including monocytes and endothelial cells. Over-expression of TF in human tumor cell lines promotes metastasis. We recently showed that hemoglobin (Hb) forms a specific complex with TF purified from human malignant melanoma cells and enhances its procoagulant activity (PCA). To further study this interaction, we examined the effect of Hb on the expression of TF on human malignant (TF+) cells and KG1 myeloid leukemia (TF-) cells. Human melanoma A375 and J82 bladder carcinoma cells, which express TF at moderate and relatively high levels, respectively, were incubated with varying concentrations (0-1.5 mg/ml) of Hb. After washing, cells were analyzed for Hb binding and TF expression using flow cytometry and confocal microscopy. Hb bound to the cells in a concentration-dependent manner, and increased both TF expression and PCA. The human A375 malignant melanoma cells incubated with Hb (1 mg/ml) expressed up to six times more TF antigen than cells without Hb. This increase in TF expression and PCA of intact cells incubated with Hb was significantly inhibited by cycloheximide at a concentration of 10 microg/ml (P < 0.01). An increase in total cellular TF antigen content was demonstrated by specific immunoassay. In contrast, Hb (5 mg/ml) did not induce TF expression and PCA on KG1 cells as determined by flow cytometry and TF (FXAA) activity. We conclude that Hb specifically binds to TF-bearing malignant cells and increases their PCA. This effect seems to be at least partly due to de novo synthesis of TF and increased surface expression. However, the exact mechanism by which Hb binds and upregulates TF expression remains to be determined.

Electromagnetic Launching for Affordable Agile Access to Space

DTIC Science & Technology

2006-04-15

requirements are advantageous compared to other EM launch technologies. 14 I Pp TRI TF1 (P) TR2 TF2 (P) ... TRM TFM (P) TF1 TRI(n) TF2 TH .)񔰣 -n F- on 71...some integer M. The distance between the rear coil TRI and the corresponding front coil TF1 is MxPT. PP: distance between coils in the projectile, PT...TRI with TFI/p), TR2 with TF2(P) ..., and also TR/("),with TF1 , TR2(n)with TF2, etc. ). * For a slender projectile (i.e. length >> diameter), it is

Report of the Secretary of Defense Task Force on DoD Nuclear Weapons Management. Phase 1. The Air Force’s Nuclear Mission

DTIC Science & Technology

2008-09-01

under- resourced. • Missile transfer vans /warhead transfer vans require upgrades. • ICBM weapon system test sets under-funded; the coding system...Air Force’s Nuclear Mission D-1 Appendix D. Current B-52 Basing Status Barksdale AFB, LA 64 B-52Hs Minot AFB, ND 27 B-52Hs Edwards AFB, CA 3...Barksdale – 64 B-52s 2 BW (ACC) 15 TF; 24 CC; 7 BAI 53 WG (ACC) 2 Test Coded 917 WG (AFRC) 8 CC; 1 BAI 7 Unfunded AR Edwards - 3 B-52s 412 TW 2 Test

Mutation in Torenia fournieri Lind. UFO homolog confers loss of TfLFY interaction and results in a petal to sepal transformation.

PubMed

Sasaki, Katsutomo; Yamaguchi, Hiroyasu; Aida, Ryutaro; Shikata, Masahito; Abe, Tomoko; Ohtsubo, Norihiro

2012-09-01

We identified a Torenia fournieri Lind. mutant (no. 252) that exhibited a sepaloid phenotype in which the second whorls were changed to sepal-like organs. This mutant had no stamens, and the floral organs consisted of sepals and carpels. Although the expression of a torenia class B MADS-box gene, GLOBOSA (TfGLO), was abolished in the 252 mutant, no mutation of TfGLO was found. Among torenia homologs such as APETALA1 (AP1), LEAFY (LFY), and UNUSUAL FLORAL ORGANS (UFO), which regulate expression of class B genes in Arabidopsis, only accumulation of the TfUFO transcript was diminished in the 252 mutant. Furthermore, a missense mutation was found in the coding region of the mutant TfUFO. Intact TfUFO complemented the mutant phenotype whereas mutated TfUFO did not; in addition, the transgenic phenotype of TfUFO-knockdown torenias coincided with the mutant phenotype. Yeast two-hybrid analysis revealed that the mutated TfUFO lost its ability to interact with TfLFY protein. In situ hybridization analysis indicated that the transcripts of TfUFO and TfLFY were partially accumulated in the same region. These results clearly demonstrate that the defect in TfUFO caused the sepaloid phenotype in the 252 mutant due to the loss of interaction with TfLFY. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

Comparative Analysis of Ultrasonic Inspection Procedures for Kaman K747 Root End Fittings

DTIC Science & Technology

1989-04-01

I.CI- IA 4cz 4c-- a- LLJ 4A ccu I46 APPENDIX III. TRANSDUCER WEDGE ANGLE DATA RESULTS No Procedure, Gain = 70 dB 45.Degre Probe REF# TF1 TF2 TF3 TAl...Degree Probe REF # TF1 TF2 TF3 TAl TA2 TA3 BF1 BF2 BF3 BAl BA2 BA3 B5328 35 33 -. . . 31 - - - - - 38 38 B5102 38 - 31 .. - - 31 - - - B5298 40 42...50 No Procedure, Gain = 70 dB 50-Degree Probe REF # TF1 TF2 TF3 TAl TA2 TA3 BF1 BF2 BF3 BAl BA2 BA3 B5328 - . . . . 32 - 40 B5102 34 .- 30

Optimum Design Methods for Structural Sandwich Panels

DTIC Science & Technology

1989-02-01

B)*ROS TF1 -STRE?4*SS**2/(Cl(CONFI)*AFA*(ROCl/ROS)**(2*A/3. )*TCI) Wlm(2* TF1 *WS*SS*ROF+TCi*WS*SS*ROCI)/1728000. IF (W1.LT.WEIGHT) THEN TF- TF1 TC-TC1...B)*ROS W1-(2* TF1 *WS*SS*ROF+TC1*WS*SS*RoC1)/172800O. IF (WI.LT.WEIGHT) THEN TF- TF1 TC-TC1 ROC-ROC1 WEIGHT-Wi FAIL-3 END IF END IF WRITE(*, 260)TC,TF...8217THE PROGRAM IS RUNNING. PL.EASE WAIT!’ DO 273 1-1,999 * TCl-P*SS/(C1 lrONFI)*YF*WS*TFI) COEFF-C5 (CONFI )*EF*P*SS* TF1 *TC1/ (CG*C6 (CONFI ) *E) COEFF

The Long Terminal Repeat Retrotransposons Tf1 and Tf2 of Schizosaccharomyces pombe.

PubMed

Esnault, Caroline; Levin, Henry L

2015-08-01

The long terminal repeat (LTR) retrotransposons Tf1 and Tf2 of Schizosaccharomyces pombe are active mobile elements of the Ty3/gypsy family. The mobilization of these retrotransposons depends on particle formation, reverse transcription and integration, processes typical of other LTR retrotransposons. However, Tf1 and Tf2 are distinct from other LTR elements in that they assemble virus-like particles from a single primary translation product, initiate reverse transcription with an unusual self-priming mechanism, and, in the case of Tf1, integrate with a pattern that favors specific promoters of RNA pol II-transcribed genes. To avoid the chromosome instability and genome damage that results from increased copy number, S. pombe applies a variety of defense mechanisms that restrict Tf1 and Tf2 activity. The mRNA of the Tf elements is eliminated by an exosome-based pathway when cells are in favorable conditions whereas nutrient deprivation triggers an RNA interference-dependent pathway that results in the heterochromatization of the elements. Interestingly, Tf1 integrates into the promoters of stress-induced genes and these insertions are capable of increasing the expression of adjacent genes. These properties of Tf1 transposition raise the possibility that Tf1 benefits cells with specific insertions by providing resistance to environmental stress.

Insulin-regulated Glut4 Translocation

PubMed Central

Brewer, Paul Duffield; Habtemichael, Estifanos N.; Romenskaia, Irina; Mastick, Cynthia Corley; Coster, Adelle C. F.

2014-01-01

The trafficking kinetics of Glut4, the transferrin (Tf) receptor, and LRP1 were quantified in adipocytes and undifferentiated fibroblasts. Six steps were identified that determine steady state cell surface Glut4: (i) endocytosis, (ii) degradation, (iii) sorting, (iv) sequestration, (v) release, and (vi) tethering/docking/fusion. Endocytosis of Glut4 is 3 times slower than the Tf receptor in fibroblasts (ken = 0.2 min−1 versus 0.6 min−1). Differentiation decreases Glut4 ken 40% (ken = 0.12 min−1). Differentiation also decreases Glut4 degradation, increasing total and cell surface Glut4 3-fold. In fibroblasts, Glut4 is recycled from endosomes through a slow constitutive pathway (kex = 0.025–0.038 min−1), not through the fast Tf receptor pathway (kex = 0.2 min−1). The kex measured in adipocytes after insulin stimulation is similar (kex = 0.027 min−1). Differentiation decreases the rate constant for sorting into the Glut4 recycling pathway (ksort) 3-fold. In adipocytes, Glut4 is also sorted from endosomes into a second exocytic pathway through Glut4 storage vesicles (GSVs). Surprisingly, transfer from endosomes into GSVs is highly regulated; insulin increases the rate constant for sequestration (kseq) 8-fold. Release from sequestration in GSVs is rate-limiting for Glut4 exocytosis in basal adipocytes. AS160 regulates this step. Tethering/docking/fusion of GSVs to the plasma membrane is regulated through an AS160-independent process. Insulin increases the rate of release and fusion of GSVs (kfuseG) 40-fold. LRP1 cycles with the Tf receptor and Glut4 in fibroblasts but predominantly with Glut4 after differentiation. Surprisingly, AS160 knockdown accelerated LRP1 exocytosis in basal and insulin-stimulated adipocytes. These data indicate that AS160 may regulate trafficking into as well as release from GSVs. PMID:24778187

Host factors that promote retrotransposon integration are similar in distantly related eukaryotes

PubMed Central

Rai, Sudhir Kumar; Sangesland, Maya; Lee, Michael; Esnault, Caroline; Cui, Yujin; Chatterjee, Atreyi Ghatak

2017-01-01

Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements. PMID:29232693

Host factors that promote retrotransposon integration are similar in distantly related eukaryotes.

PubMed

Rai, Sudhir Kumar; Sangesland, Maya; Lee, Michael; Esnault, Caroline; Cui, Yujin; Chatterjee, Atreyi Ghatak; Levin, Henry L

2017-12-01

Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements.

Decay of random correlation functions for unimodal maps

NASA Astrophysics Data System (ADS)

Baladi, Viviane; Benedicks, Michael; Maume-Deschamps, Véronique

2000-10-01

Since the pioneering results of Jakobson and subsequent work by Benedicks-Carleson and others, it is known that quadratic maps tfa( χ) = a - χ2 admit a unique absolutely continuous invariant measure for a positive measure set of parameters a. For topologically mixing tfa, Young and Keller-Nowicki independently proved exponential decay of correlation functions for this a.c.i.m. and smooth observables. We consider random compositions of small perturbations tf + ωt, with tf = tfa or another unimodal map satisfying certain nonuniform hyperbolicity axioms, and ωt chosen independently and identically in [-ɛ, ɛ]. Baladi-Viana showed exponential mixing of the associated Markov chain, i.e., averaging over all random itineraries. We obtain stretched exponential bounds for the random correlation functions of Lipschitz observables for the sample measure μωof almost every itinerary.

The aesthetic impact of enamel fluorosis on Irish adolescents.

PubMed

Browne, Deirdre; Whelton, Helen; O'Mullane, Denis; Tavener, Jacqueline; Flannery, Edel

2011-04-01

To assess the impact of differing degrees of enamel fluorosis on dental aesthetics according to Irish adolescents. The same participants also aesthetically rated other variations in dental appearances including a carious lesion, bleached teeth and a demarcated opacity. One hundred and fifty adolescents examined seven identical template photographs of an attractive dental smile displaying varying levels of enamel fluorosis (TF1, TF2, TF3), a demarcated opacity, no fluorosis (TF0), anterior caries and very white or bleached teeth. By indicating their level of agreement or disagreement with five statements on a five-point Likert scale, the participants rated the aesthetic acceptability of each of the photographs. Using paired t-tests with the Bonferroni correction, it was found that the photographs depicting the very white teeth and anterior caries were rated as the most and least aesthetically pleasing images, respectively. There was no significant difference in the ratings of the photographs displaying TF0, TF1 and TF2 levels of fluorosis indicating that these photographs were viewed similarly (P>0.002). The remaining two photographs (TF3 and the demarcated opacity) were rated similarly and significantly worse (P<0.002) than the photographs showing no or low grades of fluorosis (TF0, TF1 and TF2). TF3 level of fluorosis represented the break point at which enamel fluorosis became aesthetically objectionable to these participants. Low grades of fluorosis (TF1 and TF2) were rated similarly to the photograph depicting no fluorosis (TF0). © 2011 John Wiley & Sons A/S.

Image Quality and Diagnostic Performance of a Digital PET Prototype in Patients with Oncologic Diseases: Initial Experience and Comparison with Analog PET.

PubMed

Nguyen, Nghi C; Vercher-Conejero, Jose L; Sattar, Abdus; Miller, Michael A; Maniawski, Piotr J; Jordan, David W; Muzic, Raymond F; Su, Kuan-Hao; O'Donnell, James K; Faulhaber, Peter F

2015-09-01

We report our initial clinical experience for image quality and diagnostic performance of a digital PET prototype scanner with time-of-flight (DigitalTF), compared with an analog PET scanner with time-of-flight (GeminiTF PET/CT). Twenty-one oncologic patients, mean age 58 y, first underwent clinical (18)F-FDG PET/CT on the GeminiTF. The scanner table was then withdrawn while the patient remained on the table, and the DigitalTF was inserted between the GeminiTF PET and CT scanner. The patients were scanned for a second time using the same PET field of view with CT from the GeminiTF for attenuation correction. Two interpreters reviewed the 2 sets of PET/CT images for overall image quality, lesion conspicuity, and sharpness. They counted the number of suggestive (18)F-FDG-avid lesions and provided the TNM staging for the 5 patients referred for initial staging. Standardized uptake values (SUVs) and SUV gradients as a measure of lesion sharpness were obtained. The DigitalTF showed better image quality than the GeminiTF. In a side-by-side comparison using a 5-point scale, lesion conspicuity (4.3 ± 0.6), lesion sharpness (4.3 ± 0.6), and diagnostic confidence (3.4 ± 0.7) were better with DigitalTF than with GeminiTF (P < 0.01). In 52 representative lesions, the lesion maximum SUV was 36% higher with DigitalTF than with GeminiTF, lesion-to-blood-pool SUV ratio was 59% higher, and SUV gradient was 51% higher, with good correlation between the 2 scanners. Lesions less than 1.5 cm showed a greater increase in SUV from GeminiTF to DigitalTF than those lesions 1.5 cm or greater. In 5 of 21 patients, DigitalTF showed an additional 8 suggestive lesions that were not seen using GeminiTF. In the 15 restaging patients, the true-negative rate was 100% and true-positive rate was 78% for both scanners. In the 5 patients for initial staging, DigitalTF led to upstaging in 2 patients and showed the same staging in the other 3 patients, compared with GeminiTF. DigitalTF provides better image quality, diagnostic confidence, and accuracy than GeminiTF. DigitalTF may be the most beneficial in detecting small tumor lesions and disease staging. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Thyroid hormone and COUP-TF1 regulate kallikrein-binding protein (KBP) gene expression.

PubMed

Liu, Yan-Yun; Nakatani, Teruyo; Kogai, Takahiko; Mody, Kaizeen; Brent, Gregory A

2011-03-01

Kallikrein-binding protein (KBP) is a component of the kallikrein-kinin system that mediates vasodilation and inhibits tumor growth by antagonizing vascular endothelial growth factor-mediated angiogenesis. We demonstrate that KBP gene expression is repressed by T(3) and modulated by the orphan nuclear receptor, chicken ovalbumin upstream promoter transcription factor 1 (COUP-TF1). In hypothyroid mice, KBP mRNA expression in the testis was increased 2.1-fold compared with euthyroid mice. We have identified two negative thyroid hormone response elements (nTREs) in the mouse KBP gene, nTRE1 located in the 5' flanking region (-53 to -29) and nTRE2, located in the first intron (104-132). We used functional assays, cofactor knockdown, and chromatin immunoprecipitation assays to characterize nTRE1 and nTRE2 in hepatic (HepG2) and testes (GC-1spg) cell lines. Reporter expression directed by both elements was enhanced with addition of thyroid hormone receptor and repressed with the addition of T(3). COUP-TF1 enhanced basal expression of both elements but blunted unliganded thyroid hormone receptor enhancement and T(3) repression of nTRE1 but not nTRE2. Both nTREs bound nuclear corepressor and binding increased in response to T(3). Nuclear corepressor knockdown resulted in loss of T(3) repression of both nTRE1 and nTRE2. COUP-TF1, which usually represses T(3) induction of positive thyroid hormone response elements, reverses T(3) repression mediated by nTRE1 in the mouse KBP gene. Endogenous KBP expression is repressed by T(3) and two functional nTREs, both of which are required, have been characterized in the KBP gene. COUP-TF1 may be an important factor to modulate expression of genes that are repressed by T(3).

Thyroid Hormone and COUP-TF1 Regulate Kallikrein-Binding Protein (KBP) Gene Expression

PubMed Central

Liu, Yan-Yun; Nakatani, Teruyo; Kogai, Takahiko; Mody, Kaizeen

2011-01-01

Kallikrein-binding protein (KBP) is a component of the kallikrein-kinin system that mediates vasodilation and inhibits tumor growth by antagonizing vascular endothelial growth factor-mediated angiogenesis. We demonstrate that KBP gene expression is repressed by T3 and modulated by the orphan nuclear receptor, chicken ovalbumin upstream promoter transcription factor 1 (COUP-TF1). In hypothyroid mice, KBP mRNA expression in the testis was increased 2.1-fold compared with euthyroid mice. We have identified two negative thyroid hormone response elements (nTREs) in the mouse KBP gene, nTRE1 located in the 5′ flanking region (−53 to −29) and nTRE2, located in the first intron (104–132). We used functional assays, cofactor knockdown, and chromatin immunoprecipitation assays to characterize nTRE1 and nTRE2 in hepatic (HepG2) and testes (GC-1spg) cell lines. Reporter expression directed by both elements was enhanced with addition of thyroid hormone receptor and repressed with the addition of T3. COUP-TF1 enhanced basal expression of both elements but blunted unliganded thyroid hormone receptor enhancement and T3 repression of nTRE1 but not nTRE2. Both nTREs bound nuclear corepressor and binding increased in response to T3. Nuclear corepressor knockdown resulted in loss of T3 repression of both nTRE1 and nTRE2. COUP-TF1, which usually represses T3 induction of positive thyroid hormone response elements, reverses T3 repression mediated by nTRE1 in the mouse KBP gene. Endogenous KBP expression is repressed by T3 and two functional nTREs, both of which are required, have been characterized in the KBP gene. COUP-TF1 may be an important factor to modulate expression of genes that are repressed by T3. PMID:21266512

Relationship between rabbit transferrin electrophoretic patterns and plasma iron concentrations.

PubMed

Zaragoza, P; Arana, A; Amorena, B

1987-01-01

Rabbit transferrin (Tf) was studied electrophoretically using 1141 blood samples from individuals belonging to seven populations (Spanish Common, Spanish Giant, Butterfly, Lyoné de Bourgogne, New Zealand White, Californian and New Zealand White X Californian hybrids). No Tf polymorphism was found by starch gel electrophoresis, but six patterns, differing in the presence and/or intensity of three bands ('a', anodic; 'b', intermediate; and 'c', cathodic) were observed by polyacrylamide gel electrophoresis. No genetic model could explain these patterns, since they reflect differences in plasma Tf iron content. The electrophoretic test allowed a direct observation of the relative in vivo levels of the different Tf molecular species; saturated (band 'a', Fe2Tf); semi-saturated (band 'b', Fe1Tf); and without iron (band 'c' Fe0Tf, apotransferrin). The degree of iron saturation of Tf varied among individuals and throughout the individual's life. Specifically, in pregnant females, Fe2Tf and Fe1Tf are generally observed, except in late pregnancy (from day 25 to parturition), when mainly apotransferrin is observed. Significantly, within 24 h post-partum, high levels of Fe2Tf are reached in the female's serum.

USF-related transcription factor, HIV-TF1, stimulates transcription of human immunodeficiency virus-1.

PubMed

Maekawa, T; Sudo, T; Kurimoto, M; Ishii, S

1991-09-11

The transcription factor HIV-TF1, which binds to a region about 60 bp upstream from the enhancer of the human immunodeficiency virus-1 (HIV-1), was purified from human B cells. HIV-TF1 had a molecular weight of 39,000. Binding of HIV-TF1 to the HIV long terminal repeat (LTR) activated transcription from the HIV promoter in vitro. The HIV-TF1-binding site in HIV LTR was similar to the site recognized by upstream stimulatory factor (USF) in the adenovirus major late promoter. DNA-binding properties of HIV-TF1 suggested that HIV-TF1 might be identical or related to USF. Interestingly, treatment of purified HIV-TF1 by phosphatase greatly reduced its DNA-binding activity, suggesting that phosphorylation of HIV-TF1 was essential for DNA binding. The disruption of HIV-TF1-binding site induced a 60% decrease in the level of transcription from the HIV promoter in vivo. These results suggest that HIV-TF1 is involved in transcriptional regulation of HIV-1.

Ionic residues of human serum transferrin affect binding to the transferrin receptor and iron release.

PubMed

Steere, Ashley N; Miller, Brendan F; Roberts, Samantha E; Byrne, Shaina L; Chasteen, N Dennis; Smith, Valerie C; MacGillivray, Ross T A; Mason, Anne B

2012-01-17

Efficient delivery of iron is critically dependent on the binding of diferric human serum transferrin (hTF) to its specific receptor (TFR) on the surface of actively dividing cells. Internalization of the complex into an endosome precedes iron removal. The return of hTF to the blood to continue the iron delivery cycle relies on the maintenance of the interaction between apohTF and the TFR after exposure to endosomal pH (≤6.0). Identification of the specific residues accounting for the pH-sensitive nanomolar affinity with which hTF binds to TFR throughout the cycle is important to fully understand the iron delivery process. Alanine substitution of 11 charged hTF residues identified by available structures and modeling studies allowed evaluation of the role of each in (1) binding of hTF to the TFR and (2) TFR-mediated iron release. Six hTF mutants (R50A, R352A, D356A, E357A, E367A, and K511A) competed poorly with biotinylated diferric hTF for binding to TFR. In particular, we show that Asp356 in the C-lobe of hTF is essential to the formation of a stable hTF-TFR complex: mutation of Asp356 in the monoferric C-lobe hTF background prevented the formation of the stoichiometric 2:2 (hTF:TFR monomer) complex. Moreover, mutation of three residues (Asp356, Glu367, and Lys511), whether in the diferric or monoferric C-lobe hTF, significantly affected iron release when in complex with the TFR. Thus, mutagenesis of charged hTF residues has allowed identification of a number of residues that are critical to formation of and release of iron from the hTF-TFR complex.

Regulatory mechanisms for iron transport across the blood-brain barrier.

PubMed

Duck, Kari A; Simpson, Ian A; Connor, James R

2017-12-09

Many critical metabolic functions in the brain require adequate and timely delivery of iron. However, most studies when considering brain iron uptake have ignored the iron requirements of the endothelial cells that form the blood-brain barrier (BBB). Moreover, current models of BBB iron transport do not address regional regulation of brain iron uptake or how neurons, when adapting to metabolic demands, can acquire more iron. In this study, we demonstrate that both iron-poor transferrin (apo-Tf) and the iron chelator, deferoxamine, stimulate release of iron from iron-loaded endothelial cells in an in vitro BBB model. The role of the endosomal divalent metal transporter 1 (DMT1) in BBB iron acquisition and transport has been questioned. Here, we show that inhibition of DMT1 alters the transport of iron and Tf across the endothelial cells. These data support an endosome-mediated model of Tf-bound iron uptake into the brain and identifies mechanisms for local regional regulation of brain iron uptake. Moreover, our data provide an explanation for the disparity in the ratio of Tf to iron transport into the brain that has confounded the field. Copyright © 2017 Elsevier Inc. All rights reserved.

Survey of protein–DNA interactions in Aspergillus oryzae on a genomic scale

PubMed Central

Wang, Chao; Lv, Yangyong; Wang, Bin; Yin, Chao; Lin, Ying; Pan, Li

2015-01-01

The genome-scale delineation of in vivo protein–DNA interactions is key to understanding genome function. Only ∼5% of transcription factors (TFs) in the Aspergillus genus have been identified using traditional methods. Although the Aspergillus oryzae genome contains >600 TFs, knowledge of the in vivo genome-wide TF-binding sites (TFBSs) in aspergilli remains limited because of the lack of high-quality antibodies. We investigated the landscape of in vivo protein–DNA interactions across the A. oryzae genome through coupling the DNase I digestion of intact nuclei with massively parallel sequencing and the analysis of cleavage patterns in protein–DNA interactions at single-nucleotide resolution. The resulting map identified overrepresented de novo TF-binding motifs from genomic footprints, and provided the detailed chromatin remodeling patterns and the distribution of digital footprints near transcription start sites. The TFBSs of 19 known Aspergillus TFs were also identified based on DNase I digestion data surrounding potential binding sites in conjunction with TF binding specificity information. We observed that the cleavage patterns of TFBSs were dependent on the orientation of TF motifs and independent of strand orientation, consistent with the DNA shape features of binding motifs with flanking sequences. PMID:25883143

The pig CYP2E1 promoter is activated by COUP-TF1 and HNF-1 and is inhibited by androstenone.

PubMed

Tambyrajah, Winston S; Doran, Elena; Wood, Jeffrey D; McGivan, John D

2004-11-15

Functional analysis of the pig cytochrome P4502E1 (CYP2E1) promoter identified two major activating elements. One corresponded to the hepatic nuclear factor 1 (HNF-1) consensus binding sequence at nucleotides -128/-98 and the other was located in the region -292/-266. The binding of proteins in pig liver nuclear extracts to a synthetic double-stranded oligonucleotide corresponding to this more distal activating sequence was studied by electrophoretic mobility shift assay. The minimum protein binding sequence was identified as TGTTCTGACCTCTGGG. Gel super-shift assays identified the protein binding to this site as chick ovalbumin upstream promoter transcription factor 1 (COUP-TF1). Androstenone inhibited promoter activity in transfection experiments only with constructs which included the COUP-TF1 binding site. Androstenone inhibited COUP-TF1 binding to synthetic oligonucleotides but did not affect HNF-1 binding. The results offer an explanation for the inhibition of CYP2E1 protein expression by androstenone in isolated pig hepatocytes and may be relevant to the low expression of hepatic CYP2E1 in those pigs which accumulate high levels of androstenone in vivo.

Lentiviral Nef suppresses iron uptake in a strain specific manner through inhibition of Transferrin endocytosis

PubMed Central

2014-01-01

Background Increased cellular iron levels are associated with high mortality in HIV-1 infection. Moreover iron is an important cofactor for viral replication, raising the question whether highly divergent lentiviruses actively modulate iron homeostasis. Here, we evaluated the effect on cellular iron uptake upon expression of the accessory protein Nef from different lentiviral strains. Results Surface Transferrin receptor (TfR) levels are unaffected by Nef proteins of HIV-1 and its simian precursors but elevated in cells expressing Nefs from most other primate lentiviruses due to reduced TfR internalization. The SIV Nef-mediated reduction of TfR endocytosis is dependent on an N-terminal AP2 binding motif that is not required for downmodulation of CD4, CD28, CD3 or MHCI. Importantly, SIV Nef-induced inhibition of TfR endocytosis leads to the reduction of Transferrin uptake and intracellular iron concentration and is accompanied by attenuated lentiviral replication in macrophages. Conclusion Inhibition of Transferrin and thereby iron uptake by SIV Nef might limit viral replication in myeloid cells. Furthermore, this new SIV Nef function could represent a virus-host adaptation that evolved in natural SIV-infected monkeys. PMID:24383984

Radiation hardness of lead glasses TF1 and TF101

NASA Astrophysics Data System (ADS)

Kobayashi, Masaaki; Prokoshkin, Yuri; Singovsky, Alexandre; Takamatsu, Kunio

1994-06-01

We have measured the radiation hardness of two types of lead glasses, TF1 and TF101, for low energy γ-rays from 60Co. TF101 containing cerium is a few tens times radiation harder than TF1 which contains no cerium. The radiation hardness, or the tolerable accumulated dose, of TF101 is 2 × 10 3 rad when the degradation of the transmittance is required to be less than 1% for the unit radiation length X0 = 2.8 cm. When the present result is compared with the work of Inyakin et al., the radiation hardness of TF101 glass should be similar for both γ-rays and for high energy hadrons.

Stoichiometry of DNA binding by the bacteriophage SP01-encoded type II DNA-binding protein TF1.

PubMed

Schneider, G J; Geiduschek, E P

1990-06-25

The stoichiometry of DNA binding by the bacteriophage SP01-encoded type II DNA-binding protein TF1 has been determined. 3H-Labeled TF1 was allowed to bind to a 32P-labeled DNA fragment containing a TF1 binding site. Multiple TF1-DNA complexes were resolved from each other and from unbound DNA by native gel electrophoresis. DNA-protein complexes were cut from polyacrylamide gels, and the amounts of 3H and 32P contained in each slice were measured. A ratio of 1.12 +/- 0.06 TF1 dimer/DNA molecule was calculated for the fastest-migrating TF1-DNA complex. We conclude that TF1 has a DNA-binding unit of one dimer. More slowly migrating complexes are apparently formed by serial addition of single TF1 dimers.

The transcription factor titration effect dictates level of gene expression.

PubMed

Brewster, Robert C; Weinert, Franz M; Garcia, Hernan G; Song, Dan; Rydenfelt, Mattias; Phillips, Rob

2014-03-13

Models of transcription are often built around a picture of RNA polymerase and transcription factors (TFs) acting on a single copy of a promoter. However, most TFs are shared between multiple genes with varying binding affinities. Beyond that, genes often exist at high copy number-in multiple identical copies on the chromosome or on plasmids or viral vectors with copy numbers in the hundreds. Using a thermodynamic model, we characterize the interplay between TF copy number and the demand for that TF. We demonstrate the parameter-free predictive power of this model as a function of the copy number of the TF and the number and affinities of the available specific binding sites; such predictive control is important for the understanding of transcription and the desire to quantitatively design the output of genetic circuits. Finally, we use these experiments to dynamically measure plasmid copy number through the cell cycle. Copyright © 2014 Elsevier Inc. All rights reserved.

Palmitoylation of Sindbis Virus TF Protein Regulates Its Plasma Membrane Localization and Subsequent Incorporation into Virions.

PubMed

Ramsey, Jolene; Renzi, Emily C; Arnold, Randy J; Trinidad, Jonathan C; Mukhopadhyay, Suchetana

2017-02-01

Palmitoylation is a reversible, posttranslational modification that helps target proteins to cellular membranes. The alphavirus small membrane proteins 6K and TF have been reported to be palmitoylated and to positively regulate budding. 6K and TF are isoforms that are identical in their N termini but unique in their C termini due to a -1 ribosomal frameshift during translation. In this study, we used cysteine (Cys) mutants to test differential palmitoylation of the Sindbis virus 6K and TF proteins. We modularly mutated the five Cys residues in the identical N termini of 6K and TF, the four additional Cys residues in TF's unique C terminus, or all nine Cys residues in TF. Using these mutants, we determined that TF palmitoylation occurs primarily in the N terminus. In contrast, 6K is not palmitoylated, even on these shared residues. In the C-terminal Cys mutant, TF protein levels increase both in the cell and in the released virion compared to the wild type. In viruses with the N-terminal Cys residues mutated, TF is much less efficiently localized to the plasma membrane, and it is not incorporated into the virion. The three Cys mutants have minor defects in cell culture growth but a high incidence of abnormal particle morphologies compared to the wild-type virus as determined by transmission electron microscopy. We propose a model where the C terminus of TF modulates the palmitoylation of TF at the N terminus, and palmitoylated TF is preferentially trafficked to the plasma membrane for virus budding. Alphaviruses are a reemerging viral cause of arthritogenic disease. Recently, the small 6K and TF proteins of alphaviruses were shown to contribute to virulence in vivo Nevertheless, a clear understanding of the molecular mechanisms by which either protein acts to promote virus infection is missing. The TF protein is a component of budded virions, and optimal levels of TF correlate positively with wild-type-like particle morphology. In this study, we show that the palmitoylation of TF regulates its localization to the plasma membrane, which is the site of alphavirus budding. Mutants in which TF is not palmitoylated display drastically reduced plasma membrane localization, which effectively prevents TF from participating in budding or being incorporated into virus particles. Investigation of the regulation of TF will aid current efforts in the alphavirus field searching for approaches to mitigate alphaviral disease in humans. Copyright © 2017 American Society for Microbiology.

Immunological and biochemical analysis of glycosylated surface antigens and lipophosphoglycan of Tritrichomonas foetus.

PubMed

Singh, B N; BonDurant, R H; Campero, C M; Corbeil, L B

2001-08-01

Immunoaffinity-purified TF1.17 adhesin antigen was compared biochemically and antigenically to Tritrichomonas foetus (TF) lipophosphoglycan (LPG) and a soluble glycosylated antigen (SGA) released from T. foetus and implicated in pathogenesis and immunity. The monoclonal antibodies (Mabs TF1.15 and TF1.17) specific for a glycosylated TF1.17 antigen were previously shown to prevent adhesion of the T. foetus parasites to bovine vaginal epithelial cells and to mediate killing by bovine complement. SGA was isolated from T. foetus-conditioned buffer and purified by octyl-Sepharose hydrophobic column chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of SGA showed a major SGA1 component (approximately 190 kDa) and a minor SGA2 component (50-70 kDa), which migrated close to TF-LPG and TF1.17. The carbohydrate and lipid compositional analyses of affinity-purified TF1.17 and SGA2 by high-performance liquid chromatography (HPLC) and gas-liquid chromatography revealed the presence of monosaccharides and fatty acids as found in TF-LPG. All antigens contained terminal fucose as determined by alpha-fucosidase digestion followed by HPLC. ELISA and western blots were used to further characterize these glycosylated antigens and to analyze their relationships. The Mabs TF1.15 and TF1.17 reacted very strongly to TF-LPG and SGA2. as well as TF1.17 antigen, indicating that these molecules share common epitopes. These Mabs did not react with the SGA1 component either in ELISA and western blot analyses. Also, the monosaccharide composition of SGA1 was very different from the other three antigen, suggesting SGA1 was different from LPG, SGA2 and TF1.17. Although LPG reacted with Mabs to native TF1.17 antigen, LPG did not induce an immune response in cattle with the same route and adjuvant used to produce strong antibody responses to the native antigen. The latter response suggests that the tightly bound peptide present in the immunoaffinity-purified antigen is necessary for induction of a response to (an) epitope(s) in TF-LPG and TF1.17. Furthermore, vaginal fluid from T. foetus-infected heifers and serum from a cow with a T. foetus-associated pyometra recognized both TF1.17 and TF-LPG in western blots. These results suggest that T. foetus LPG and SGA2 are related to TF1.17 antigen, which was previously shown to play an important role in the pathogenesis and host response in bovine trichomoniasis.

Comparison of transfemoral transcatheter aortic valve replacement performed in the catheterization laboratory (minimalist approach) versus hybrid operating room (standard approach): outcomes and cost analysis.

PubMed

Babaliaros, Vasilis; Devireddy, Chandan; Lerakis, Stamatios; Leonardi, Robert; Iturra, Sebastian A; Mavromatis, Kreton; Leshnower, Bradley G; Guyton, Robert A; Kanitkar, Mihir; Keegan, Patricia; Simone, Amy; Stewart, James P; Ghasemzadeh, Nima; Block, Peter; Thourani, Vinod H

2014-08-01

The aim of this study was to compare transfemoral transcatheter aortic valve replacement (TF TAVR) performed in a catheterization laboratory (minimalist approach [MA]) with TF TAVR performed in a hybrid operating room (standard approach [SA]). A MA-TF TAVR can be performed without general anesthesia, transesophageal echocardiography, or a surgical hybrid room. The outcomes and cost of MA-TF TAVR compared with those of the SA have not been described. Patients who underwent elective, percutaneous TF TAVR using the Edwards Sapien valve (Edwards Lifesciences, Irvine, California) were studied. Baseline characteristics, outcomes, and hospital costs of MA-TF TAVR and SA-TF TAVR were compared. A total of 142 patients were studied (MA-TF TAVR, n = 70 and SA-TF TAVR, n = 72). There were no differences in baseline comorbidities (Society of Thoracic Surgeons score, 10.6 ± 4.3 vs. 11.4 ± 5.8; p = 0.35). All procedures in the MA-TF TAVR group were successful; 1 patient was intubated. Three patients in the SA-TF TAVR group had procedure-related death. Procedure room time (150 ± 48 min vs. 218 ± 56 min, p < 0.001), total intensive care unit time (22 h vs. 28 h, p < 0.001), length of stay from procedure to discharge (3 days vs. 5 days, p < 0.001), and cost ($45,485 ± 14,397 vs. $55,377 ± 22,587, p < 0.001) were significantly less in the MA-TF TAVR group. Mortality at 30 days was not significantly different in the MA-TF TAVR group (0 vs. 6%, p = 0.12) and 30-day stroke/transient ischemic attack was similar (4.3% vs. 1.4%, p = 0.35). Moderate or severe paravalvular leak and device success were similar in the MA-TF TAVR and SA-TF TAVR groups (3% vs. 5.8%, p = 0.4 and 90% vs. 88%, p = 0.79, respectively) at 30 days. At a median follow-up of 435 days, there was no significant difference in survival (MA-TF TAVR, 83% vs. SA-TF TAVR, 82%; p = 0.639). MA-TF TAVR can be performed with minimal morbidity and mortality and equivalent effectiveness compared with SA-TF TAVR. The shorter length of stay and lower resource use with MA-TF TAVR significantly lowers hospital costs. Copyright © 2014 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Analysis of the time-varying energy of brain responses to an oddball paradigm using short-term smoothed Wigner-Ville distribution.

PubMed

Tağluk, M E; Cakmak, E D; Karakaş, S

2005-04-30

Cognitive brain responses to external stimuli, as measured by event related potentials (ERPs), have been analyzed from a variety of perspectives to investigate brain dynamics. Here, the brain responses of healthy subjects to auditory oddball paradigms, standard and deviant stimuli, recorded on an Fz electrode site were studied using a short-term version of the smoothed Wigner-Ville distribution (STSW) method. A smoothing kernel was designed to preserve the auto energy of the signal with maximum time and frequency resolutions. Analysis was conducted mainly on the time-frequency distributions (TFDs) of sweeps recorded during successive trials including the TFD of averaged single sweeps as the evoked time-frequency (ETF) brain response and the average of TFDs of single sweeps as the time-frequency (TF) brain response. Also the power entropy and the phase angles of the signal at frequency f and time t locked to the stimulus onset were studied across single trials as the TF power-locked and the TF phase-locked brain responses, respectively. TFDs represented in this way demonstrated the ERP spectro-temporal characteristics from multiple perspectives. The time-varying energy of the individual components manifested interesting TF structures in the form of amplitude modulated (AM) and frequency modulated (FM) energy bursts. The TF power-locked and phase-locked brain responses provoked ERP energies in a manner modulated by cognitive functions, an observation requiring further investigation. These results may lead to a better understanding of integrative brain dynamics.

Soil-to-soybean transfer of (99)Tc and its underground distribution in differently contaminated upland soils.

PubMed

Choi, Yong-Ho; Lim, Kwang-Muk; Jun, In; Kim, Byung-Ho; Keum, Dong-Kwon; Kim, In-Gyu

2014-06-01

Pot experiments were performed in a greenhouse to investigate the soil-to-soybean transfer of (99)Tc in two different upland soils labeled with (99)TcO4(-) in two contrasting ways. One was to mix the soil with a (99)TcO4(-) solution 26 d before sowing (pre-sowing deposition: PSD), and the other was to apply the solution onto the soil surface 44 d after sowing (growing-period deposition: GPD). The soil-to-plant transfer was quantified with the transfer factor (TF, ratio of the plant concentration to the average of at-planting and at-harvest soil concentrations) or the aggregated transfer factor (TFag, ratio of the plant concentration to the deposition density). For both the depositions, the transfer of (99)Tc to aerial parts decreased in the order of leaf > stem > pod > seed. TF values (dimensionless) from the PSD were 0.22 and 0.27 (no statistically significant difference) for mature dry seeds in the respective soils, whereas a 600-fold higher value occurred for dry leaves. The post-harvest concentrations of the PSD (99)Tc in the top 20 cm soils as a whole were about half the initial concentrations. Around 25% of the total applied activity remained in the GPD soils after the harvest. The post-harvest depth profiles of the GPD (99)Tc in the two soils showed similar patterns of logarithmic activity decrease with increasing soil depths. Only 1.5-4.3% of the total applied activity was removed through the harvested biomass (seeds, pods and stems), and it was estimated that a great part of the total pant uptake returned to the soil through the fallen leaves. TFag values (m(2) kg(-1)) were about 2-4 times higher for the GPD than for the PSD. This finding and generally high root uptake of Tc may indicate that the use of empirical deposition time-dependent TFag data is particularly important for predicting the plant concentrations of Tc after its growing-period deposition. Copyright © 2014 Elsevier Ltd. All rights reserved.

Binding affinity of aluminium to human serum transferrin and effects of carbohydrate chain modification as studied by HPLC/high-resolution ICP-MS--speciation of aluminium in human serum.

PubMed

Nagaoka, Megumi Hamano; Maitani, Tamio

2005-09-01

Aluminium (Al) in the blood is bound to transferrin (Tf), a glycoprotein of about 80kDa that is characterized by its need for a synergistic anion. In this focused review, the binding affinity of Al to Tf is surveyed in the context of our recent studies using on-line high-performance liquid chromatography/high-resolution inductively coupled plasma mass spectrometry (HPLC/HR-ICP-MS). Al in human serum without any in vitro Al-spikes was present in a form bound to the N-lobe site of Tf. The influences of sialic acid in the carbohydrate chain of human serum Tf (hTf) were studied using asialo-hTf, obtained by treatment with sialidase. The binding affinity of Fe was similar between asialo-hTf and native-hTf, while that of Al for asialo-hTf was larger than that for native-hTf, especially in the presence of oxalate, a synergistic anion. The above findings are discussed in relation to diseases in which the serum concentrations of carbohydrate-deficient Tf and oxalate are augmented.

Programme Presentation on TF 1.

ERIC Educational Resources Information Center

Casile, Nicole

1979-01-01

Reports a survey of the role and function of French television announcers. Possibilities for increasing the personalization, naturalness, and efficiency in communications between announcer and audience are explored. (RAO)

Demonstration of thin film pair distribution function analysis (tfPDF) for the study of local structure in amorphous and crystalline thin films

DOE PAGES

Jensen, K. M.Ø.; Blichfeld, A. B.; Bauers, S. R.; ...

2015-07-05

By means of normal incidence, high flux and high energy x-rays, we have obtained total scattering data for Pair Distribution Function (PDF) analysis from thin films (tf), suitable for local structure analysis. By using amorphous substrates as support for the films, the standard Rapid Acquisition PDF setup can be applied and the scattering signal from the film can be isolated from the total scattering data through subtraction of an independently measured background signal. No angular corrections to the data are needed, as would be the case for grazing incidence measurements. We illustrate the ‘tfPDF’ method through studies of as depositedmore » (i.e. amorphous) and crystalline FeSb 3 films, where the local structure analysis gives insight into the stabilization of the metastable skutterudite FeSb 3 phase. The films were prepared by depositing ultra-thin alternating layers of Fe and Sb, which interdiffuse and after annealing crystallize to form the FeSb 3 structure. The tfPDF data show that the amorphous precursor phase consists of corner-sharing FeSb 6 octahedra with motifs highly resembling the local structure in crystalline FeSb 3. Analysis of the amorphous structure allows predicting whether the final crystalline product will form the FeSb 3 phase with or without excess Sb present. The study thus illustrates how analysis of the local structure in amorphous precursor films can help to understand crystallization processes of metastable phases and opens for a range of new local structure studies of thin films.« less

Demonstration of thin film pair distribution function analysis (tfPDF) for the study of local structure in amorphous and crystalline thin films

PubMed Central

Jensen, Kirsten M. Ø.; Blichfeld, Anders B.; Bauers, Sage R.; Wood, Suzannah R.; Dooryhée, Eric; Johnson, David C.; Iversen, Bo B.; Billinge, Simon J. L.

2015-01-01

By means of normal-incidence, high-flux and high-energy X-rays, total scattering data for pair distribution function (PDF) analysis have been obtained from thin films (tf), suitable for local structure analysis. By using amorphous substrates as support for the films, the standard Rapid Acquisition PDF setup can be applied and the scattering signal from the film can be isolated from the total scattering data through subtraction of an independently measured background signal. No angular corrections to the data are needed, as would be the case for grazing incidence measurements. The ‘tfPDF’ method is illustrated through studies of as-deposited (i.e. amorphous) and crystalline FeSb3 films, where the local structure analysis gives insight into the stabilization of the metastable skutterudite FeSb3 phase. The films were prepared by depositing ultra-thin alternating layers of Fe and Sb, which interdiffuse and after annealing crystallize to form the FeSb3 structure. The tfPDF data show that the amorphous precursor phase consists of corner-sharing FeSb6 octahedra with motifs highly resembling the local structure in crystalline FeSb3. Analysis of the amorphous structure allows the prediction of whether the final crystalline product will form the FeSb3 phase with or without excess Sb present. The study thus illustrates how analysis of the local structure in amorphous precursor films can help to understand crystallization processes of metastable phases and opens for a range of new local structure studies of thin films. PMID:26306190

CTF Theory Manual

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

Avramova, Maria N.; Salko, Robert K.

Coolant-Boiling in Rod Arrays|Two Fluids (COBRA-TF) is a thermal/ hydraulic (T/H) simulation code designed for light water reactor (LWR) vessel analysis. It uses a two-fluid, three-field (i.e. fluid film, fluid drops, and vapor) modeling approach. Both sub-channel and 3D Cartesian forms of 9 conservation equations are available for LWR modeling. The code was originally developed by Pacific Northwest Laboratory in 1980 and had been used and modified by several institutions over the last few decades. COBRA-TF also found use at the Pennsylvania State University (PSU) by the Reactor Dynamics and Fuel Management Group (RDFMG) and has been improved, updated, andmore » subsequently re-branded as CTF. As part of the improvement process, it was necessary to generate sufficient documentation for the open-source code which had lacked such material upon being adopted by RDFMG. This document serves mainly as a theory manual for CTF, detailing the many two-phase heat transfer, drag, and important accident scenario models contained in the code as well as the numerical solution process utilized. Coding of the models is also discussed, all with consideration for updates that have been made when transitioning from COBRA-TF to CTF. Further documentation outside of this manual is also available at RDFMG which focus on code input deck generation and source code global variable and module listings.« less

Tissue factor deficiency increases alveolar hemorrhage and death in influenza A virus-infected mice.

PubMed

Antoniak, S; Tatsumi, K; Hisada, Y; Milner, J J; Neidich, S D; Shaver, C M; Pawlinski, R; Beck, M A; Bastarache, J A; Mackman, N

2016-06-01

Essentials H1N1 Influenza A virus (IAV) infection is a hemostatic challenge for the lung. Tissue factor (TF) on lung epithelial cells maintains lung hemostasis after IAV infection. Reduced TF-dependent activation of coagulation leads to alveolar hemorrhage. Anticoagulation might increase the risk for hemorrhages into the lung during severe IAV infection. Background Influenza A virus (IAV) infection is a common respiratory tract infection that causes considerable morbidity and mortality worldwide. Objective To investigate the effect of genetic deficiency of tissue factor (TF) in a mouse model of IAV infection. Methods Wild-type mice, low-TF (LTF) mice and mice with the TF gene deleted in different cell types were infected with a mouse-adapted A/Puerto Rico/8/34 H1N1 strain of IAV. TF expression was measured in the lungs, and bronchoalveolar lavage fluid (BALF) was collected to measure extracellular vesicle TF, activation of coagulation, alveolar hemorrhage, and inflammation. Results IAV infection of wild-type mice increased lung TF expression, activation of coagulation and inflammation in BALF, but also led to alveolar hemorrhage. LTF mice and mice with selective deficiency of TF in lung epithelial cells had low basal levels of TF and failed to increase TF expression after infection; these two strains of mice had more alveolar hemorrhage and death than controls. In contrast, deletion of TF in either myeloid cells or endothelial cells and hematopoietic cells did not increase alveolar hemorrhage or death after IAV infection. These results indicate that TF expression in the lung, particularly in epithelial cells, is required to maintain alveolar hemostasis after IAV infection. Conclusion Our study indicates that TF-dependent activation of coagulation is required to limit alveolar hemorrhage and death after IAV infection. © 2016 International Society on Thrombosis and Haemostasis.

p53 determines prognostic significance of the carbohydrate stem cell marker TF1 (CD176) in ovarian cancer.

PubMed

Heublein, Sabine; Page, Sabina K; Mayr, Doris; Ditsch, Nina; Jeschke, Udo

2016-06-01

The oncofoetal Thomsen-Friedenreich (TF1, CD176) epitope is a carbohydrate cancer stem cell (CSC) antigen, and TF1-mediated cancer progression can be widely reversed by anti-TF1 antibodies. Particularly, CSC-like cells are regarded to be tumorigenic and chemoresistant. Aberrant p53 is probably the factor most closely associated with chemoresistance and tumour aggressiveness in ovarian tumours. We thus questioned whether TF1 in combination with p53 or as a single marker may be related to clinico-pathological features and survival of ovarian cancer patients. Both markers were quantified in ovarian cancer tissue (n = 151) by immunohistochemistry. p53 staining was subdivided into three subgroups [n (completely negative) = 57, n (moderately stained) = 28, n (overexpressing) = 66]. TF1 was scored as positive (n = 30) versus negative (n = 121). Only in those cancers classified with moderate p53 staining-and thus most likely displaying with wild-type TP53-TF1 positivity turned out to be a predictor for shortened overall survival (univariate: p < 0.001, multivariate: p = 0.001). By screening 17 different protein markers for correlation with TF1, only mucin-1 emerged as a potential TF1 carrier protein. It is hypothesized that TF1 may confer tumour-promoting features, especially in a TP53 wild-type genetic background. In addition, TF1 is an attractive immunotherapeutic target. Whether those cases classified as TF1 positive and at the same time as moderately stained for p53 might particularly benefit from a future anti-TF1 antibody treatment or from TF1 vaccination therapy remains to be determined.

Differential effects of somatostatin on circulating tissue factor procoagulant activity and protein.

PubMed

Boden, Guenther; Vaidyula, Vijender; Homko, Carol; Mozzoli, Maria; Rao, A Koneti

2007-05-01

The tissue factor (TF) pathway is the primary mechanism for initiation of blood coagulation. Circulating blood contains TF, which originates mainly from monocytes and is thrombogenic. The presence of somatostatin (SMS) receptors on monocytes suggests the possibility that SMS may regulate TF synthesis and/or release. Circulating TF procoagulant activity (TF-PCA), factor VIIa activity (FVIIa; clotting assays), TF antigen (TF-Ag; ELISA), prothrombin fragment 1.2 (F1.2), thrombin-antithrombin complexes (ELISAs), CD40 ligand expression on platelets, and monocyte-platelet aggregates (flow cytometry) were determined in blood from normal volunteers undergoing 24 h of basal glucose/basal insulin (BG/BI) clamps and high-glucose/high-insulin (HG/HI) clamps with and without SMS. Infusions of SMS under basal conditions (BG/BI) raised TF-PCA 1.8-fold (P < 0.03), TF-Ag 2.3-fold (P < 0.001), and TF expression on monocytes by 36% (P < 0.001) and decreased plasma levels of FVIIa by 30% (P < 0.001). Infusion of SMS reduced the 8.6-fold HG/HI-induced increase in TF-Ag by 26% and the 8.6-fold increase in TF-PCA by 100%. SMS also prevented the 60% increase in TF expression on monocytes, the 2.2-fold increase in F1.2, the 40% increase in CD40L expression on platelets, and the 17% increase in monocyte-platelet aggregates seen during HG/HI. We conclude that SMS completely prevented HG/HI-induced TF activation in normal volunteers and may be of use to reduce the procoagulant state and acute vascular events in hyperinsulinemic insulin-resistant patients with type 2 diabetes.

Intracellular concentrations of 65 species of transcription factors with known regulatory functions in Escherichia coli.

PubMed

Ishihama, Akira; Kori, Ayako; Koshio, Etsuko; Yamada, Kayoko; Maeda, Hiroto; Shimada, Tomohiro; Makinoshima, Hideki; Iwata, Akira; Fujita, Nobuyuki

2014-08-01

The expression pattern of the Escherichia coli genome is controlled in part by regulating the utilization of a limited number of RNA polymerases among a total of its approximately 4,600 genes. The distribution pattern of RNA polymerase changes from modulation of two types of protein-protein interactions: the interaction of core RNA polymerase with seven species of the sigma subunit for differential promoter recognition and the interaction of RNA polymerase holoenzyme with about 300 different species of transcription factors (TFs) with regulatory functions. We have been involved in the systematic search for the target promoters recognized by each sigma factor and each TF using the newly developed Genomic SELEX system. In parallel, we developed the promoter-specific (PS)-TF screening system for identification of the whole set of TFs involved in regulation of each promoter. Understanding the regulation of genome transcription also requires knowing the intracellular concentrations of the sigma subunits and TFs under various growth conditions. This report describes the intracellular levels of 65 species of TF with known function in E. coli K-12 W3110 at various phases of cell growth and at various temperatures. The list of intracellular concentrations of the sigma factors and TFs provides a community resource for understanding the transcription regulation of E. coli under various stressful conditions in nature. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

The Intracellular Trafficking Pathway of Transferrin

PubMed Central

Mayle, Kristine M.; Le, Alexander M.; Kamei, Daniel T.

2011-01-01

Background Transferrin (Tf) is an iron-binding protein that facilitates iron-uptake in cells. Iron-loaded Tf first binds to the Tf receptor (TfR) and enters the cell through clathrin-mediated endocytosis. Inside the cell, Tf is trafficked to early endosomes, delivers iron, and then is subsequently directed to recycling endosomes to be taken back to the cell surface. Scope of Review We aim to review the various methods and techniques that researchers have employed for elucidating the Tf trafficking pathway and the cell-machinery components involved. These experimental methods can be categorized as microscopy, radioactivity, and surface plasmon resonance (SPR). Major Conclusions Qualitative experiments, such as total internal reflectance fluorescence (TIRF), electron, laser-scanning confocal, and spinning-disk confocal microscopy, have been utilized to determine the roles of key components in the Tf trafficking pathway. These techniques allow temporal resolution and are useful for imaging Tf endocytosis and recycling, which occur on the order of seconds to minutes. Additionally, radiolabeling and SPR methods, when combined with mathematical modeling, have enabled researchers to estimate quantitative kinetic parameters and equilibrium constants associated with Tf binding and trafficking. General Significance Both qualitative and quantitative data can be used to analyze the Tf trafficking pathway. The valuable information that is obtained about the Tf trafficking pathway can then be combined with mathematical models to identify design criteria to improve the ability of Tf to deliver anticancer drugs. PMID:21968002

Tree species related functional properties of dissolved and total organic matter in throughfall, stemflow and forest floor solutions

NASA Astrophysics Data System (ADS)

Michalzik, Beate; Bischoff, Sebastian; Schwarz, Martin; Siemens, Jan; Thieme, Lisa; Wilcke, Wolfgang

2016-04-01

The amount and chemical nature of water-bound organic matter is a prerequisite for advancing our understanding of the C and nutrient cycling and associated ecosystem processes. While many investigations have addressed the nature and dynamics of DOM in terrestrial ecosystems, only a few have investigated the dynamics and composition of water-bound total OM (TOM) including the particulate organic matter fraction (POM; 0.45 μm < POM < 500 μm). Since water-bound element and nutrient concentrations are conventionally measured after 0.45 μm-filtration, the exclusion of the POM fraction results in misleading inferences and budgeting gaps of nutrient and energy fluxes in terrestrial ecosystems. Furthermore, tree species differ in leaf composition (e.g. nutrient, polyphenols content) and leaf litter quality, which in turn affect a variety of ecosystem processes. Nevertheless, the composition and amount of DOM and TOM derived from living plant material via throughfall (TF), stemflow (SF) and its compositional fate traversing the forest floor (FF) are insufficiently understood. In particular we asked: How do tree species and forest types affect the amount of dissolved and particulate C and N in TF and FF solutions and thus the input into the mineral soil? Do functional properties (e.g. aromaticity) of DOM and TOM differ in TF, SF and FF solutions collected in beech and spruce stands and among different beech stands across Germany? To monitor (mineral) soil input fluxes of DOM and POM in different spruce and beech forests, we fortnightly sampled TF and FF solution over three years (2010-2012) in the "Hainich-Dün-Exploratory", Thuringia, Central Germany, which forms part of the DFG SPP 1374 "Exploratories for Large-scale and Long-term Functional Biodiversity Research". To characterize chemical properties of DOM and TOM, we applied solid-state 13C NMR spectroscopy to TF, SF and FF solutions from three European beech regions across Germany and from Norway spruce sites of the Hainich-Dün-Exploratory. Fluxes of POC and PN were highly variable between years and added significantly to the annual budgets of DOC and DN in TF and FF solutions especially in beech forests. The non-consideration of these particle-bound element fluxes remarkable underestimates the TOC input to the soil by 30 to 40% and those of TN by 10 to 20%. We therefore emphasize the imperative to include POC and PN fluxes into C and N budgeting of forest ecosystems. 13C NMR spectroscopy revealed remarkable tree-species related differences in the composition of DOM and TOM. Compared to DOM, TOM generally showed higher intensities for the alkyl C region and lower ones for lignin-derived and aromatic C of the aryl C region resulting in lower aromaticity indices and a diminished degree of humification. Differences in the structural composition of DOM and TOM under beech lessened in the order: throughfall > stemflow > forest floor leachate. Compared to spruce, TF DOM under beech concordantly showed the highest intensities of aromatic and phenolic C and lowest ones of alkyl-C. Phenolic compounds are known for their allelopathic potential successfully impairing competing plants and hence altering ecosystem structure and functions - mechanisms being still imperfectly understood.

Characterization of early and late endocytic compartments of the transferrin cycle. Transferrin receptor antibody blocks erythroid differentiation by trapping the receptor in the early endosome.

PubMed

Killisch, I; Steinlein, P; Römisch, K; Hollinshead, R; Beug, H; Griffiths, G

1992-09-01

We describe a detailed morphological characterization of the endocytic pathway in differentiating chicken erythroblasts transformed by a temperature-sensitive mutant of avian erythroblastosis virus (AEV). These cells express high levels of transferrin receptors (TfR) when induced to differentiate at 42 degrees C. Biochemical analysis showed that most (approximately 90%) of the internalized 125I-Tf recycled within approximately 30 min while a smaller fraction of 125I-Tf required up to 2 h for recycling. By immunocytochemistry, the bulk of Tf and TfR was localized at the plasma membrane and in tubuloreticular early endosomes. This structure contained coated buds that labelled with an antibody specific for the clathrin light chain. Decreasing amounts of both Tf and TfR were detected in two distal compartments, spherical endosome vesicles resembling multivesicular bodies and the prelysosomal compartment (PLC) enriched in cation-independent mannose 6-phosphate receptor. As shown by fluorescent (FITC-Tf) labelling of living cells, the movement of Tf/TfR complex into these late structures was accompanied by a significant drop in pH from about 6, the value displayed by early endosomes, to values below pH 5.0. Since no detectable 125I-Tf degradation was observed during a 4 h period we believe that the Tf/TfR detected in these late endocytic structures avoids degradation and recycles back to the cell surface. The addition of an anti-TfR monoclonal antibody to the culture medium of these cells blocks their differentiation. Under this condition the antibody-TfR complex was trapped in an early endosome compartment that enlarged to more than twice its normal size. However, this condition did not affect the transport kinetics of horseradish peroxidase from the medium to the PLC.

Increased brain uptake of targeted nanoparticles by adding an acid-cleavable linkage between transferrin and the nanoparticle core.

PubMed

Clark, Andrew J; Davis, Mark E

2015-10-06

Most therapeutic agents are excluded from entering the central nervous system by the blood-brain barrier (BBB). Receptor mediated transcytosis (RMT) is a common mechanism used by proteins, including transferrin (Tf), to traverse the BBB. Here, we prepared Tf-containing, 80-nm gold nanoparticles with an acid-cleavable linkage between the Tf and the nanoparticle core to facilitate nanoparticle RMT across the BBB. These nanoparticles are designed to bind to Tf receptors (TfRs) with high avidity on the blood side of the BBB, but separate from their multidentate Tf-TfR interactions upon acidification during the transcytosis process to allow release of the nanoparticle into the brain. These targeted nanoparticles show increased ability to cross an in vitro model of the BBB and, most important, enter the brain parenchyma of mice in greater amounts in vivo after systemic administration compared with similar high-avidity nanoparticles containing noncleavable Tf. In addition, we investigated this design with nanoparticles containing high-affinity antibodies (Abs) to TfR. With the Abs, the addition of the acid-cleavable linkage provided no improvement to in vivo brain uptake for Ab-containing nanoparticles, and overall brain uptake was decreased for all Ab-containing nanoparticles compared with Tf-containing ones. These results are consistent with recent reports of high-affinity anti-TfR Abs trafficking to the lysosome within BBB endothelium. In contrast, high-avidity, Tf-containing nanoparticles with the acid-cleavable linkage avoid major endothelium retention by shedding surface Tf during their transcytosis.

Directed Energy Beam Jitter Mitigation Using the Line-of-Sight Reference Frame

DTIC Science & Technology

2011-05-10

tg,’Connected’); C4 = ’Yes’ TF1 =strcmp(C1, C2);TF2=strcmp(C3, C4); if ~ TF1 ; unload(tg); load(tg,’FFD_9’); tg=xpctarget.xpc; end if...C1 = (get(tg,’Application’));C2=’FFD_9’C3 = get(tg,’Connected’); C4 = ’Yes’ TF1 =strcmp(C1, C2);TF2=strcmp(C3, C4); if ~ TF1 ; unload(tg

On the Design of VLSI Circuits for the Winograd Fourier Transform Algorithm

DTIC Science & Technology

1991-12-01

3-:3 T’able 8: Twiddle factors in TF1 (real side) ... .. .. .. .. .... ... .. .. ...- 4 T;l1)a1e 9: Twiddle factors I n... TF1 (imaginary side) .. .. .. .. ... ... .... .. 13-5 ’fable 10: Twiddle factors in TF2 (r’eal side) ... .. .. .. .. .... ... .... .. 13-6 ’Table 11...reads its twiddle factor from Y. The four other possibilities (TFO, TF1 , TF2, and TF3) correspond to the fixed values that are necessary for computing 20

Lead suppresses chimeric human transferrin gene expression in transgenic mouse liver.

PubMed

Adrian, G S; Rivera, E V; Adrian, E K; Lu, Y; Buchanan, J; Herbert, D C; Weaker, F J; Walter, C A; Bowman, B H

1993-01-01

The major iron-transport protein in serum is transferrin (TF) which also has the capacity to transport other metals. This report presents evidence that synthesis of human TF can be regulated by the metal lead. Transgenic mice carrying chimeric human TF-chloramphenicol acetyl transferase (CAT) genes received lead or sodium salts by intraperitoneal injections or in drinking water. Transgene expression in liver was suppressed 31 to 50% by the lead treatment. Lead regulates human TF transgenes at the mRNA level since liver CAT enzyme activity, CAT protein, and TF-CAT mRNA levels were all suppressed. The dosages of lead did not alter synthesis of the other liver proteins, mouse TF and albumin, as measured by Northern blot analysis of total liver RNA and rocket immunoelectrophoresis of mouse sera. Moderate levels of lead exposure were sufficient to evoke the human TF transgene response; blood lead levels in mice that received lead acetate in drinking water ranged from 30 micrograms/dl to 56 micrograms/dl. In addition to suppressing expression of TF-CAT genes in transgenic mice, lead also suppressed synthesis of TF protein in cultured human hepatoma HepG2 cells. The regulation of human TF apparently differs from the regulation of mouse TF which is unresponsive to lead exposure.

Aortic pulse wave velocity and reflecting distance estimation from peripheral waveforms in humans: detection of age- and exercise training-related differences.

PubMed

Pierce, Gary L; Casey, Darren P; Fiedorowicz, Jess G; Seals, Douglas R; Curry, Timothy B; Barnes, Jill N; Wilson, DeMaris R; Stauss, Harald M

2013-07-01

We hypothesized that demographic/anthropometric parameters can be used to estimate effective reflecting distance (EfRD), required to derive aortic pulse wave velocity (APWV), a prognostic marker of cardiovascular risk, from peripheral waveforms and that such estimates can discriminate differences in APWV and EfRD with aging and habitual endurance exercise in healthy adults. Ascending aortic pressure waveforms were derived from peripheral waveforms (brachial artery pressure, n = 25; and finger volume pulse, n = 15) via a transfer function and then used to determine the time delay between forward- and backward-traveling waves (Δtf-b). True EfRDs were computed as directly measured carotid-femoral pulse wave velocity (CFPWV) × 1/2Δtf-b and then used in regression analysis to establish an equation for EfRD based on demographic/anthropometric data (EfRD = 0.173·age + 0.661·BMI + 34.548 cm, where BMI is body mass index). We found good agreement between true and estimated APWV (Pearson's R² = 0.43; intraclass correlation = 0.64; both P < 0.05) and EfRD (R² = 0.24; intraclass correlation = 0.40; both P < 0.05). In young sedentary (22 ± 2 years, n = 6), older sedentary (62 ± 1 years, n = 24), and older endurance-trained (61 ± 2 years, n = 14) subjects, EfRD (from demographic/anthropometric parameters), APWV, and 1/2Δtf-b (from brachial artery pressure waveforms) were 52.0 ± 0.5, 61.8 ± 0.4, and 60.6 ± 0.5 cm; 6.4 ± 0.3, 9.6 ± 0.2, and 8.1 ± 0.2 m/s; and 82 ± 3, 65 ± 1 and 76 ± 2 ms (all P < 0.05), respectively. Our results demonstrate that APWV derived from peripheral waveforms using age and BMI to estimate EfRD correlates with CFPWV in healthy adults. This method can reliably detect the distal shift of the reflecting site with age and the increase in APWV with sedentary aging that is attenuated with habitual endurance exercise.

Inversion of substrate stereoselectivity of horse liver alcohol dehydrogenase by substitutions of Ser-48 and Phe-93

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

Kim, Keehyuk; Plapp, Bryce V.

The substrate specificities of alcohol dehydrogenases (ADH) are of continuing interest for understanding the physiological functions of these enzymes. Ser-48 and Phe-93 have been identified as important residues in the substrate binding sites of ADHs, but more comprehensive structural and kinetic studies are required. The S48T substitution in horse ADH1E has small effects on kinetic constants and catalytic efficiency (V/Km) with ethanol, but decreases activity with benzyl alcohol and affinity for 2,2,2-trifluoroethanol (TFE) and 2,3,4,5,6-pentafluorobenzyl alcohol (PFB). Nevertheless, atomic resolution crystal structures of the S48T enzyme complexed with NAD+ and TFE or PFB are very similar to the structures formore » the wild-type enzyme. (The S48A substitution greatly diminishes catalytic activity.) The F93A substitution significantly decreases catalytic efficiency (V/Km) for ethanol and acetaldehyde while increasing activity for larger secondary alcohols and the enantioselectivity for the R-isomer relative to the S-isomer of 2-alcohols. The doubly substituted S48T/F93A enzyme has kinetic constants for primary and secondary alcohols similar to those for the F93A enzyme, but the effect of the S48T substitution is to decrease V/Km for (S)-2-alcohols without changing V/Km for (R)-2-alcohols. Thus, the S48T/F93A substitutions invert the enantioselectivity for alcohol oxidation, increasing the R/S ratio by 10, 590, and 200-fold for 2-butanol, 2-octanol, and sec-phenethyl alcohol, respectively. Transient kinetic studies and simulations of the ordered bi bi mechanism for the oxidation of the 2-butanols by the S48T/F93A ADH show that the rate of hydride transfer is increased about 7-fold for both isomers (relative to wild-type enzyme) and that the inversion of enantioselectivity is due to more productive binding for (R)-2-butanol than for (S)-2-butanol in the ternary complex. Molecular modeling suggests that both of the sec-phenethyl alcohols could bind to the enzyme and that dynamics must affect the rates of catalysis.« less

Landsat 7 thermal-IR image sharpening using an artificial neural network and sensor model

USGS Publications Warehouse

Lemeshewsky, G.P.; Schowengerdt, R.A.; ,

2001-01-01

The enhanced thematic mapper (plus) (ETM+) instrument on Landsat 7 shares the same basic design as the TM sensors on Landsats 4 and 5, with some significant improvements. In common are six multispectral bands with a 30-m ground-projected instantaneous field of view (GIFOV). However, the thermaL-IR (TIR) band now has a 60-m GIFOV, instead of 120-m. Also, a 15-m panchromatic band has been added. The artificial neural network (NN) image sharpening method described here uses data from the higher spatial resolution ETM+ bands to enhance (sharpen) the spatial resolution of the TIR imagery. It is based on an assumed correlation over multiple scales of resolution, between image edge contrast patterns in the TIR band and several other spectral bands. A multilayer, feedforward NN is trained to approximate TIR data at 60m, given degraded (from 30-m to 60-m) spatial resolution input from spectral bands 7, 5, and 2. After training, the NN output for full-resolution input generates an approximation of a TIR image at 30-m resolution. Two methods are used to degrade the spatial resolution of the imagery used for NN training, and the corresponding sharpening results are compared. One degradation method uses a published sensor transfer function (TF) for Landsat 5 to simulate sensor coarser resolution imagery from higher resolution imagery. For comparison, the second degradation method is simply Gaussian low pass filtering and subsampling, wherein the Gaussian filter approximates the full width at half maximum amplitude characteristics of the TF-based spatial filter. Two fixed-size NNs (that is, number of weights and processing elements) were trained separately with the degraded resolution data, and the sharpening results compared. The comparison evaluates the relative influence of the degradation technique employed and whether or not it is desirable to incorporate a sensor TF model. Preliminary results indicate some improvements for the sensor model-based technique. Further evaluation using a higher resolution reference image and strict application of sensor model to data is recommended.

Thermal-hydraulic analysis of the coil test facility for CFETR.

PubMed

Ren, Yong; Liu, Xiaogang; Li, Junjun; Wang, Zhaoliang; Qiu, Lilong; Du, Shijun; Li, Guoqiang; Gao, Xiang

2016-01-01

Performance test of the China Fusion Engineering Test Reactor (CFETR) central solenoid (CS) and toroidal field (TF) insert coils is of great importance to evaluate the CFETR magnet performance in relevant operation conditions. The superconducting magnet of the coil test facility for CFETR is being designed with the aim of providing a background magnetic field to test the CFETR CS insert and TF insert coils. The superconducting magnet consists of the inner module with Nb 3 Sn coil and the outer module with NbTi coil. The superconducting magnet is designed to have a maximum magnetic field of 12.59 T and a stored energy of 436.6 MJ. An active quench protection circuit and the positive temperature coefficient dump resistor were adopted to transfer the stored magnetic energy. The temperature margin behavior of the test facility for CFETR satisfies the design criteria. The quench analysis of the test facility shows that the cable temperature and the helium pressure inside the jacket are within the design criteria.

Role of Multiple Hosts in the Cross-Species Transmission and Emergence of a Pandemic Parvovirus

PubMed Central

Allison, Andrew B.; Harbison, Carole E.; Pagan, Israel; Stucker, Karla M.; Kaelber, Jason T.; Brown, Justin D.; Ruder, Mark G.; Keel, M. Kevin; Dubovi, Edward J.; Holmes, Edward C.

2012-01-01

Understanding the mechanisms of cross-species virus transmission is critical to anticipating emerging infectious diseases. Canine parvovirus type 2 (CPV-2) emerged as a variant of a feline parvovirus when it acquired mutations that allowed binding to the canine transferrin receptor type 1 (TfR). However, CPV-2 was soon replaced by a variant virus (CPV-2a) that differed in antigenicity and receptor binding. Here we show that the emergence of CPV involved an additional host range variant virus that has circulated undetected in raccoons for at least 24 years, with transfers to and from dogs. Raccoon virus capsids showed little binding to the canine TfR, showed little infection of canine cells, and had altered antigenic structures. Remarkably, in capsid protein (VP2) phylogenies, most raccoon viruses fell as evolutionary intermediates between the CPV-2 and CPV-2a strains, suggesting that passage through raccoons assisted in the evolution of CPV-2a. This highlights the potential role of alternative hosts in viral emergence. PMID:22072763

Role of multiple hosts in the cross-species transmission and emergence of a pandemic parvovirus.

PubMed

Allison, Andrew B; Harbison, Carole E; Pagan, Israel; Stucker, Karla M; Kaelber, Jason T; Brown, Justin D; Ruder, Mark G; Keel, M Kevin; Dubovi, Edward J; Holmes, Edward C; Parrish, Colin R

2012-01-01

Understanding the mechanisms of cross-species virus transmission is critical to anticipating emerging infectious diseases. Canine parvovirus type 2 (CPV-2) emerged as a variant of a feline parvovirus when it acquired mutations that allowed binding to the canine transferrin receptor type 1 (TfR). However, CPV-2 was soon replaced by a variant virus (CPV-2a) that differed in antigenicity and receptor binding. Here we show that the emergence of CPV involved an additional host range variant virus that has circulated undetected in raccoons for at least 24 years, with transfers to and from dogs. Raccoon virus capsids showed little binding to the canine TfR, showed little infection of canine cells, and had altered antigenic structures. Remarkably, in capsid protein (VP2) phylogenies, most raccoon viruses fell as evolutionary intermediates between the CPV-2 and CPV-2a strains, suggesting that passage through raccoons assisted in the evolution of CPV-2a. This highlights the potential role of alternative hosts in viral emergence.

Condensation Heat-Transfer Measurements of Refrigerants on Externally Enhanced Tubes.

DTIC Science & Technology

1987-06-01

Pf Density of condensate at Tf (kgjm3 ) e Insulated angle em Rotation angle of normal to fin surface Of Surface tension of condensate (N/m) a Nusselt ...reported data for the condensation of steam at near atmospheric pressure on smooth tubes and roped tubes with and without a helical , external wrap of...Their model, a Nusselt -type equation based on the equivalent diameter of the finned tube, lives the average condensing coefficient by the following

Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF

PubMed Central

Cong, Yingnan; Chan, Yao-ban; Phillips, Charles A.; Langston, Michael A.; Ragan, Mark A.

2017-01-01

Bacteria and archaea can exchange genetic material across lineages through processes of lateral genetic transfer (LGT). Collectively, these exchange relationships can be modeled as a network and analyzed using concepts from graph theory. In particular, densely connected regions within an LGT network have been defined as genetic exchange communities (GECs). However, it has been problematic to construct networks in which edges solely represent LGT. Here we apply term frequency-inverse document frequency (TF-IDF), an alignment-free method originating from document analysis, to infer regions of lateral origin in bacterial genomes. We examine four empirical datasets of different size (number of genomes) and phyletic breadth, varying a key parameter (word length k) within bounds established in previous work. We map the inferred lateral regions to genes in recipient genomes, and construct networks in which the nodes are groups of genomes, and the edges natively represent LGT. We then extract maximum and maximal cliques (i.e., GECs) from these graphs, and identify nodes that belong to GECs across a wide range of k. Most surviving lateral transfer has happened within these GECs. Using Gene Ontology enrichment tests we demonstrate that biological processes associated with metabolism, regulation and transport are often over-represented among the genes affected by LGT within these communities. These enrichments are largely robust to change of k. PMID:28154557

Toll-like receptor (TLR)-4 mediates anti-β2GPI/β2GPI-induced tissue factor expression in THP-1 cells

PubMed Central

Zhou, H; Yan, Y; Xu, G; Zhou, B; Wen, H; Guo, D; Zhou, F; Wang, H

2011-01-01

Our previous study demonstrated that annexin A2 (ANX2) on cell surface could function as a mediator and stimulate tissue factor (TF) expression of monocytes by anti-β2-glycoprotein I/β2-glycoprotein I complex (anti-β2GPI/β2GPI). However, ANX2 is not a transmembrane protein and lacks the intracellular signal transduction pathway. Growing evidence suggests that Toll-like receptor 4 (TLR-4) might act as an ‘adaptor’ for intracellular signal transduction in anti-β2GPI/β2GPI-induced TF expressing cells. In the current study, we investigated the roles of TLR-4 and its related molecules, myeloid differentiation protein 2 (MD-2) and myeloid differentiation factor 88 (MyD88), in anti-β2GPI/β2GPI-induced TF expressing human monocytic-derived THP-1 (human acute monocytic leukaemia) cells. The relationship of TLR-4 and ANX2 in this process was also explored. Along with TF, expression of TLR-4, MD-2 and MyD88 in THP-1 cells increased significantly when treated by anti-β2GPI (10 µg/ml)/β2GPI (100 µg/ml) complex. The addition of paclitaxel, which competes with the MD-2 ligand, could inhibit the effects of anti-β2GPI/β2GPI on TLR-4, MD-2, MyD88 and TF expression. Both ANX2 and TLR-4 in THP-1 cell lysates could bind to β2GPI that had been conjugated to a column (β2GPI-Affi-Gel). Furthermore, TLR-4, MD-2, MyD88 and TF expression was remarkably diminished in THP-1 cells infected with ANX2-specific RNA interference (RNAi) lentivirus (LV-RNAi-ANX2), in spite of treatment with a similar concentration of anti-β2GPI/β2GPI complex. These results indicate that TLR-4 and its signal transduction pathway contribute to anti-β2GPI/β2GPI-induced TF expression in THP-1 cells, and the effects of TLR-4 with ANX2 are tightly co-operative. PMID:21091668

Spectroscopic studies of the interaction between alprazolam and apo-human serum transferrin as a drug carrier protein.

PubMed

Karimian Amroabadi, Marzieh; Taheri-Kafrani, Asghar; Heidarpoor Saremi, Leily; Rastegari, Ali Asghar

2018-03-01

The interaction between apo-human serum transferrin (Apo-hTf) and alprazolam was investigated using various spectroscopic techniques. The drug quenched the fluorescence intensity of Apo-hTf and the mechanism behind the quenching was static. The thermodynamic parameters (ΔG, ΔH, and ΔS) that obtained from tryptophan fluorescence study revealed that the interactions between alprazolam and Apo-hTf were spontaneous. Collectively, hydrophobic interactions and hydrogen bonding most likely played major roles in Apo-hTf/alprazolam interactions. Also, the absorption spectra of Apo-hTf increased in the presence of increasing concentration of alprazolam, reflecting Apo-hTf structural alteration after drug's binding. The CD results demonstrated that the Apo-hTf/alprazolam interaction does not affect the protein secondary and tertiary structure significantly until the molar ratios (alprazolam/Apo-hTf) of 10, but the conformational changes become visible at higher molar ratios. The DSC results suggested that alprazolam stabilized the Apo-hTf at alprazolam/Apo-hTf molar ratio of 20. Based on the achieved results, this potentially therapeutic agent can significantly bind to Apo-hTf which also further confirmed by molecular docking study. This study on the interaction of the drug with Apo-hTf should be helpful for understanding the transportation and distribution of drugs in vivo, as well as the action mechanism and dynamics of a drug at the molecular level. Copyright © 2017 Elsevier B.V. All rights reserved.

Stepped care versus standard trauma-focused cognitive behavioral therapy for young children

PubMed Central

Salloum, Alison; Wang, Wei; Robst, John; Murphy, Tanya K.; Scheeringa, Michael S.; Cohen, Judith A.; Storch, Eric A.

2015-01-01

Background Compare the effectiveness and cost of stepped care trauma-focused cognitive behavioral therapy (SC-TF-CBT), a new service delivery method designed to address treatment barriers, to standard TF-CBT among young children who were experiencing posttraumatic stress symptoms (PTSS). Methods A total of 53 children (ages 3-7 years) who were experiencing PTSS were randomly assigned (2:1) to receive SC-TF-CBT or TF-CBT. Assessments by a blinded evaluator occurred at screening/baseline, after Step One for SC-TF-CBT, post-treatment, and 3-month follow-up. Trial registration: ClinicalTrials.gov: https://www.clinicaltrials.gov/ct2/show/NCT01603563 Results There were comparable improvements over time in PTSS and secondary outcomes in both conditions. Non-inferiority of SC-TF-CBT compared to TF-CBT was supported for the primary outcome of PTSS, and the secondary outcomes of severity and internalizing symptoms, but not for externalizing symptoms. There were no statistical differences in comparisons of changes over time from pre- to post-treatment and pre- to 3 month follow-up for PTSD diagnostic status, treatment response or remission. Parent satisfaction was high for both conditions. Costs were 51.3% lower for children in SC-TF-CBT compared to TF-CBT. Conclusions Although future research is needed, preliminary evidence suggests that SC-TF-CBT is comparable to TF-CBT, and delivery costs are significantly less than standard care. SC-TF-CBT may be a viable service delivery system to address treatment barriers. PMID:26443493

Stepped and Standard Care for Childhood Trauma: A Pilot Randomized Clinical Trial

ERIC Educational Resources Information Center

Salloum, Alison; Small, Brent J.; Robst, John; Scheeringa, Michael S.; Cohen, Judith A.; Storch, Eric A.

2017-01-01

Objective: This study explored the feasibility of stepped care trauma-focused cognitive behavioral therapy (SC-TF-CBT) relative to TF-CBT with children (aged 8--12). Method: Children (N = 33) with post-traumatic stress symptoms (PTSS) were randomly assigned (2:1) to SC-TF-CBT or TF-CBT. SC-TF-CBT consisted of Step 1, parent-led therapist-assisted…

Design, synthesis, nuclear localization, and biological activity of a fluorescent duocarmycin analog, HxTfA.

PubMed

Kiakos, Konstantinos; Englinger, Bernhard; Yanow, Stephanie K; Wernitznig, Debora; Jakupec, Michael A; Berger, Walter; Keppler, Bernhard K; Hartley, John A; Lee, Moses; Patil, Pravin C

2018-05-01

HxTfA 4 is a fluorescent analog of a potent cytotoxic and antimalarial agent, TfA 3, which is currently being investigated for the development of an antimalarial vaccine, PlasProtect®. HxTfA contains a p-anisylbenzimidazole or Hx moiety, which is endowed with a blue emission upon excitation at 318 nm; thus enabling it to be used as a surrogate for probing the cellular fate of TfA using confocal microscopy, and addressing the question of nuclear localization. HxTfA exhibits similar selectivity to TfA for A-tract sequences of DNA, alkylating adenine-N3, albeit at 10-fold higher concentrations. It also possesses in vitro cytotoxicity against A549 human lung carcinoma cells and Plasmodium falciparum. Confocal microscopy studies showed for the first time that HxTfA, and by inference TfA, entered A549 cells and localized in the nucleus to exert its biological activity. At biologically relevant concentrations, HxTfA elicits DNA damage response as evidenced by a marked increase in the levels of γH2AX observed by confocal microscopy and immunoblotting studies, and ultimately induces apoptosis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Blood-brain barrier drug delivery of IgG fusion proteins with a transferrin receptor monoclonal antibody.

PubMed

Pardridge, William M

2015-02-01

Biologic drugs are large molecules that do not cross the blood- brain barrier (BBB). Brain penetration is possible following the re-engineering of the biologic drug as an IgG fusion protein. The IgG domain is a MAb against an endogenous BBB receptor such as the transferrin receptor (TfR). The TfRMAb acts as a molecular Trojan horse to ferry the fused biologic drug into the brain via receptor-mediated transport on the endogenous BBB TfR. This review discusses TfR isoforms, models of BBB transport of transferrin and TfRMAbs, and the genetic engineering of TfRMAb fusion proteins, including BBB penetrating IgG-neurotrophins, IgG-decoy receptors, IgG-lysosomal enzyme therapeutics and IgG-avidin fusion proteins, as well as BBB transport of bispecific antibodies formed by fusion of a therapeutic antibody to a TfRMAb targeting antibody. Also discussed are quantitative aspects of the plasma pharmacokinetics and brain uptake of TfRMAb fusion proteins, as compared to the brain uptake of small molecules, and therapeutic applications of TfRMAb fusion proteins in mouse models of neural disease, including Parkinson's disease, stroke, Alzheimer's disease and lysosomal storage disorders. The review covers the engineering of TfRMAb-avidin fusion proteins for BBB targeted delivery of biotinylated peptide radiopharmaceuticals, low-affinity TfRMAb Trojan horses and the safety pharmacology of chronic administration of TfRMAb fusion proteins. The BBB delivery of biologic drugs is possible following re-engineering as a fusion protein with a molecular Trojan horse such as a TfRMAb. The efficacy of this technology will be determined by the outcome of future clinical trials.

Properties of a recombinant bovine tissue factor expressed by Silkworm pupae and its performance as an Owren-type prothrombin time reagent for warfarin monitoring.

PubMed

Okuda, Masahiro; Taniguchi, Tomokuni; Takamiya, Osamu

2012-09-01

Tissue factor (TF), or thromboplastin, is a glycoprotein that triggers the extrinsic coagulation pathway. In blood coagulation testing, TF has been used as a natural source for determining Quick prothrombin time (PT) or the Owren PT (OBT). Currently, natural sources are being replaced with recombinant proteins because of their uniform characteristics and the possibility of stable mass production of PT reagents. Because bovine spongiform encephalopathy (BSE)-infected cows are widespread in Japan, we prepared a recombinant bovine TF (rbTF) with a baculovirus expression system using silkworms. To overcome the limitations of natural TF, especially in bovine brain, we expressed a full-length rbTF protein in Silkworm pupae with a baculovirus expression system. Baculovirus inactivation and the presence of DNA fragments in the rbTF fraction were confirmed using Reed-Muench and polymerase chain reaction methods after inactivation with a detergent. The rbTF fraction prepared by an immobilized anti-Silkworm pupae fluid protein Sepharose 4B column was identified as a visible band on western blots with a polyclonal antibody against human TF with cross-reactivity with TFs. The inhibition of the polyclonal antibody against human TF by the clotting assay for PT was identified, and amidolytic biological activity through activated factor VII on S-2288 substrate was observed. In conclusion, the rbTF expressed by the baculovirus system using Silkworm pupae was uniformly specific for bovine TF. The OBT reagent incorporated by this rbTF was similar to those of commercial reagents. It also showed a suitable International Sensitivity Index and reproducibility precision, thereby allowing for diagnostic use. Copyright © 2012 Elsevier Ltd. All rights reserved.

The requirement of iron transport for lymphocyte function.

PubMed

Lo, Bernice

2016-01-01

Iron is essential in multiple cellular processes and is especially critical for cellular respiration and division. A new study identified a mutation affecting the iron import receptor TfR1 as the cause of a human primary immunodeficiency, illuminating the importance of iron in immune cell function.

A dual brain-targeting curcumin-loaded polymersomes ameliorated cognitive dysfunction in intrahippocampal amyloid-β1-42-injected mice.

PubMed

Jia, Tingting; Sun, Zhiguo; Lu, Ying; Gao, Jie; Zou, Hao; Xie, Fangyuan; Zhang, Guoqing; Xu, Hao; Sun, Duxin; Yu, Yuan; Zhong, Yanqiang

2016-01-01

Due to the impermeability of the blood-brain barrier and the nonselective distribution of drugs in the brain, the therapeutic access to intractable neurological disorders is challenging. In this study, dual brain-targeting polymersomes (POs) functionalized by transferrin and Tet-1 peptide (Tf/Tet-1-POs) promoted the transportation of curcumin into the brain and provided neuroprotection. The modification of the ligands that bind to the surface of POs was revealed by X-ray photoelectron spectroscopy analysis. The cell uptake of a coculture model of mouse brain capillary endothelial cells with neurons showed that the Tf/Tet-1-POs had significant transportation properties and possessed affinity for neurons. The pharmacokinetic analysis showed that the blood-brain barrier permeability-surface efficiency of the Tf/Tet-1-POs was 0.28 mL/h/g and that the brain tissue uptake rate (% ID/g) was 0.08, which were significant compared with the controls (P<0.05). The curcumin-encapsulated Tf/Tet-1-POs provided neuroprotection and ameliorated cognitive dysfunction in intrahippocampal amyloid-β1-42-injected mice. These results suggest that the dual brain-targeting POs are more capable of drug delivery to the brain that can be exploited as a multiple noninvasive vehicle for targeting therapeutics.

Development and evaluation of an intelligent traceability system for frozen tilapia fillet processing.

PubMed

Xiao, Xinqing; Fu, Zetian; Qi, Lin; Mira, Trebar; Zhang, Xiaoshuan

2015-10-01

The main export varieties in China are brand-name, high-quality bred aquatic products. Among them, tilapia has become the most important and fast-growing species since extensive consumer markets in North America and Europe have evolved as a result of commodity prices, year-round availability and quality of fresh and frozen products. As the largest tilapia farming country, China has over one-third of its tilapia production devoted to further processing and meeting foreign market demand. Using by tilapia fillet processing, this paper introduces the efforts for developing and evaluating ITS-TF: an intelligent traceability system integrated with statistical process control (SPC) and fault tree analysis (FTA). Observations, literature review and expert questionnaires were used for system requirement and knowledge acquisition; scenario simulation was applied to evaluate and validate ITS-TF performance. The results show that traceability requirement is evolved from a firefighting model to a proactive model for enhancing process management capacity for food safety; ITS-TF transforms itself as an intelligent system to provide functions on early warnings and process management by integrated SPC and FTA. The valuable suggestion that automatic data acquisition and communication technology should be integrated into ITS-TF was achieved for further system optimization, perfection and performance improvement. © 2014 Society of Chemical Industry.

Expression of the Thomsen-Friedenreich (TF) tumor antigen in human abort placentas.

PubMed

Richter, D U; Jeschke, U; Bergemann, C; Makovitzky, J; Lüthen, F; Karsten, U; Briese, V

2005-01-01

The Thomsen-Friedenreich antigen (TF), or more precisely epitope, has been known as a pancarcinoma antigen. It consists of galactose-beta1-3-N-acetylgalactose. We have already described the expression of TF in the normal placenta. TF is expressed by the syncytium and by extravillous trophoblast cells. In this study, we investigated the expression of TF in the abort placenta. Frozen samples of human abort placentas (12 placentas), obtained from the first and second trimesters of pregnancy and, for comparison, samples of normal placentas (17 placentas) from the first, second and third trimesters of pregnancy, were used. Expression of TF was investigated by immunohistochemical methods. For identification of TF-positive cells in abort placentas, immunofluorescence methods were used. Evaluation of simple and double immunofluorescence was performed on a laser scanning microscope. Furthermore, we isolated trophoblast cells from first and third trimester placentas and evaluated cytokeratin 7 and Muc1 expression by immunofluorescence methods. We observed expression of TF antigen in the syncytiotrophoblasts layer of the placenta in all three trimesters of pregnancy in normal and abort placentas evaluated by immunohistochemical methods. There was no expression of TF antigen in the decidua of abort placentas. Immunofluorescence double staining of TF antigen and cytokeratin 7 showed reduced expression of both antigens in the abort decidua and co-expression of both antigens in the syncytiotrophoblast layer of normal and abort placentas. TF expression in the syncytiotrophoblast was reduced in abort placentas. In the isolated trophoblast cells, no TF expression was found, however, Muc1 expression was visualized. Expression of TF antigen was reduced in the first and second trimester abort decidua compared to the normal decidua during the same time of pregnancy. TF antigen was restricted to the syncytiotrophoblast and extravillous trophoblast cells in the decidua. Abort placentas expressed TF antigen on the syncytiotrophoblast layer, but with lower intensity compared to normal placentas. We found a significantly reduced co-expression of TF antigen and cytokeratin 7 in the decidua of abort placentas. These data suggested a reduction of extravillous trophoblast cells in the decidua of abort placentas. In addition, we found higher numbers of CD45-positive cells in the abort decidua compared to normal placentas.

Structural basis for receptor recognition by New World hemorrhagic fever arenaviruses

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

Abraham, Jonathan; Corbett, Kevin D.; Farzan, Michael

New World hemorrhagic fever arenaviruses are rodent-borne agents that cause severe human disease. The GP1 subunit of the surface glycoprotein mediates cell attachment through transferrin receptor 1 (TfR1). We report the structure of Machupo virus (MACV) GP1 bound with human TfR1. Atomic details of the GP1-TfR1 interface clarify the importance of TfR1 residues implicated in New World arenavirus host specificity. Analysis of sequence variation among New World arenavirus GP1s and their host-species receptors, in light of the molecular structure, indicates determinants of viral zoonotic transmission. Infectivities of pseudoviruses in cells expressing mutated TfR1 confirm that contacts at the tip ofmore » the TfR1 apical domain determine the capacity of human TfR1 to mediate infection by particular New World arenaviruses. We propose that New World arenaviruses that are pathogenic to humans fortuitously acquired affinity for human TfR1 during adaptation to TfR1 of their natural hosts.« less

Ion transport with charge-protected and non-charge-protected cations using the compensated Arrhenius formalism. Part 2. Relationship between ionic conductivity and diffusion.

PubMed

Petrowsky, Matt; Fleshman, Allison; Bopege, Dharshani N; Frech, Roger

2012-08-09

Temperature-dependent ionic conductivities and cation/anion self-diffusion coefficients are measured for four electrolyte families: TbaTf-linear primary alcohols, LiTf-linear primary alcohols, TbaTf-n-alkyl acetates, and LiTf-n-alkyl acetates. The Nernst-Einstein equation does not adequately describe the data. Instead, the compensated Arrhenius formalism is applied to both conductivity and diffusion data. General trends based on temperature and alkyl chain length are observed when conductivity is plotted against cation or anion diffusion coefficient, but there is no clear pattern to the data. However, plotting conductivity exponential prefactors against those for diffusion results in four distinct curves, one each for the alcohol and acetate families described above. Furthermore, the TbaTf-alcohol and TbaTf-acetate data are "in line" with each other. The conductivity prefactors for the LiTf-alcohol data are smaller than those for the TbaTf data. The LiTf-acetate data have the lowest conductivity prefactors. This trend in prefactors mirrors the observed trend in degree of ionic association for these electrolytes.

"Hit-and-Run" leaves its mark: catalyst transcription factors and chromatin modification.

PubMed

Varala, Kranthi; Li, Ying; Marshall-Colón, Amy; Para, Alessia; Coruzzi, Gloria M

2015-08-01

Understanding how transcription factor (TF) binding is related to gene regulation is a moving target. We recently uncovered genome-wide evidence for a "Hit-and-Run" model of transcription. In this model, a master TF "hits" a target promoter to initiate a rapid response to a signal. As the "hit" is transient, the model invokes recruitment of partner TFs to sustain transcription over time. Following the "run", the master TF "hits" other targets to propagate the response genome-wide. As such, a TF may act as a "catalyst" to mount a broad and acute response in cells that first sense the signal, while the recruited TF partners promote long-term adaptive behavior in the whole organism. This "Hit-and-Run" model likely has broad relevance, as TF perturbation studies across eukaryotes show small overlaps between TF-regulated and TF-bound genes, implicating transient TF-target binding. Here, we explore this "Hit-and-Run" model to suggest molecular mechanisms and its biological relevance. © 2015 The Authors. Bioessays published by WILEY Periodicals, Inc.

Specificity of the weak binding between the phage SPO1 transcription-inhibitory protein, TF1, and SPO1 DNA.

PubMed

Johnson, G G; Geiduschek, E P

1977-04-05

The interaction of the phage SPO1 protein transcription factor 1 (TF1), with DNA has been analyzed by membrane filter binding and by sedimentation methods. Substantially specific binding of TF1 to helical SPO1 DNA can be demonstrated by nitrocellulose filter-binding assays at relatively low ionic strength (0.08). However, TF1-DNA complexes dissociate and reequilibrate relatively rapidly and this makes filter-binding assays unsuitable for quantitative measurements of binding equilibra. Accordingly, the sedimentation properties of TF1-DNA complexes have been explored and a short-column centrifugation assay has been elaborated for quantitative measurements. Preferential binding of TF1 to the hydroxymethyluracil-containing SPO1 DNA has also been demonstrated by short-column centrifugation. TF1 binds relatively weakly and somewhat cooperatively to SPO1 DNA at many sites; TF1-DNA complexes dissociate and reequilibrate rapidly. At 20 degrees C in 0.01 M phosphate, pH 7.5, 0.15 KC1, one molecule of TF1 can bind to approximately every 60 nucleotide pairs of SPO1 DNA.

Large enhancement of functional activity of active site-inhibited factor VIIa due to protein dimerization: insights into mechanism of assembly/disassembly from tissue factor.

PubMed

Stone, Matthew D; Harvey, Stephen B; Martinez, Michael B; Bach, Ronald R; Nelsestuen, Gary L

2005-04-26

Active site-inhibited blood clotting factor VIIa (fVIIai) binds to tissue factor (TF), a cell surface receptor that is exposed upon injury and initiates the blood clotting cascade. FVIIai blocks binding of the corresponding enzyme (fVIIa) or zymogen (fVII) forms of factor VII and inhibits coagulation. Although several studies have suggested that fVIIai may have superior anticoagulation effects in vivo, a challenge for use of fVIIai is cost of production. This study reports the properties of dimeric forms of fVIIai that are cross-linked through their active sites. Dimeric wild-type fVIIai was at least 75-fold more effective than monomeric fVIIai in blocking fVIIa association with TF. The dimer of a mutant fVIIai with higher membrane affinity was 1600-fold more effective. Anticoagulation by any form of fVIIai differed substantially from agents such as heparin and showed a delayed mode of action. Coagulation proceeded normally for the first minutes, and inhibition increased as equilibrium binding was established. It is suggested that association of fVIIa(i) with TF in a collision-dependent reaction gives equal access of inhibitor and enzyme to TF. Assembly was not influenced by the higher affinity and slower dissociation of the dimer. As a result, anticoagulation was delayed until the reaction reached equilibrium. Properties of different dissociation experiments suggested that dissociation of fVIIai from TF occurred by a two-step mechanism. The first step was separation of TF-fVIIa(i) while both proteins remained bound to the membrane, and the second step was dissociation of the fVIIa(i) from the membrane. These results suggest novel actions of fVIIai that distinguish it from most of the anticoagulants that block later steps of the coagulation cascade.

β cell membrane remodelling and procoagulant events occur in inflammation-driven insulin impairment: a GLP-1 receptor dependent and independent control.

PubMed

Gleizes, Céline; Kreutter, Guillaume; Abbas, Malak; Kassem, Mohamad; Constantinescu, Andrei Alexandru; Boisramé-Helms, Julie; Yver, Blandine; Toti, Florence; Kessler, Laurence

2016-02-01

Inflammation and hyperglycaemia are associated with a prothrombotic state. Cell-derived microparticles (MPs) are the conveyors of active procoagulant tissue factor (TF) and circulate at high concentration in diabetic patients. Liraglutide, a glucagon-like peptide (GLP)-1 analogue, is known to promote insulin secretion and β-cell preservation. In this in vitro study, we examined the link between insulin impairment, procoagulant activity and plasma membrane remodelling, under inflammatory conditions. Rin-m5f β-cell function, TF activity mediated by MPs and their modulation by 1 μM liraglutide were examined in a cell cross-talk model. Methyl-β-cyclodextrine (MCD), a cholesterol depletor, was used to evaluate the involvement of raft on TF activity, MP shedding and insulin secretion as well as Soluble N-éthylmaleimide-sensitive-factor Attachment protein Receptor (SNARE)-dependent exocytosis. Cytokines induced a two-fold increase in TF activity at MP surface that was counteracted by liraglutide. Microparticles prompted TF activity on the target cells and a two-fold decrease in insulin secretion via protein kinase A (PKA) and p38 signalling, that was also abolished by liraglutide. Large lipid raft clusters were formed in response to cytokines and liraglutide or MCD-treated cells showed similar patterns. Cells pre-treated by saturating concentration of the GLP-1r antagonist exendin (9-39), showed a partial abolishment of the liraglutide-driven insulin secretion and liraglutide-decreased TF activity. Measurement of caspase 3 cleavage and MP shedding confirmed the contribution of GLP-1r-dependent and -independent pathways. Our results confirm an integrative β-cell response to GLP-1 that targets receptor-mediated signalling and membrane remodelling pointing at the coupling of insulin secretion and inflammation-driven procoagulant events. © 2015 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Genetic Basis for Developmental Homeostasis of Germline Stem Cell Niche Number: A Network of Tramtrack-Group Nuclear BTB Factors

PubMed Central

Chalvet, Fabienne; Netter, Sophie; Dos Santos, Nicolas; Poisot, Emilie; Paces-Fessy, Mélanie; Cumenal, Delphine; Peronnet, Frédérique; Pret, Anne-Marie; Théodore, Laurent

2012-01-01

The potential to produce new cells during adult life depends on the number of stem cell niches and the capacity of stem cells to divide, and is therefore under the control of programs ensuring developmental homeostasis. However, it remains generally unknown how the number of stem cell niches is controlled. In the insect ovary, each germline stem cell (GSC) niche is embedded in a functional unit called an ovariole. The number of ovarioles, and thus the number of GSC niches, varies widely among species. In Drosophila, morphogenesis of ovarioles starts in larvae with the formation of terminal filaments (TFs), each made of 8–10 cells that pile up and sort in stacks. TFs constitute organizers of individual germline stem cell niches during larval and early pupal development. In the Drosophila melanogaster subgroup, the number of ovarioles varies interspecifically from 8 to 20. Here we show that pipsqueak, Trithorax-like, batman and the bric-à-brac (bab) locus, all encoding nuclear BTB/POZ factors of the Tramtrack Group, are involved in limiting the number of ovarioles in D. melanogaster. At least two different processes are differentially perturbed by reducing the function of these genes. We found that when the bab dose is reduced, sorting of TF cells into TFs was affected such that each TF contains fewer cells and more TFs are formed. In contrast, psq mutants exhibited a greater number of TF cells per ovary, with a normal number of cells per TF, thereby leading to formation of more TFs per ovary than in the wild type. Our results indicate that two parallel genetic pathways under the control of a network of nuclear BTB factors are combined in order to negatively control the number of germline stem cell niches. PMID:23185495

SND1 Transcription Factor–Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa[C][W

PubMed Central

Lin, Ying-Chung; Li, Wei; Sun, Ying-Hsuan; Kumari, Sapna; Wei, Hairong; Li, Quanzi; Tunlaya-Anukit, Sermsawat; Sederoff, Ronald R.; Chiang, Vincent L.

2013-01-01

Wood is an essential renewable raw material for industrial products and energy. However, knowledge of the genetic regulation of wood formation is limited. We developed a genome-wide high-throughput system for the discovery and validation of specific transcription factor (TF)–directed hierarchical gene regulatory networks (hGRNs) in wood formation. This system depends on a new robust procedure for isolation and transfection of Populus trichocarpa stem differentiating xylem protoplasts. We overexpressed Secondary Wall-Associated NAC Domain 1s (Ptr-SND1-B1), a TF gene affecting wood formation, in these protoplasts and identified differentially expressed genes by RNA sequencing. Direct Ptr-SND1-B1–DNA interactions were then inferred by integration of time-course RNA sequencing data and top-down Graphical Gaussian Modeling–based algorithms. These Ptr-SND1-B1-DNA interactions were verified to function in differentiating xylem by anti-PtrSND1-B1 antibody-based chromatin immunoprecipitation (97% accuracy) and in stable transgenic P. trichocarpa (90% accuracy). In this way, we established a Ptr-SND1-B1–directed quantitative hGRN involving 76 direct targets, including eight TF and 61 enzyme-coding genes previously unidentified as targets. The network can be extended to the third layer from the second-layer TFs by computation or by overexpression of a second-layer TF to identify a new group of direct targets (third layer). This approach would allow the sequential establishment, one two-layered hGRN at a time, of all layers involved in a more comprehensive hGRN. Our approach may be particularly useful to study hGRNs in complex processes in plant species resistant to stable genetic transformation and where mutants are unavailable. PMID:24280390

Efficient -2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein.

PubMed

Fang, Ying; Treffers, Emmely E; Li, Yanhua; Tas, Ali; Sun, Zhi; van der Meer, Yvonne; de Ru, Arnoud H; van Veelen, Peter A; Atkins, John F; Snijder, Eric J; Firth, Andrew E

2012-10-23

Programmed -1 ribosomal frameshifting (-1 PRF) is a gene-expression mechanism used to express many viral and some cellular genes. In contrast, efficient natural utilization of -2 PRF has not been demonstrated previously in eukaryotic systems. Like all nidoviruses, members of the Arteriviridae (a family of positive-stranded RNA viruses) express their replicase polyproteins pp1a and pp1ab from two long ORFs (1a and 1b), where synthesis of pp1ab depends on -1 PRF. These polyproteins are posttranslationally cleaved into at least 13 functional nonstructural proteins. Here we report that porcine reproductive and respiratory syndrome virus (PRRSV), and apparently most other arteriviruses, use an additional PRF mechanism to access a conserved alternative ORF that overlaps the nsp2-encoding region of ORF1a in the +1 frame. We show here that this ORF is translated via -2 PRF at a conserved G_GUU_UUU sequence (underscores separate ORF1a codons) at an estimated efficiency of around 20%, yielding a transframe fusion (nsp2TF) with the N-terminal two thirds of nsp2. Expression of nsp2TF in PRRSV-infected cells was verified using specific Abs, and the site and direction of frameshifting were determined via mass spectrometric analysis of nsp2TF. Further, mutagenesis showed that the frameshift site and an unusual frameshift-stimulatory element (a conserved CCCANCUCC motif 11 nucleotides downstream) are required to direct efficient -2 PRF. Mutations preventing nsp2TF expression impair PRRSV replication and produce a small-plaque phenotype. Our findings demonstrate that -2 PRF is a functional gene-expression mechanism in eukaryotes and add another layer to the complexity of arterivirus genome expression.

Transposon integration enhances expression of stress response genes.

PubMed

Feng, Gang; Leem, Young-Eun; Levin, Henry L

2013-01-01

Transposable elements possess specific patterns of integration. The biological impact of these integration profiles is not well understood. Tf1, a long-terminal repeat retrotransposon in Schizosaccharomyces pombe, integrates into promoters with a preference for the promoters of stress response genes. To determine the biological significance of Tf1 integration, we took advantage of saturated maps of insertion activity and studied how integration at hot spots affected the expression of the adjacent genes. Our study revealed that Tf1 integration did not reduce gene expression. Importantly, the insertions activated the expression of 6 of 32 genes tested. We found that Tf1 increased gene expression by inserting enhancer activity. Interestingly, the enhancer activity of Tf1 could be limited by Abp1, a host surveillance factor that sequesters transposon sequences into structures containing histone deacetylases. We found the Tf1 promoter was activated by heat treatment and, remarkably, only genes that themselves were induced by heat could be activated by Tf1 integration, suggesting a synergy of Tf1 enhancer sequence with the stress response elements of target promoters. We propose that the integration preference of Tf1 for the promoters of stress response genes and the ability of Tf1 to enhance the expression of these genes co-evolved to promote the survival of cells under stress.

Transposon integration enhances expression of stress response genes

PubMed Central

Feng, Gang; Leem, Young-Eun; Levin, Henry L.

2013-01-01

Transposable elements possess specific patterns of integration. The biological impact of these integration profiles is not well understood. Tf1, a long-terminal repeat retrotransposon in Schizosaccharomyces pombe, integrates into promoters with a preference for the promoters of stress response genes. To determine the biological significance of Tf1 integration, we took advantage of saturated maps of insertion activity and studied how integration at hot spots affected the expression of the adjacent genes. Our study revealed that Tf1 integration did not reduce gene expression. Importantly, the insertions activated the expression of 6 of 32 genes tested. We found that Tf1 increased gene expression by inserting enhancer activity. Interestingly, the enhancer activity of Tf1 could be limited by Abp1, a host surveillance factor that sequesters transposon sequences into structures containing histone deacetylases. We found the Tf1 promoter was activated by heat treatment and, remarkably, only genes that themselves were induced by heat could be activated by Tf1 integration, suggesting a synergy of Tf1 enhancer sequence with the stress response elements of target promoters. We propose that the integration preference of Tf1 for the promoters of stress response genes and the ability of Tf1 to enhance the expression of these genes co-evolved to promote the survival of cells under stress. PMID:23193295

Generation and gene expression profiling of 48 transcription-factor-inducible mouse embryonic stem cell lines.

PubMed

Yamamizu, Kohei; Sharov, Alexei A; Piao, Yulan; Amano, Misa; Yu, Hong; Nishiyama, Akira; Dudekula, Dawood B; Schlessinger, David; Ko, Minoru S H

2016-05-06

Mouse embryonic stem cells (ESCs) can differentiate into a wide range - and possibly all cell types in vitro, and thus provide an ideal platform to study systematically the action of transcription factors (TFs) in cell differentiation. Previously, we have generated and analyzed 137 TF-inducible mouse ESC lines. As an extension of this "NIA Mouse ESC Bank," we generated and characterized 48 additional mouse ESC lines, in which single TFs in each line could be induced in a doxycycline-controllable manner. Together, with the previous ESC lines, the bank now comprises 185 TF-manipulable ESC lines (>10% of all mouse TFs). Global gene expression (transcriptome) profiling revealed that the induction of individual TFs in mouse ESCs for 48 hours shifts their transcriptomes toward specific differentiation fates (e.g., neural lineages by Myt1 Isl1, and St18; mesodermal lineages by Pitx1, Pitx2, Barhl2, and Lmx1a; white blood cells by Myb, Etv2, and Tbx6, and ovary by Pitx1, Pitx2, and Dmrtc2). These data also provide and lists of inferred target genes of each TF and possible functions of these TFs. The results demonstrate the utility of mouse ESC lines and their transcriptome data for understanding the mechanism of cell differentiation and the function of TFs.

A global view of regulatory networks in lung cancer: An approach to understand homogeneity and heterogeneity.

PubMed

Lu, Jiapei; Wang, William; Xu, Menglin; Li, Yuping; Chen, Chengshui; Wang, Xiangdong

2017-02-01

A number of new biotechnologies are used to identify potential biomarkers for the early detection of lung cancer, enabling a personalized therapy to be developed in response. The combinatorial cross-regulation of hundreds of biological function-specific transcription factors (TFs) is defined as the understanding of regulatory networks of molecules within the cell. Here we integrated global databases with 537 patients with lung adenocarcinoma (ADC), 140 with lung squamous carcinoma (SCC), 9 with lung large-cell carcinoma (LCC), 56 with small-cell lung cancer (SCLC), and 590 without cancer with the understanding of TF functions. The present review aims at the homogeneity or heterogeneity of gene expression profiles among subtypes of lung cancer. About 5, 136, 52, or 16 up-regulated or 19, 24, 122, or 97down-regulated type-special TF genes were identified in ADC, SCC, LCC or SCLC, respectively. DNA-binding and transcription regulator activity associated genes play a dominant role in the differentiation of subtypes in lung cancer. Subtype-specific TF gene regulatory networks with elements should be an alternative for diagnostic and therapeutic targets for early identification of lung cancer and can provide insightful clues to etiology and pathogenesis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dual-Functional Nanographene Oxide as Cancer-Targeted Drug-Delivery System to Selectively Induce Cancer-Cell Apoptosis.

PubMed

Zhou, Binwei; Huang, Yanyu; Yang, Fang; Zheng, Wenjie; Chen, Tianfeng

2016-04-05

Construction of bioresponsive drug-delivery nanosystems could enhance the anticancer efficacy of anticancer agents and reduce their toxic side effects. Herein, by using transferrin (Tf) as a surface decorator, we constructed a cancer-targeted nanographene oxide (NGO) nanosystem for use in drug delivery. This nanosystem (Tf-NGO@HPIP) drastically enhanced the cellular uptake, retention, and anticancer efficacy of loaded drugs but showed much lower toxicity to normal cells. The nanosystem was internalized through receptor-mediated endocytosis and triggered pH-dependent drug release in acidic environments and in the presence of cellular enzymes. Moreover, Tf-NGO@HPIP effectively induced cancer-cell apoptosis through activation of superoxide-mediated p53 and MAPK pathways along with inactivation of ERK and AKT. Taken together, this study demonstrates a good strategy for the construction of bioresponsive NGO drug-delivery nanosystems and their use as efficient anticancer drug carriers. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transferrin-functionalized nanographene oxide for delivery of platinum complexes to enhance cancer-cell selectivity and apoptosis-inducing efficacy.

PubMed

Zhu, Hai; Zhou, Binwei; Chan, Leung; Du, Yanxin; Chen, Tianfeng

2017-01-01

Rational design and construction of delivery nanosystems for anticancer metal complexes is a crucial strategy to improve solubility under physiological conditions and permeability and retention behavior in tumor cells. Therefore, in this study, we designed and synthesize a transferrin (Tf)-conjugated nanographene oxide (NGO) nanosystem as a cancer-targeted nanocarrier of Pt complexes (Tf-NGO@Pt). This nanodelivery system exhibited good solubility under physiological conditions. Moreover, Tf-NGO@Pt showed higher anticancer efficacy against MCF human breast cancer cells than the free Pt complex, and effectively inhibited cancer-cell migration and invasion, with involvement of reactive oxygen species overproduction. In addition, nanolization also enhanced the penetration ability and inhibitory effect of the Pt complex toward MCF7 breast cancer-cell tumor spheroids. The enhancement of anticancer efficacy was positively correlated with increased cellular uptake and cellular drug retention. This study provides a new strategy to facilitate the future application of metal complexes in cancer therapy.

Rational Design of a Transferrin-Binding Peptide Sequence Tailored to Targeted Nanoparticle Internalization.

PubMed

Santi, Melissa; Maccari, Giuseppe; Mereghetti, Paolo; Voliani, Valerio; Rocchiccioli, Silvia; Ucciferri, Nadia; Luin, Stefano; Signore, Giovanni

2017-02-15

The transferrin receptor (TfR) is a promising target in cancer therapy owing to its overexpression in most solid tumors and on the blood-brain barrier. Nanostructures chemically derivatized with transferrin are employed in TfR targeting but often lose their functionality upon injection in the bloodstream. As an alternative strategy, we rationally designed a peptide coating able to bind transferrin on suitable pockets not involved in binding to TfR or iron by using an iterative multiscale-modeling approach coupled with quantitative structure-activity and relationship (QSAR) analysis and evolutionary algorithms. We tested that selected sequences have low aspecific protein adsorption and high binding energy toward transferrin, and one of them is efficiently internalized in cells with a transferrin-dependent pathway. Furthermore, it promotes transferrin-mediated endocytosis of gold nanoparticles by modifying their protein corona and promoting oriented adsorption of transferrin. This strategy leads to highly effective nanostructures, potentially useful in diagnostic and therapeutic applications, which exploit (and do not suffer) the protein solvation for achieving a better targeting.

DNA Looping Facilitates Targeting of a Chromatin Remodeling Enzyme

PubMed Central

Yadon, Adam N; Singh, Badri Nath; Hampsey, Michael; Tsukiyama, Toshio

2013-01-01

Summary ATP-dependent chromatin remodeling enzymes are highly abundant and play pivotal roles regulating DNA-dependent processes. The mechanisms by which they are targeted to specific loci have not been well understood on a genome-wide scale. Here we present evidence that a major targeting mechanism for the Isw2 chromatin remodeling enzyme to specific genomic loci is through sequence-specific transcription factor (TF)-dependent recruitment. Unexpectedly, Isw2 is recruited in a TF-dependent fashion to a large number of loci without TF binding sites. Using the 3C assay, we show that Isw2 can be targeted by Ume6- and TFIIB-dependent DNA looping. These results identify DNA looping as a previously unknown mechanism for the recruitment of a chromatin remodeling enzyme and defines a novel function for DNA looping. We also present evidence suggesting that Ume6-dependent DNA looping is involved in chromatin remodeling and transcriptional repression, revealing a mechanism by which the three-dimensional folding of chromatin affects DNA-dependent processes. PMID:23478442

Zinc-finger protein-targeted gene regulation: Genomewide single-gene specificity

PubMed Central

Tan, Siyuan; Guschin, Dmitry; Davalos, Albert; Lee, Ya-Li; Snowden, Andrew W.; Jouvenot, Yann; Zhang, H. Steven; Howes, Katherine; McNamara, Andrew R.; Lai, Albert; Ullman, Chris; Reynolds, Lindsey; Moore, Michael; Isalan, Mark; Berg, Lutz-Peter; Campos, Bradley; Qi, Hong; Spratt, S. Kaye; Case, Casey C.; Pabo, Carl O.; Campisi, Judith; Gregory, Philip D.

2003-01-01

Zinc-finger protein transcription factors (ZFP TFs) can be designed to control the expression of any desired target gene, and thus provide potential therapeutic tools for the study and treatment of disease. Here we report that a ZFP TF can repress target gene expression with single-gene specificity within the human genome. A ZFP TF repressor that binds an 18-bp recognition sequence within the promoter of the endogenous CHK2 gene gives a >10-fold reduction in CHK2 mRNA and protein. This level of repression was sufficient to generate a functional phenotype, as demonstrated by the loss of DNA damage-induced CHK2-dependent p53 phosphorylation. We determined the specificity of repression by using DNA microarrays and found that the ZFP TF repressed a single gene (CHK2) within the monitored genome in two different cell types. These data demonstrate the utility of ZFP TFs as precise tools for target validation, and highlight their potential as clinical therapeutics. PMID:14514889

Overview of Research Activities on Time and Frequency at the National Institute of Information and Communications Technology

DTIC Science & Technology

2004-12-01

FREQUENCY TRANSFER ( TWSTFT ) TWSTFT network in the Asia-Pacific region has developed by the collaboration of NICT and major T&F institutes in the...region [7]. A multi-channel TWSTFT modem has been developed by NICT. The performance evaluation shows that it is capable of sub-nanosecond time...intercomparison of NICT modem TWSTFT , ATLANTIS modem TWSTFT , and GPS common view (CV) in the case of the NICT-TL link is shown in Figure 4, and the stability

Increased circulating procoagulant and anticoagulant factors as TF and TFPI according to severity or infecting serotypes in human dengue infection.

PubMed

Leal de Azeredo, Elzinandes; Solórzano, Victor Edgar Fiestas; de Oliveira, Débora Batista; Marinho, Cintia Ferreira; de Souza, Luiz José; da Cunha, Rivaldo Venâncio; Damasco, Paulo Vieira; Kubelka, Claire Fernandes; de-Oliveira-Pinto, Luzia Maria

2017-01-01

Tissue Factor (TF) is the initiator of coagulation and Tissue Factor Inhibitor (TFPI) is the physiological inhibitor of the TF/FVIIa complex. Circulating levels of TF and TFPI were quantified in dengue patients and the relationships with disease severity and infecting serotype analysed. A significant decrease in TF and TPFI plasma levels was observed in mild DF patients compared with severe dengue. Furthermore, both factors were associated with haemorrhagic manifestations. Finally, TF levels were significantly increased in DENV-1/2 infected patients as compared with DENV-4. These findings suggest that activation of TF-pathway is an important component of DENV -related coagulation disorders. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Glycogen Synthase Kinase 3β Promotes the Endocytosis of Transferrin in the African Trypanosome.

PubMed

Guyett, Paul J; Xia, Shuangluo; Swinney, David C; Pollastri, Michael P; Mensa-Wilmot, Kojo

2016-07-08

Human parasite Trypanosoma brucei proliferates in the blood of its host, where it takes up iron via receptor-mediated endocytosis of transferrin (Tf). Mechanisms of Tf endocytosis in the trypanosome are not fully understood. Small molecule lapatinib inhibits Tf endocytosis in T. brucei and associates with protein kinase GSK3β (TbGSK3β). Therefore, we hypothesized that Tf endocytosis may be regulated by TbGSK3β, and we used three approaches (both genetic and small molecule) to test this possibility. First, the RNAi knock-down of TbGSK3β reduced Tf endocytosis selectively, without affecting the uptake of haptaglobin-hemoglobin (Hp-Hb) or bovine serum albumin (BSA). Second, the overexpression of TbGSK3β increased the Tf uptake. Third, small-molecule inhibitors of TbGSK3β, TWS119 (IC50 = 600 nM), and GW8510 (IC50 = 8 nM) reduced Tf endocytosis. Furthermore, TWS119, but not GW8510, selectively blocked Tf uptake. Thus, TWS119 phenocopies the selective endocytosis effects of a TbGSK3β knockdown. Two new inhibitors of TbGSK3β, LY2784544 (IC50 = 0.6 μM) and sorafenib (IC50 = 1.7 μM), were discovered in a focused screen: at low micromolar concentrations, they prevented Tf endocytosis as well as trypanosome proliferation (GI50's were 1.0 and 3.1 μM, respectively). These studies show that (a) TbGSK3β regulates Tf endocytosis, (b) TWS119 is a small-molecule tool for investigating the endocytosis of Tf, (c) endocytosis of GPI-anchored TfR and HpHbR are differentially regulated, and (d) the imidazopyridazine aminopyrazole scaffold of LY2784544 is attractive for a hit-to-lead optimization program in antitrypanosome drug discovery.

Regulation of tissue factor in NT2 germ cell tumor cells by cisplatin chemotherapy.

PubMed

Jacobsen, Christine; Oechsle, Karin; Hauschild, Jessica; Steinemann, Gustav; Spath, Brigitte; Bokemeyer, Carsten; Ruf, Wolfram; Honecker, Friedemann; Langer, Florian

2015-09-01

Patients with germ cell tumors (GCTs) receiving cisplatin-based chemotherapy are at increased risk of thrombosis, but the underlying cellular and molecular mechanisms remain obscure. To study baseline tissue factor (TF) expression by GCT cell lines and its modulation by cisplatin treatment. TF expression was assessed by single-stage clotting and thrombin generation assay, flow cytometry, ELISA, and Western blot analysis. Cell cycle analysis and detection of phosphatidylserine (PS) membrane exposure were carried out by flow cytometry. TF mRNA was analyzed by quantitative RT-PCR. Significant expression of TF-specific procoagulant activity (PCA) was detected on three non-seminoma (NT2, 2102Ep, NCCIT) and one seminoma cell line (TCam-2). Treatment with 0.4μM cisplatin (corresponding to the IC50) for 48hrs increased TF PCA on NT2 cells 3-fold, an effect that was largely independent of PS exposure and that could not be explained by translocation of active TF from intracellular storage pools. Cisplatin-induced TF PCA expression in NT2 cells did not occur before 12hrs, but was steady thereafter and accompanied by a 2-fold increase in total and surface-located TF antigen. Importantly, increased TF gene transcription or production and release of an intermediate factor were not involved in this process. Cell cycle analysis suggested that cisplatin-induced G2/M arrest resulted in an accumulation of procoagulant TF on the membrane surface of NT2 cells. In addition to induction of apoptosis/necrosis with PS-mediated activation of preformed TF, cisplatin may alter the procoagulant phenotype of GCT cells through an increase in total cellular TF antigen. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

Almus, F.E.; Rao, L.V.; Fleck, R.A.

An umbilical vein model was designed in which washed vein segments are filled with a reaction mixture containing factor VIIa, Ca(+)+, and a substrate, either 3H-factor IX or 3H-factor X. The vein wall provides the tissue factor (TF) for factor VIIa/TF complexes that activate the substrates as measured by activation peptide release. The model was developed to study TF induced on venous endothelium in situ. However, unlike previous studies with TF expressed on cultured umbilical vein endothelial cells, factors IX and X were activated without first having to expose the vein wall to a perturbing stimulus. Histologic studies revealed thatmore » washing the vein and mixing the reaction mixture before subsampling had disrupted the endothelium. Immunostaining with anti-TF antibodies revealed no staining of endothelium but intense staining in extensions of Wharton's jelly penetrating fenestrations of the muscularis media of the vein. Thus, the model provided data on factor VIIa/TF formed, not on endothelium, but within the mucoid connective tissue of Wharton's jelly. It is known that factor VIIa/TF formed with TF in suspension or with TF expressed on the surface of cultured cells activates factor X more rapidly than factor IX. In contrast, in the umbilical vein model, when each substrate was present in an 88 nmol/L concentration, factors IX and X were activated at equivalent rates (mean activation rate for factor IX, 18.8 +/- 3.6 nmol/L/h; for factor X, 17.8 +/- 2.9 nmol/L/h; n = 9 paired vein segments). These data strengthen the evidence that factor VIIa/TF activation of factor IX represents a key initial reaction of coagulation in tissues. These results also show that data obtained with factor VIIa/TF complexes formed on the surface of cultured cells need not hold for factor VIIa/TF complexes formed in extracellular matrix.« less

Regulation of the Incorporation of Tissue Factor into Microparticles by Serine Phosphorylation of the Cytoplasmic Domain of Tissue Factor*

PubMed Central

Collier, Mary E. W.; Ettelaie, Camille

2011-01-01

The mechanisms that regulate the incorporation and release of tissue factors (TFs) into cell-derived microparticles are as yet unidentified. In this study, we have explored the regulation of TF release into microparticles by the phosphorylation of serine residues within the cytoplasmic domain of TF. Wild-type and mutant forms of TF, containing alanine and aspartate substitutions at Ser253 and Ser258, were overexpressed in coronary artery and dermal microvascular endothelial cells and microparticle release stimulated with PAR2 agonist peptide (PAR2-AP). The release of TF antigen and activity was then monitored. In addition, the phosphorylation state of the two serine residues within the released microparticles and the cells was monitored for 150 min. The release of wild-type TF as procoagulant microparticles peaked at 90 min and declined thereafter in both cell types. The TF within these microparticles was phosphorylated at Ser253 but not at Ser258. Aspartate substitution of Ser253 resulted in rapid release of TF antigen but not activity, whereas TF release was reduced and delayed by alanine substitution of Ser253 or aspartate substitution of Ser258. Alanine substitution of Ser258 prolonged the release of TF following PAR2-AP activation. The release of TF was concurrent with phosphorylation of Ser253 and was followed by dephosphorylation at 120 min and phosphorylation of Ser258. We propose a sequential mechanism in which the phosphorylation of Ser253 through PAR2 activation results in the incorporation of TF into microparticles, simultaneously inducing Ser258 phosphorylation. Phosphorylation of Ser258 in turn promotes the dephosphorylation of Ser253 and suppresses the release of TF. PMID:21310953

Simulated infrared spectra of triflic acid during proton dissociation.

PubMed

Laflamme, Patrick; Beaudoin, Alexandre; Chapaton, Thomas; Spino, Claude; Soldera, Armand

2012-05-05

Vibrational analysis of triflic acid (TfOH) at different water uptakes was conducted. This molecule mimics the sulfonate end of the Nafion side-chain. As the proton leaves the sulfonic acid group, structural changes within the Nafion side-chain take place. They are revealed by signal shifts in the infrared spectrum. Molecular modeling is used to follow structural modifications that occur during proton dissociation. To confirm the accuracy of the proposed structures, infrared spectra were computed via quantum chemical modeling based on density functional theory. The requirement to use additional diffuse functions in the basis set is discussed. Comparison between simulated infrared spectra of 1 and 2 acid molecules with different water contents and experimental data was performed. An accurate description of infrared spectra for systems containing 2 TfOH was obtained. Copyright © 2012 Wiley Periodicals, Inc.

Inferring genome-wide functional modulatory network: a case study on NF-κB/RelA transcription factor.

PubMed

Li, Xueling; Zhu, Min; Brasier, Allan R; Kudlicki, Andrzej S

2015-04-01

How different pathways lead to the activation of a specific transcription factor (TF) with specific effects is not fully understood. We model context-specific transcriptional regulation as a modulatory network: triplets composed of a TF, target gene, and modulator. Modulators usually affect the activity of a specific TF at the posttranscriptional level in a target gene-specific action mode. This action may be classified as enhancement, attenuation, or inversion of either activation or inhibition. As a case study, we inferred, from a large collection of expression profiles, all potential modulations of NF-κB/RelA. The predicted modulators include many proteins previously not reported as physically binding to RelA but with relevant functions, such as RNA processing, cell cycle, mitochondrion, ubiquitin-dependent proteolysis, and chromatin modification. Modulators from different processes exert specific prevalent action modes on distinct pathways. Modulators from noncoding RNA, RNA-binding proteins, TFs, and kinases modulate the NF-κB/RelA activity with specific action modes consistent with their molecular functions and modulation level. The modulatory networks of NF-κB/RelA in the context epithelial-mesenchymal transition (EMT) and burn injury have different modulators, including those involved in extracellular matrix (FBN1), cytoskeletal regulation (ACTN1), and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a long intergenic nonprotein coding RNA, and tumor suppression (FOXP1) for EMT, and TXNIP, GAPDH, PKM2, IFIT5, LDHA, NID1, and TPP1 for burn injury.

DNA-bending properties of TF1.

PubMed

Schneider, G J; Sayre, M H; Geiduschek, E P

1991-10-05

Transcription factor 1 (TF1) is the Bacillus subtilis phage SPO1-encoded member of the family of DNA-binding proteins that includes Escherichia coli HU and integration host factor, IHF. A gel electrophoretic retardation method has been used to show that a TF1 dimer binding to one of its preferred sites in (5-hydroxymethyl)uracil (hmUra)-containing DNA sharply bends the latter. In fact, the DNA-bending properties of TF1 and E. coli IHF are indistinguishable. Substitutions at amino acid 61 in the DNA-binding "arm" of TF1 are known to affect DNA-binding affinity and site selectivity. Experiments described here show that these substitutions also affect DNA bending. The selectivity of TF1 binding is very greatly diminished and the affinity is reduced when hmUra is replaced in DNA by thymine (T). An extension of the gel retardation method that permits an analysis of DNA bending by non-specifically bound TF1 is proposed. Under the assumptions of this analysis, the reduced affinity of TF1 for T-containing DNA is shown to be associated with bending that is still sharp. The analysis of the TF1-DNA interaction has also been extended by hydroxyl radical (.OH) and methylation interference footprinting at two DNA sites. At each of these sites, and on each strand, TF1 strongly protects three segments of DNA from attack by OH. Patches of protected DNA are centered approximately ten base-pairs apart and fall on one side of the B-helix. Methylation in either the major or minor groove in the central ten base-pairs of the two TF1 binding sites quantitatively diminishes, but does not abolish, TF1 binding. We propose that multiple protein contacts allow DNA to wrap around the relatively small TF1 dimer, considerably deforming the DNA B-helix in the process.

Quantitative analysis of collagens and fibronectin expression in human right ventricular hypertrophy.

PubMed

Peters, T H; Sharma, H S; Yilmaz, E; Bogers, A J

1999-06-30

One of the main features in human tetralogy of Fallot (TF) is right ventricular hypertrophy (RVH) due to pressure (sub-pulmonary stenosis) and volume overload (ventricular septal defect). Currently, primary correction at a young age is the treatment of choice. To unravel the role of extracellular matrix in RVH, we examined myocardial expression of collagens and fibronectin in TF patients with primary correction (TF1, age 0.7 +/- 0.2 yr.), secondary surgery (TF2, age 36.9 +/- 4.6 yr), and in age-matched control patients. Sirius red staining quantified by video imaging showed significantly increased interstitial staining for collagens in both TF1 and TF2 groups as compared to respective controls. Fibronectin was expressed in extracellular spaces, perivascular regions, and in some cardiomyocytes. Quantitative analysis of fibronectin revealed increased expression in only TF1 group as compared to respective control. Our results indicate an increased amount of myocardial extracellular matrix deposition as a sign of fibrosis during RVH in patients with TF.

Soluble Form of Canine Transferrin Receptor Inhibits Canine Parvovirus Infection In Vitro and In Vivo

PubMed Central

Wen, Jiexia; Pan, Sumin; Liang, Shuang; Zhong, Zhenyu; He, Ying; Lin, Hongyu; Li, Wenyan; Wang, Liyue; Li, Xiujin; Zhong, Fei

2013-01-01

Canine parvovirus (CPV) disease is an acute, highly infectious disease threatening the dog-raising industry. So far there are no effective therapeutic strategies to control this disease. Although the canine transferrin receptor (TfR) was identified as a receptor for CPV infection, whether extracellular domain of TfR (called soluble TfR (sTfR)) possesses anti-CPV activities remains elusive. Here, we used the recombinant sTfR prepared from HEK293T cells with codon-optimized gene structure to investigate its anti-CPV activity both in vitro and in vivo. Our results indicated that codon optimization could significantly improve sTfR expression in HEK293T cells. The prepared recombinant sTfR possessed a binding activity to both CPV and CPV VP2 capsid proteins and significantly inhibited CPV infection of cultured feline F81 cells and decreased the mortality of CPV-infected dogs, which indicates that the sTfR has the anti-CPV activity both in vitro and in vivo. PMID:24089666

Targeted release of transcription factors for cell reprogramming by a natural micro-syringe.

PubMed

Berthoin, Lionel; Toussaint, Bertrand; Garban, Frédéric; Le Gouellec, Audrey; Caulier, Benjamin; Polack, Benoît; Laurin, David

2016-11-20

Ectopic expression of defined transcription factors (TFs) for cell fate handling has proven high potential interest in reprogramming differentiated cells, in particular for regenerative medicine, ontogenesis study and cell based modelling. Pluripotency or transdifferentiation induction as TF mediated differentiation is commonly produced by transfer of genetic information with safety concerns. The direct delivery of proteins could represent a safer alternative but still needs significant advances to be efficient. We have successfully developed the direct delivery of proteins by an attenuated bacterium with a type 3 secretion system that does not require challenging and laborious steps for production and purification of recombinant molecules. Here we show that this natural micro-syringe is able to inject TFs to primary human fibroblasts and cord blood CD34 + hematopoietic stem cells. The signal sequence for vectorization of the TF Oct4 has no effect on DNA binding to its nucleic target. As soon as one hour after injection, vectorized TFs are detectable in the nucleus. The injection process is not associated with toxicity and the bacteria can be completely removed from cell cultures. A three days targeted release of Oct4 or Sox2 embryonic TFs results in the induction of the core pluripotency genes expression in fibroblasts and CD34 + hematopoietic stem cells. This micro-syringe vectorization represents a new strategy for TF delivery and has potential applications for cell fate reprogramming. Copyright © 2016 Elsevier B.V. All rights reserved.

Tracing artificial trans fat in popular foods in Europe: a market basket investigation.

PubMed

Stender, Steen; Astrup, Arne; Dyerberg, Jørn

2014-05-20

To minimise the intake of industrial artificial trans fat (I-TF), nearly all European countries rely on food producers to voluntarily reduce the I-TF content in food. The objective of this study was to investigate the effect of this strategy on I-TF content in prepackaged biscuits/cakes/wafers in 2012-2013 in 20 European countries. The I-TF content was assessed in a market basket investigation. Three large supermarkets were visited in each capital, and in some countries, three additional ethnic shops were included. A total of 598 samples of biscuits/cakes/wafers with 'partially hydrogenated vegetable fat' or a similar term high on the list of ingredients were analysed, 312 products had more than 2% of fat as I-TF, exceeding the legislatively determined I-TF limit in Austria and Denmark; the mean (SD) was 19 (7)%. In seven countries, no I-TF was found, whereas nine predominantly Eastern European countries had products with very high I-TF content, and the remaining four countries had intermediate levels. Of the five countries that were examined using the same procedure as in 2006, three had unchanged I-TF levels in 2013, and two had lower levels. The 18 small ethnic shops examined in six Western European countries sold 83 products. The mean (SD) was 23 (12)% of the fat as I-TF, all imported from countries in Balkan. In Sweden, this type of food imported from Balkan was also available in large supermarkets. The findings suggest that subgroups of the population in many countries in Europe still consume I-TF in amounts that increase their risk of coronary heart disease. Under current European Union (EU) legislation, the sale of products containing I-TF is legal but conflicts with the WHO recommendation to minimise the intake of I-TF. An EU-legislative limit on I-TF content in foods is expected to be an effective strategy to achieve this goal. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

An analysis of subunit exchange in the dimeric DNA-binding and DNA-bending protein, TF1.

PubMed

Andera, L; Schneider, G J; Geiduschek, E P

1994-01-01

TF1 is the Bacillus subtilis bacteriophage-encoded dimeric type II DNA-binding protein. This relative of the eubacterial HU proteins and of the Escherichia coli integration host factor binds preferentially to 5-(hydroxymethyluracil)-containing DNA. We have examined the dynamics of exchange of monomer subunits between molecules of dimeric TF1. The analysis takes advantage of the fact that replacement of phenylalanine with arginine at amino acid 61 in the beta-loop 'arm' of TF1 alters DNA-bending and -binding properties, generating DNA complexes with distinctively different mobilities in gel electrophoresis. New species of DNA-protein complexes were formed by mixtures of wild type and mutant TF1, reflecting the formation of heterodimeric TF1, and making the dynamics of monomer exchange between TF1 dimers accessible to a simple gel retardation analysis. Exchange was rapid at high protein concentrations, even at 0 degrees C, and is proposed to be capable of proceeding through an interaction of molecules of TF1 dimer rather than exclusively through dissociation into monomer subunits. Evidence suggesting that DNA-bound TF1 dimers do not exchange subunits readily is also presented.

Incremental Drag due to Grooves and Threads for KE (Kinetic Energy) Projectiles

DTIC Science & Technology

1989-03-01

RFI • CTsB TF * - MF (3a) q L where TF1 is the Thread Factor defined as: TF 0.84 + 0.117 P - o (3b) where p is the groove pitch in inches, MF1 is...g2) MF RF CD (4) where TF11 and TF1 2 are the thread factors for the threads of pitch p, and P2, respectively. 5 One can notice the large

Dynamic Transcription Factor Networks in Epithelial-Mesenchymal Transition in Breast Cancer Models

PubMed Central

Siletz, Anaar; Schnabel, Michael; Kniazeva, Ekaterina; Schumacher, Andrew J.; Shin, Seungjin; Jeruss, Jacqueline S.; Shea, Lonnie D.

2013-01-01

The epithelial-mesenchymal transition (EMT) is a complex change in cell differentiation that allows breast carcinoma cells to acquire invasive properties. EMT involves a cascade of regulatory changes that destabilize the epithelial phenotype and allow mesenchymal features to manifest. As transcription factors (TFs) are upstream effectors of the genome-wide expression changes that result in phenotypic change, understanding the sequential changes in TF activity during EMT provides rich information on the mechanism of this process. Because molecular interactions will vary as cells progress from an epithelial to a mesenchymal differentiation program, dynamic networks are needed to capture the changing context of molecular processes. In this study we applied an emerging high-throughput, dynamic TF activity array to define TF activity network changes in three cell-based models of EMT in breast cancer based on HMLE Twist ER and MCF-7 mammary epithelial cells. The TF array distinguished conserved from model-specific TF activity changes in the three models. Time-dependent data was used to identify pairs of TF activities with significant positive or negative correlation, indicative of interdependent TF activity throughout the six-day study period. Dynamic TF activity patterns were clustered into groups of TFs that change along a time course of gene expression changes and acquisition of invasive capacity. Time-dependent TF activity data was combined with prior knowledge of TF interactions to construct dynamic models of TF activity networks as epithelial cells acquire invasive characteristics. These analyses show EMT from a unique and targetable vantage and may ultimately contribute to diagnosis and therapy. PMID:23593114

Dynamic transcription factor networks in epithelial-mesenchymal transition in breast cancer models.

PubMed

Siletz, Anaar; Schnabel, Michael; Kniazeva, Ekaterina; Schumacher, Andrew J; Shin, Seungjin; Jeruss, Jacqueline S; Shea, Lonnie D

2013-01-01

The epithelial-mesenchymal transition (EMT) is a complex change in cell differentiation that allows breast carcinoma cells to acquire invasive properties. EMT involves a cascade of regulatory changes that destabilize the epithelial phenotype and allow mesenchymal features to manifest. As transcription factors (TFs) are upstream effectors of the genome-wide expression changes that result in phenotypic change, understanding the sequential changes in TF activity during EMT provides rich information on the mechanism of this process. Because molecular interactions will vary as cells progress from an epithelial to a mesenchymal differentiation program, dynamic networks are needed to capture the changing context of molecular processes. In this study we applied an emerging high-throughput, dynamic TF activity array to define TF activity network changes in three cell-based models of EMT in breast cancer based on HMLE Twist ER and MCF-7 mammary epithelial cells. The TF array distinguished conserved from model-specific TF activity changes in the three models. Time-dependent data was used to identify pairs of TF activities with significant positive or negative correlation, indicative of interdependent TF activity throughout the six-day study period. Dynamic TF activity patterns were clustered into groups of TFs that change along a time course of gene expression changes and acquisition of invasive capacity. Time-dependent TF activity data was combined with prior knowledge of TF interactions to construct dynamic models of TF activity networks as epithelial cells acquire invasive characteristics. These analyses show EMT from a unique and targetable vantage and may ultimately contribute to diagnosis and therapy.

A complex structure in the mRNA of Tf1 is recognized and cleaved to generate the primer of reverse transcription.

PubMed

Lin, J H; Levin, H L

1997-01-15

All retroviruses and LTR-containing retrotransposons are thought to require specific tRNA molecules to serve as primers of reverse transcription. An exception is the LTR-containing retrotransposon Tf1, isolated from Schizosaccharomyces pombe. Instead of requiring a tRNA, the reverse transcriptase of Tf1 uses the first 11 bases of the Tf1 transcript as the primer for reverse transcription. The primer is generated by a cleavage that occurs between bases 11 and 12 of the Tf1 mRNA. Sequence analysis of the 5' untranslated region of the Tf1 mRNA resulted in the identification of a region with the potential to form an RNA structure of 89 bases that included the primer binding site and the first 11 bases of the Tf1 mRNA. Systematic mutagenesis of this region revealed 34 single-point mutants in the structure that resulted in reduced transposition activity. The defects in transposition correlated with reduced level of Tf1 reverse transcripts as determined by DNA blot analysis. Evidence that the RNA structure did form in vivo included the result that strains with second site mutations that restored complementarity resulted in increased levels of reverse transcripts and Tf1 transposition. The majority of the mutants defective for reverse transcription were unable to cleave the Tf1 mRNA between bases 11 and 12. These data indicate that formation of an extensive RNA structure was required for the cleavage reaction that generated the primer for Tf1 reverse transcription.

Investigating the interaction of anticancer drug temsirolimus with human transferrin: Molecular docking and spectroscopic approach.

PubMed

Shamsi, Anas; Ahmed, Azaj; Khan, Mohd Shahnawaz; Husain, Fohad Mabood; Amani, Samreen; Bano, Bilqees

2018-05-16

In our present study, binding between an important anti renal cancer drug temsirolimus and human transferrin (hTF) was investigated employing spectroscopic and molecular docking approach. In the presence of temsirolimus, hyper chromaticity is observed in hTF in UV spectroscopy suggestive of complex formation between hTF and temsirolimus. Fluorescence spectroscopy revealed the occurrence of quenching in hTF in the presence of temsirolimus implying complex formation taking place between hTF and temsirolimus. Further, the mode of interaction between hTF and temsirolimus was revealed to be static by fluorescence quenching analysis at 3 different temperatures. Binding constant values obtained employing fluorescence spectroscopy depicts strong interaction between hTF and temsirolimus; temsirolimus binds to hTF at 298 K with a binding constant of .32 × 10 4  M -1 implying the strength of this interaction. The negative Gibbs free energy obtained through quenching experiments is evident of the fact that the binding is spontaneous. CD spectra of hTF also showed a downward shift in the presence of temsirolimus as compared with free hTF implying complex formation between hTF and temsirolimus. Molecular docking was performed with a view to find out which residues are key players in this interaction. The importance of our study stems from the fact it will provide an insight into binding pattern of commonly administered renal cancer drug with an important protein that plays a pivotal role in many physiological processes. Copyright © 2018 John Wiley & Sons, Ltd.

Generation of a Multivariate Distribution for Specified Univariate Marginals and Covariance Structure.

DTIC Science & Technology

1981-05-28

x2-+,(y) . F7. y1 (-i! Tf1 ’ 2) 2 f. 2;X (3 1(2 X T= t I (Y) F= I (yI) .(-l I f ill ; X ( 2 ) Combining the one-to-one property of Tf, with (B-4...transformation of probability, dT; (y) g(Y) - f( Tf1 (Y)). ldet ( dY )I = f(TfI (Y))/f(Tf (Y)) =1 Remarks m 1. It immediately follows that Y is uniformly

Modes of Large-Scale Brain Network Organization during Threat Processing and Posttraumatic Stress Disorder Symptom Reduction during TF-CBT among Adolescent Girls.

PubMed

Cisler, Josh M; Sigel, Benjamin A; Kramer, Teresa L; Smitherman, Sonet; Vanderzee, Karin; Pemberton, Joy; Kilts, Clinton D

2016-01-01

Posttraumatic stress disorder (PTSD) is often chronic and disabling across the lifespan. The gold standard treatment for adolescent PTSD is Trauma-Focused Cognitive-Behavioral Therapy (TF-CBT), though treatment response is variable and mediating neural mechanisms are not well understood. Here, we test whether PTSD symptom reduction during TF-CBT is associated with individual differences in large-scale brain network organization during emotion processing. Twenty adolescent girls, aged 11-16, with PTSD related to assaultive violence completed a 12-session protocol of TF-CBT. Participants completed an emotion processing task, in which neutral and fearful facial expressions were presented either overtly or covertly during 3T fMRI, before and after treatment. Analyses focused on characterizing network properties of modularity, assortativity, and global efficiency within an 824 region-of-interest brain parcellation separately during each of the task blocks using weighted functional connectivity matrices. We similarly analyzed an existing dataset of healthy adolescent girls undergoing an identical emotion processing task to characterize normative network organization. Pre-treatment individual differences in modularity, assortativity, and global efficiency during covert fear vs neutral blocks predicted PTSD symptom reduction. Patients who responded better to treatment had greater network modularity and assortativity but lesser efficiency, a pattern that closely resembled the control participants. At a group level, greater symptom reduction was associated with greater pre-to-post-treatment increases in network assortativity and modularity, but this was more pronounced among participants with less symptom improvement. The results support the hypothesis that modularized and resilient brain organization during emotion processing operate as mechanisms enabling symptom reduction during TF-CBT.

Transferrin Receptor 1 Facilitates Poliovirus Permeation of Mouse Brain Capillary Endothelial Cells.

PubMed

Mizutani, Taketoshi; Ishizaka, Aya; Nihei, Coh-Ichi

2016-02-05

As a possible route for invasion of the CNS, circulating poliovirus (PV) in the blood is believed to traverse the blood-brain barrier (BBB), resulting in paralytic poliomyelitis. However, the underlying mechanism is poorly understood. In this study, we demonstrated that mouse transferrin receptor 1 (mTfR1) is responsible for PV attachment to the cell surface, allowing invasion into the CNS via the BBB. PV interacts with the apical domain of mTfR1 on mouse brain capillary endothelial cells (MBEC4) in a dose-dependent manner via its capsid protein (VP1). We found that F-G, G-H, and H-I loops in VP1 are important for this binding. However, C-D, D-E, and E-F loops in VP1-fused Venus proteins efficiently penetrate MBEC4 cells. These results imply that the VP1 functional domain responsible for cell attachment is different from that involved in viral permeation of the brain capillary endothelium. We observed that co-treatment of MBEC4 cells with excess PV particles but not dextran resulted in blockage of transferrin transport into cells. Using the Transwell in vitro BBB model, transferrin co-treatment inhibited permeation of PV into MBEC4 cells and delayed further viral permeation via mTfR1 knockdown. With mTfR1 as a positive mediator of PV-host cell attachment and PV permeation of MBEC4 cells, our results indicate a novel role of TfR1 as a cellular receptor for human PV receptor/CD155-independent PV invasion of the CNS. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full cyclic testing in SULTAN: III. The importance of strand surface roughness in long twist pitch conductors

DOE PAGES

Sanabria, Charlie; Lee, Peter J.; Starch, William; ...

2016-05-31

As part of the ITER conductor qualification process, 3 m long Cable-in-Conduit Conductors (CICCs) were tested at the SULTAN facility under conditions simulating ITER operation so as to establish the current sharing temperature, T cs, as a function of multiple full Lorentz force loading cycles. After a comprehensive evaluation of both the Toroidal Field (TF) and the Central Solenoid (CS) conductors, it was found that T cs degradation was common in long twist pitch TF conductors while short twist pitch CS conductors showed some T cs increase. However, one kind of TF conductors containing superconducting strand fabricated by the Bochvarmore » Institute of Inorganic Materials (VNIINM) avoided T cs degradation despite having long twist pitch. In our earlier metallographic autopsies of long and short twist pitch CS conductors, we observed a substantially greater transverse strand movement under Lorentz force loading for long twist pitch conductors, while short twist pitch conductors had negligible transverse movement. With help from the literature, we concluded that the transverse movement was not the source of T cs degradation but rather an increase of the compressive strain in the Nb 3Sn filaments possibly induced by longitudinal movement of the wires. Like all TF conductors this TF VNIINM conductor showed large transverse motions under Lorentz force loading, but Tcs actually increased, as in all short twist pitch CS conductors. We here propose that the high surface roughness of the VNIINM strand may be responsible for the suppression of the compressive strain enhancement (characteristic of long twist pitch conductors). Furthermore, it appears that increasing strand surface roughness could improve the performance of long twist pitch CICCs.« less

Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full cyclic testing in SULTAN: III. The importance of strand surface roughness in long twist pitch conductors

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

Sanabria, Charlie; Lee, Peter J.; Starch, William

As part of the ITER conductor qualification process, 3 m long Cable-in-Conduit Conductors (CICCs) were tested at the SULTAN facility under conditions simulating ITER operation so as to establish the current sharing temperature, T cs, as a function of multiple full Lorentz force loading cycles. After a comprehensive evaluation of both the Toroidal Field (TF) and the Central Solenoid (CS) conductors, it was found that T cs degradation was common in long twist pitch TF conductors while short twist pitch CS conductors showed some T cs increase. However, one kind of TF conductors containing superconducting strand fabricated by the Bochvarmore » Institute of Inorganic Materials (VNIINM) avoided T cs degradation despite having long twist pitch. In our earlier metallographic autopsies of long and short twist pitch CS conductors, we observed a substantially greater transverse strand movement under Lorentz force loading for long twist pitch conductors, while short twist pitch conductors had negligible transverse movement. With help from the literature, we concluded that the transverse movement was not the source of T cs degradation but rather an increase of the compressive strain in the Nb 3Sn filaments possibly induced by longitudinal movement of the wires. Like all TF conductors this TF VNIINM conductor showed large transverse motions under Lorentz force loading, but Tcs actually increased, as in all short twist pitch CS conductors. We here propose that the high surface roughness of the VNIINM strand may be responsible for the suppression of the compressive strain enhancement (characteristic of long twist pitch conductors). Furthermore, it appears that increasing strand surface roughness could improve the performance of long twist pitch CICCs.« less

[Effect of Leonurus Heterophyllus Sweet on tissue factor transcription and expression in human umbilical vein endothelial cells in vitro].

PubMed

Zheng, Lian; Fang, Chi-hua

2007-06-01

To investigate the effect of Leonurus Heterophyllus Sweet, (LHS) on tissue factor (TF) transcription and expression induced by thrombin in human umbilical vein endothelial cells (HUVECs). HUVECs were incubated with different concentrations of LHS and the TF mRNA expression was detected by reverse transcript-polymerase chain reaction (RT-PCR). LHS treatment of HUVECs at different concentrations and for different times resulted in significant differences in TF expression (Plt;0.01). The transcription of TF in LHS-treated cells was significantly different from that of the blank control group (Plt;0.01). LHS can decrease the expression of TF and intervene with TF transcription in HUVECs in vitro.

Diaphragm assessment by two dimensional speckle tracking imaging in normal subjects.

PubMed

Orde, Sam R; Boon, Andrea J; Firth, Daniel G; Villarraga, Hector R; Sekiguchi, Hiroshi

2016-07-25

Conventionally, ultrasonographic assessment of diaphragm contractility has involved measuring respiratory changes in diaphragm thickness (thickening fraction) using B-mode or caudal displacement with M-mode. Two-dimensional speckle-tracking has been increasingly used to assess muscle deformation ('strain') in echocardiography. We sought to determine in a pilot study if this technology could be utilized to analyze diaphragmatic contraction. Fifty healthy adult volunteers with normal exercise capacity underwent ultrasound imaging. A linear array transducer was used for the assessment of diaphragm thickness, thickening fraction (TF), and strain in the right anterior axillary line at approximately the ninth intercostal space. A phased array transducer was applied subcostally for the assessment of diaphragm displacement on the right mid-clavicular line. Diaphragmatic images were recorded from the end of expiration through the end of inspiration at 60 % maximal inspiratory capacity. Diaphragm strain was analyzed off-line by speckle tracking imaging. Blinded inter- and intra-rater variability was tested in 10 cases. Mean right diaphragm thickness at end-expiration (±SD: standard deviation) was 0.24 cm (±0.1), with TF of 45.1 % (±12) at 60 % peak inspiratory effort. Mean right diaphragm caudal displacement was 4.9 cm (±1). Mean right diaphragm strain was -40.3 % (±9). A moderate correlation was seen between longitudinal strain and TF (R(2) 0.44, p < 0.0001). A weak correlation was seen between strain and caudal displacement (R(2) 0.14, p < 0.01), and an even weaker correlation was seen between caudal displacement and TF (R(2) 0.1, p = 0.04). Age, gender, and body mass index were not significantly associated with right diaphragm strain or TF. Although inter- and intra-rater variability was overall good for TF, caudal displacement, and strain (inter-rater R(2); 0.8, 0.9, and 0.7, respectively [p < 0.01], intra-rater R(2); 0.9, 0.7, and 0.9, respectively [p < 0.01]), strain values did have a slightly lower inter-rater repeatability. Diaphragmatic strain estimated by speckle tracking imaging was associated with conventional ultrasound measures of diaphragmatic function (TF and caudal displacement). Further clinical studies are warranted to investigate its clinical utility.

The unrecognized burden of typhoid fever.

PubMed

Obaro, Stephen K; Iroh Tam, Pui-Ying; Mintz, Eric Daniel

2017-03-01

Typhoid fever (TF), caused by Salmonella enterica serovar Typhi, is the most common cause of enteric fever, responsible for an estimated 129,000 deaths and more than 11 million cases annually. Although several reviews have provided global and regional TF disease burden estimates, major gaps in our understanding of TF epidemiology remain. Areas covered: We provide an overview of the gaps in current estimates of TF disease burden and offer suggestions for addressing them, so that affected communities can receive the full potential of disease prevention offered by vaccination and water, sanitation, and hygiene interventions. Expert commentary: Current disease burden estimates for TF do not capture cases from certain host populations, nor those with atypical presentations of TF, which may lead to substantial underestimation of TF cases and deaths. These knowledge gaps pose major obstacles to the informed use of current and new generation typhoid vaccines.

Time-Frequency Masking for Speech Separation and Its Potential for Hearing Aid Design

PubMed Central

Wang, DeLiang

2008-01-01

A new approach to the separation of speech from speech-in-noise mixtures is the use of time-frequency (T-F) masking. Originated in the field of computational auditory scene analysis, T-F masking performs separation in the time-frequency domain. This article introduces the T-F masking concept and reviews T-F masking algorithms that separate target speech from either monaural or binaural mixtures, as well as microphone-array recordings. The review emphasizes techniques that are promising for hearing aid design. This article also surveys recent studies that evaluate the perceptual effects of T-F masking techniques, particularly their effectiveness in improving human speech recognition in noise. An assessment is made of the potential benefits of T-F masking methods for the hearing impaired in light of the processing constraints of hearing aids. Finally, several issues pertinent to T-F masking are discussed. PMID:18974204

MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation

PubMed Central

Peng, Xianlu L.; So, Karl K.; He, Liangqiang; Zhao, Yu; Zhou, Jiajian; Li, Yuying; Yao, Mingze; Xu, Bo; Zhang, Suyang; Yao, Hongjie; Hu, Ping

2017-01-01

Abstract Super-enhancers (SEs) are cis-regulatory elements enriching lineage specific key transcription factors (TFs) to form hotspots. A paucity of identification and functional dissection promoted us to investigate SEs during myoblast differentiation. ChIP-seq analysis of histone marks leads to the uncovering of SEs which remodel progressively during the course of differentiation. Further analyses of TF ChIP-seq enable the definition of SE hotspots co-bound by the master TF, MyoD and other TFs, among which we perform in-depth dissection for MyoD/FoxO3 interaction in driving the hotspots formation and SE activation. Furthermore, using Myogenin as a model locus, we elucidate the hierarchical and complex interactions among hotspots during the differentiation, demonstrating SE function is propelled by the physical and functional cooperation among hotspots. Finally, we show MyoD and FoxO3 are key in orchestrating the Myogenin hotspots interaction and activation. Altogether our results identify muscle-specific SEs and provide mechanistic insights into the functionality of SE. PMID:28575289

Demonstration of retrotransposition of the Tf1 element in fission yeast.

PubMed

Levin, H L; Boeke, J D

1992-03-01

Tf1, a retrotransposon from fission yeast, has LTRs and coding sequences resembling the protease, reverse transcriptase and integrase domains of retroviral pol genes. A unique aspect of Tf1 is that it contains a single open reading frame whereas other retroviruses and retrotransposons usually possess two or more open reading frames. To determine whether Tf1 can transpose, we overproduced Tf1 transcripts encoded by a plasmid copy of the element marked with a neo gene. Approximately 0.1-4.0% of the cell population acquired chromosomally inherited resistance to G418. DNA blot analysis demonstrated that such strains had acquired both Tf1 and neo specific sequences within a restriction fragment of the same size; the size of this restriction fragment varied between different isolates. Structural analysis of the cloned DNA flanking the Tf1-neo element of two transposition candidates with the same regions in the parent strain showed that the ability to grow on G418 was due to transposition of Tf1-neo and not other types of recombination events.

Prospective Design of Anti‐Transferrin Receptor Bispecific Antibodies for Optimal Delivery into the Human Brain

PubMed Central

Kanodia, JS; Gadkar, K; Bumbaca, D; Zhang, Y; Tong, RK; Luk, W; Hoyte, K; Lu, Y; Wildsmith, KR; Couch, JA; Watts, RJ; Dennis, MS; Ernst, JA; Scearce‐Levie, K; Atwal, JK; Joseph, S

2016-01-01

Anti‐transferrin receptor (TfR)‐based bispecific antibodies have shown promise for boosting antibody uptake in the brain. Nevertheless, there are limited data on the molecular properties, including affinity required for successful development of TfR‐based therapeutics. A complex nonmonotonic relationship exists between affinity of the anti‐TfR arm and brain uptake at therapeutically relevant doses. However, the quantitative nature of this relationship and its translatability to humans is heretofore unexplored. Therefore, we developed a mechanistic pharmacokinetic‐pharmacodynamic (PK‐PD) model for bispecific anti‐TfR/BACE1 antibodies that accounts for antibody‐TfR interactions at the blood‐brain barrier (BBB) as well as the pharmacodynamic (PD) effect of anti‐BACE1 arm. The calibrated model correctly predicted the optimal anti‐TfR affinity required to maximize brain exposure of therapeutic antibodies in the cynomolgus monkey and was scaled to predict the optimal affinity of anti‐TfR bispecifics in humans. Thus, this model provides a framework for testing critical translational predictions for anti‐TfR bispecific antibodies, including choice of candidate molecule for clinical development. PMID:27299941

Soil-to-plant transfer factors of natural radionuclides (226Ra and 40K) in selected Thai medicinal plants.

PubMed

Saenboonruang, Kiadtisak; Phonchanthuek, Endu; Prasandee, Kamonkhuan

2018-04-01

A soil-to-plant transfer factor (TF) is an important parameter that could be used to estimate radionuclides levels in medicinal plants. This work reports concentrations of natural radionuclides ( 226 Ra and 40 K) and TFs in six Thai medicinal plants grown in central Thailand using an HPGe gamma ray spectrometer. Either root, leaf, or flower parts of each medicinal plant were selected for use in the investigation according to their practical uses in traditional medicine. The results showed that due to K being essential in plants, 40 K had higher arithmetic means of activity concentrations and geometric means of TFs (geometric standard deviations in parentheses) of 610 ± 260 Bq kg -1 dry weight (DW) and 2.0 (1.4), respectively, than 226 Ra, which had the activity concentrations and TFs of 4.8 ± 2.6 Bq kg -1 DW and 0.17 (1.8), respectively. The results also showed that the leaves of medicinal plants had higher activity concentrations and TFs than root and flower parts, probably due to higher metabolic activities in leaves. Furthermore, there was good agreement between the results from the current work and other similar reports on medicinal plants. The information obtained from this work could strengthen knowledge of natural radionuclides in plants and particularly increase available TF data on Thai medicinal plants. Copyright © 2018 Elsevier Ltd. All rights reserved.

Tissue factor expression by myeloid cells contributes to protective immune response against Mycobacterium tuberculosis infection.

PubMed

Venkatasubramanian, Sambasivan; Tripathi, Deepak; Tucker, Torry; Paidipally, Padmaja; Cheekatla, Satyanarayana; Welch, Elwyn; Raghunath, Anjana; Jeffers, Ann; Tvinnereim, Amy R; Schechter, Melissa E; Andrade, Bruno B; Mackman, Nizel; Idell, Steven; Vankayalapati, Ramakrishna

2016-02-01

Tissue factor (TF) is a transmembrane glycoprotein that plays an essential role in hemostasis by activating coagulation. TF is also expressed by monocytes/macrophages as part of the innate immune response to infections. In the current study, we determined the role of TF expressed by myeloid cells during Mycobacterium tuberculosis (M. tb) infection by using mice lacking the TF gene in myeloid cells (TF(Δ) ) and human monocyte derived macrophages (MDMs). We found that during M. tb infection, a deficiency of TF in myeloid cells was associated with reduced inducible nitric oxide synthase (iNOS) expression, enhanced arginase 1 (Arg1) expression, enhanced IL-10 production and reduced apoptosis in infected macrophages, which augmented M. tb growth. Our results demonstrate that a deficiency of TF in myeloid cells promotes M2-like phenotype in M .tb infected macrophages. A deficiency in TF expression by myeloid cells was also associated with reduced fibrin deposition and increased matrix metalloproteases (MMP)-2 and MMP-9 mediated inflammation in M. tb infected lungs. Our studies demonstrate that TF expressed by myeloid cells has newly recognized abilities to polarize macrophages and to regulate M. tb growth. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Innate lymphoid cells in normal and disease: An introductory overview.

PubMed

Moretta, Lorenzo; Locatelli, Franco

2016-11-01

Innate lymphoid cells (ILC) represent a novel group of lymphocytes that, different from T and B-lymphocytes lack recombinant activating genes (RAG-1 or RAG-2) and thus do not express rearranged antigen-specific receptors. Members of this family, i.e. NK cells, have been known since long time, while the other ILCs have been discovered only in recent years, possibly because of their predominant localization in tissues, primarily in mucosal tissues, skin and mucosa-associated lymphoid organs. ILC have been grouped in three major subsets on the basis of their phenotypic and functional features as well as of their dependency on given transcription factors (TF). Briefly, ILC-1 are dependent on T-bet TF and produce interferon (IFN)-γ. Group 2 ILC (ILC2) express GATA-3 TF and produce IL-5, IL-4 and IL-13 (Type 2) cytokines while group 3 ILC (ILC3) express RORγt TF and produce IL-17 and IL-22. ILC provide early defenses against pathogens and intervene in the repair of damaged tissues. ILC activation is mediated by cytokines (specifically acting on different ILC groups) and/or by activating receptors that are, at least in part, the same that had been previously identified in NK cells [1]. Copyright © 2016 European Federation of Immunological Societies. Published by Elsevier B.V. All rights reserved.

Sp8 and COUP-TF1 reciprocally regulate patterning and Fgf signaling in cortical progenitors.

PubMed

Borello, Ugo; Madhavan, Mayur; Vilinsky, Ilya; Faedo, Andrea; Pierani, Alessandra; Rubenstein, John; Campbell, Kenneth

2014-06-01

To gain new insights into the transcriptional regulation of cortical development, we examined the role of the transcription factor Sp8, which is downstream of Fgf8 signaling and known to promote rostral cortical development. We have used a binary transgenic system to express Sp8 throughout the mouse telencephalon in a temporally restricted manner. Our results show that misexpression of Sp8 throughout the telencephalon, at early but not late embryonic stages, results in cortical hypoplasia, which is accompanied by increased cell death, reduced proliferation, and precocious neuronal differentiation. Misexpression of Sp8 at early developmental stages represses COUP-TF1 expression, a negative effector of Fgf signaling and a key promoter of posterior cortical identity, while ablation of Sp8 has the opposite effect. In addition, transgenic misexpression of COUP-TF1 resulted in downregulation of Sp8, indicating a reciprocal cross-regulation between these 2 transcription factors. Although Sp8 has been suggested to induce and/or maintain Fgf8 expression in the embryonic telencephalon, neither Fgf8 nor Fgf15 was upregulated using our gain-of-function approach. However, misexpression of Sp8 greatly increased the expression of Fgf target molecules, suggesting enhanced Fgf signaling. Thus, we propose that Sp8 promotes rostral and dorsomedial cortical development by repressing COUP-TF1 and promoting Fgf signaling in pallial progenitors.

Sp8 and COUP-TF1 Reciprocally Regulate Patterning and Fgf Signaling in Cortical Progenitors

PubMed Central

Borello, Ugo; Madhavan, Mayur; Vilinsky, Ilya; Faedo, Andrea; Pierani, Alessandra; Rubenstein, John; Campbell, Kenneth

2014-01-01

To gain new insights into the transcriptional regulation of cortical development, we examined the role of the transcription factor Sp8, which is downstream of Fgf8 signaling and known to promote rostral cortical development. We have used a binary transgenic system to express Sp8 throughout the mouse telencephalon in a temporally restricted manner. Our results show that misexpression of Sp8 throughout the telencephalon, at early but not late embryonic stages, results in cortical hypoplasia, which is accompanied by increased cell death, reduced proliferation, and precocious neuronal differentiation. Misexpression of Sp8 at early developmental stages represses COUP-TF1 expression, a negative effector of Fgf signaling and a key promoter of posterior cortical identity, while ablation of Sp8 has the opposite effect. In addition, transgenic misexpression of COUP-TF1 resulted in downregulation of Sp8, indicating a reciprocal cross-regulation between these 2 transcription factors. Although Sp8 has been suggested to induce and/or maintain Fgf8 expression in the embryonic telencephalon, neither Fgf8 nor Fgf15 was upregulated using our gain-of-function approach. However, misexpression of Sp8 greatly increased the expression of Fgf target molecules, suggesting enhanced Fgf signaling. Thus, we propose that Sp8 promotes rostral and dorsomedial cortical development by repressing COUP-TF1 and promoting Fgf signaling in pallial progenitors. PMID:23307639

Impact of Dental Fluorosis, Socioeconomic Status and Self-Perception in Adolescents Exposed to a High Level of Fluoride in Water.

PubMed

Molina-Frechero, Nelly; Nevarez-Rascón, Martina; Nevarez-Rascón, Alfredo; González-González, Rogelio; Irigoyen-Camacho, María Esther; Sánchez-Pérez, Leonor; López-Verdin, Sandra; Bologna-Molina, Ronell

2017-01-12

Objective : To identify adolescents' self-perception of dental fluorosis from two areas with different socioeconomic levels. Methods : A cross-sectional, descriptive study was conducted with 15-year-old youths by applying a questionnaire designed and validated to assess self-perceptions of dental fluorosis in two areas with different socioeconomic statuses (SESs). Fluorosis was clinically evaluated by applying the Thylstrup and Fejerkov (TF) index on the upper front teeth. Results : A total of 308 adolescents were included in the study. The medium-SES population, which was exposed to 2.5 ppm of fluoride in water, and the low-SES population, which was exposed to 5.1 ppm, presented the following levels of dental fluorosis: TF 2-3 (50%), TF 4-5 (45.6%) and TF 6-7 (4.4%) for medium SES and TF 2-3 (12.3%), TF 4-5 (67.1%) and TF 67 (20.6%) for low SES. A significant association was found between self-perception and dental fluorosis in those with medium and low SESs ( p < 0.05). The multiple regression model found differences between TF levels and self-perception, with a 6-7 TF level for concerns about color (OR = 1.6), smile (OR = 1.2) and appearance (OR = 3.36). Conclusions : Self-perceptions of dental fluorosis affect adolescents such that adolescents with a medium SES have more negative perceptions than those with a low SES. Such perceptions increase as the TF index increases.

Mapping of the Pim-1 oncogene in mouse t-haplotypes and its use to define the relative map positions of the tcl loci t0(t6) and tw12 and the marker tf (tufted).

PubMed

Ark, B; Gummere, G; Bennett, D; Artzt, K

1991-06-01

Pim-1 is an oncogene activated in mouse T-cell lymphomas induced by Moloney and AKR mink cell focus (MCF) viruses. Pim-1 was previously mapped to chromosome 17 by somatic cell hybrids, and subsequently to the region between the hemoglobin alpha-chain pseudogene 4 (Hba-4ps) and the alpha-crystalline gene (Crya-1) by Southern blot analysis of DNA obtained from panels of recombinant inbred strains. We have now mapped Pim-1 more accurately in t-haplotypes by analysis of recombinant t-chromosomes. The recombinants were derived from Tts6tf/t12 parents backcrossed to + tf/ + tf, and scored for recombination between the loci of T and tf. For simplicity all t-complex lethal genes properly named tcl-tx are shortened to tx. The Pim-1 gene was localized 0.6 cM proximal to the tw12 lethal gene, thus placing the Pim-1 gene 5.2 cM distal to the H-2 region in t-haplotypes. Once mapped, the Pim-1 gene was used as a marker for further genetic analysis of t-haplotypes. tw12 is so close to tf that even with a large number of recombinants it was not possible to determine whether it is proximal or distal to tf. Southern blot analysis of DNA from T-tf recombinants with a separation of tw12 and tf indicated that tw12 is proximal to tf. The mapping of two allelic t-lethals, t0 and t6 with respect to tw12 and tf has also been a problem.(ABSTRACT TRUNCATED AT 250 WORDS)

Decreasing TfR1 expression reverses anemia and hepcidin suppression in β-thalassemic mice

PubMed Central

Li, Huihui; Choesang, Tenzin; Bao, Weili; Chen, Huiyong; Feola, Maria; Garcia-Santos, Daniel; Li, Jie; Sun, Shuming; Follenzi, Antonia; Pham, Petra; Liu, Jing; Zhang, Jinghua; Ponka, Prem; An, Xiuli; Mohandas, Narla; Fleming, Robert E.; Rivella, Stefano; Li, Guiyuan

2017-01-01

Iron availability for erythropoiesis and its dysregulation in β-thalassemia are incompletely understood. We previously demonstrated that exogenous apotransferrin leads to more effective erythropoiesis, decreasing erythroferrone (ERFE) and derepressing hepcidin in β-thalassemic mice. Transferrin-bound iron binding to transferrin receptor 1 (TfR1) is essential for cellular iron delivery during erythropoiesis. We hypothesize that apotransferrin’s effect is mediated via decreased TfR1 expression and evaluate TfR1 expression in β-thalassemic mice in vivo and in vitro with and without added apotransferrin. Our findings demonstrate that β-thalassemic erythroid precursors overexpress TfR1, an effect that can be reversed by the administration of exogenous apotransferrin. In vitro experiments demonstrate that apotransferrin inhibits TfR1 expression independent of erythropoietin- and iron-related signaling, decreases TfR1 partitioning to reticulocytes during enucleation, and enhances enucleation of defective β-thalassemic erythroid precursors. These findings strongly suggest that overexpressed TfR1 may play a regulatory role contributing to iron overload and anemia in β-thalassemic mice. To evaluate further, we crossed TfR1+/− mice, themselves exhibiting iron-restricted erythropoiesis with increased hepcidin, with β-thalassemic mice. Resultant double-heterozygote mice demonstrate long-term improvement in ineffective erythropoiesis, hepcidin derepression, and increased erythroid enucleation in relation to β-thalassemic mice. Our data demonstrate for the first time that TfR1+/− haploinsufficiency reverses iron overload specifically in β-thalassemic erythroid precursors. Taken together, decreasing TfR1 expression during β-thalassemic erythropoiesis, either directly via induced haploinsufficiency or via exogenous apotransferrin, decreases ineffective erythropoiesis and provides an endogenous mechanism to upregulate hepcidin, leading to sustained iron-restricted erythropoiesis and preventing systemic iron overload in β-thalassemic mice. PMID:28151426

Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach.

PubMed

Kumar, Anuj; Kumar, Sanjay; Kumar, Upendra; Suravajhala, Prashanth; Gajula, M N V Prasad

2016-10-01

Triticum aestivum L. known as common wheat is one of the most important cereal crops feeding a large and growing population. Various environmental stress factors including drought, high salinity and heat etc. adversely affect wheat production in a significant manner. Dehydration-responsive element-binding (DREB1A) factors, a class of transcription factors (TF) play an important role in combating drought stress. It is known that DREB1A specifically interacts with the dehydration responsive elements (DRE/CRT) inducing expression of genes involved in environmental stress tolerance in plants. Despite its critical interplay in plants, the structural and functional aspects of DREB1A TF in wheat remain unresolved. Previous studies showed that wheat DREBs (DREB1 and DREB2) were isolated using various methods including yeast two-hybrid screens but no extensive structural models were reported. In this study, we made an extensive in silico study to gain insight into DREB1A TF and reported the location of novel DREB1A in wheat chromosomes. We inferred the three-dimensional structural model of DREB1A using homology modelling and further evaluated them using molecular dynamics(MD) simulations yielding refined modelled structures. Our biochemical function predictions suggested that the wheat DREB1A orthologs have similar biochemical functions and pathways to that of AtDREB1A. In conclusion, the current study presents a structural perspective of wheat DREB1A and helps in understanding the molecular basis for the mechanism of DREB1A in response to environmental stress. Copyright © 2016 Elsevier Ltd. All rights reserved.

Template-independent DNA synthesis activity associated with the reverse transcriptase of the long terminal repeat retrotransposon Tf1.

PubMed

Oz-Gleenberg, Iris; Herzig, Eytan; Hizi, Amnon

2012-01-01

Reverse transcriptases (RTs) possess a non-templated addition (NTA) activity while synthesizing DNA with blunt-ended DNA primer/templates. Interestingly, the RT of the long terminal repeat retrotransposon Tf1 has an NTA activity that is substantially higher than that of HIV-1 or murine leukemia virus RTs. By performing steady state kinetics, we found that the differences between the NTA activities of Tf1 and HIV-1 RTs can be explained by the substantially lower K(M) value for the incoming dNTP of Tf1 RT (while the differences between the apparent k(cat) values of these two RTs are relatively small). Furthermore, the K(M) values, calculated for both RTs with the same dNTP, are much lower for the template-dependent synthesis (TDS) than those of NTA. However, TDS of HIV-1 RT is higher than that of Tf1 RT. The overall relative order of the apparent k(cat)/K(M) values for dATP is: HIV-1 RT (TDS) > Tf1 RT (TDS) > Tf1 RT (NTA) > HIV-1 RT (NTA). Under the employed conditions, Tf1 RT can add up to seven nucleotides to the blunt-ended substrate, while the other RTs add mostly a single nucleotide. The NTA activity of Tf1 RT is restricted to DNA primers. Furthermore, the NTA activity of Tf1 and HIV-1 RTs is suppressed by ATP, as it competes with the incoming dATP (although ATP is not incorporated by the NTA activity of the RTs). The unusually high NTA activity of Tf1 RT can explain why, after completing cDNA synthesis, the in vivo generated Tf1 cDNA has relatively long extra sequences beyond the highly conserved CA at its 3'-ends. © 2011 The Authors Journal compilation © 2011 FEBS.

On the connection between inherent DNA flexure and preferred binding of hydroxymethyluracil-containing DNA by the type II DNA-binding protein TF1.

PubMed

Grove, A; Galeone, A; Mayol, L; Geiduschek, E P

1996-07-12

TF1 is a member of the family of type II DNA-binding proteins, which also includes the bacterial HU proteins and the Escherichia coli integration host factor (IHF). Distinctive to TF1, which is encoded by the Bacillus subtilis bacteriophage SPO1, is its preferential binding to DNA in which thymine is replaced by 5-hydroxymethyluracil (hmU), as it is in the phage genome. TF1 binds to preferred sites within the phage genome and generates pronounced DNA bending. The extent to which DNA flexibility contributes to the sequence-specific binding of TF1, and the connection between hmU preference and DNA flexibility has been examined. Model flexible sites, consisting of consecutive mismatches, increase the affinity of thymine-containing DNA for TF1. In particular, tandem mismatches separated by nine base-pairs generate an increase, by orders of magnitude, in the affinity of TF1 for T-containing DNA with the sequence of a preferred TF1 binding site, and fully match the affinity of TF1 for this cognate site in hmU-containing DNA (Kd approximately 3 nM). Other placements of loops generate suboptimal binding. This is consistent with a significant contribution of site-specific DNA flexibility to complex formation. Analysis of complexes with hmU-DNA of decreasing length shows that a major part of the binding affinity is generated within a central 19 bp segment (delta G0 = 41.7 kJ mol-1) with more-distal DNA contributing modestly to the affinity (delta delta G = -0.42 kJ mol-1 bp-1 on increasing duplex length to 37 bp). However, a previously characterised thermostable and more tightly binding mutant TF1, TF1(E15G/T32I), derives most of its extra affinity from interaction with flanking DNA. We propose that inherent but sequence-dependent deformability of hmU-containing DNA underlies the preferential binding of TF1 and that TF1-induced DNA bendings is a result of distortions at two distinct sites separated by 9 bp of duplex DNA.

PET Imaging of Tissue Factor in Pancreatic Cancer Using 64Cu-Labeled Active Site-Inhibited Factor VII.

PubMed

Nielsen, Carsten H; Jeppesen, Troels E; Kristensen, Lotte K; Jensen, Mette M; El Ali, Henrik H; Madsen, Jacob; Wiinberg, Bo; Petersen, Lars C; Kjaer, Andreas

2016-07-01

Tissue factor (TF) is the main initiator of the extrinsic coagulation cascade. However, TF also plays an important role in cancer. TF expression has been reported in 53%-89% of all pancreatic adenocarcinomas, and the expression level of TF has in clinical studies correlated with advanced stage, increased microvessel density, metastasis, and poor overall survival. Imaging of TF expression is of clinical relevance as a prognostic biomarker and as a companion diagnostic for TF-directed therapies currently under clinical development. Factor VII (FVII) is the natural ligand to TF. The purpose of this study was to investigate the possibility of using active site-inhibited FVII (FVIIai) labeled with (64)Cu for PET imaging of TF expression. FVIIai was conjugated to 2-S-(4-isothiocyanatobenzyl)-1,4,7-triazacyclononane-1,4,7-triacetic acid (p-SCN-Bn-NOTA) and labeled with (64)Cu ((64)Cu-NOTA-FVIIai). Longitudinal in vivo PET imaging was performed at 1, 4, 15, and 36 h after injection of (64)Cu-NOTA-FVIIai in mice with pancreatic adenocarcinomas (BxPC-3). The specificity of TF imaging with (64)Cu-NOTA-FVIIai was investigated in subcutaneous pancreatic tumor models with different levels of TF expression and in a competition experiment. In addition, imaging of orthotopic pancreatic tumors was performed using (64)Cu-NOTA-FVIIai and PET/MRI. In vivo imaging data were supported by ex vivo biodistribution, flow cytometry, and immunohistochemistry. Longitudinal PET imaging with (64)Cu-NOTA-FVIIai showed a tumor uptake of 2.3 ± 0.2, 3.7 ± 0.3, 3.4 ± 0.3, and 2.4 ± 0.3 percentage injected dose per gram at 1, 4, 15, and 36 h after injection, respectively. An increase in tumor-to-normal-tissue contrast was observed over the imaging time course. Competition with unlabeled FVIIai significantly (P < 0.001) reduced the tumor uptake. The tumor uptake observed in models with different TF expression levels was significantly different from each other (P < 0.001) and was in agreement with the TF level evaluated by TF immunohistochemistry staining. Orthotopic tumors were clearly visible on the PET/MR images, and the uptake of (64)Cu-NOTA-FVIIai was colocalized with viable tumor tissue. (64)Cu-NOTA-FVIIai is well suited for PET imaging of tumor TF expression, and imaging is capable of distinguishing the TF expression level of various pancreatic tumor models. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

A transcription factor collective defines the HSN serotonergic neuron regulatory landscape

PubMed Central

Artacho, Alejandro; Jimeno-Martín, Ángela; Chirivella, Laura; Weinberg, Peter

2018-01-01

Cell differentiation is controlled by individual transcription factors (TFs) that together activate a selection of enhancers in specific cell types. How these combinations of TFs identify and activate their target sequences remains poorly understood. Here, we identify the cis-regulatory transcriptional code that controls the differentiation of serotonergic HSN neurons in Caenorhabditis elegans. Activation of the HSN transcriptome is directly orchestrated by a collective of six TFs. Binding site clusters for this TF collective form a regulatory signature that is sufficient for de novo identification of HSN neuron functional enhancers. Among C. elegans neurons, the HSN transcriptome most closely resembles that of mouse serotonergic neurons. Mouse orthologs of the HSN TF collective also regulate serotonergic differentiation and can functionally substitute for their worm counterparts which suggests deep homology. Our results identify rules governing the regulatory landscape of a critically important neuronal type in two species separated by over 700 million years. PMID:29553368

Intracellular Delivery of a Planar DNA Origami Structure by the Transferrin-Receptor Internalization Pathway.

PubMed

Schaffert, David H; Okholm, Anders H; Sørensen, Rasmus S; Nielsen, Jesper S; Tørring, Thomas; Rosen, Christian B; Kodal, Anne Louise B; Mortensen, Michael R; Gothelf, Kurt V; Kjems, Jørgen

2016-05-01

DNA origami provides rapid access to easily functionalized, nanometer-sized structures making it an intriguing platform for the development of defined drug delivery and sensor systems. Low cellular uptake of DNA nanostructures is a major obstacle in the development of DNA-based delivery platforms. Herein, significant strong increase in cellular uptake in an established cancer cell line by modifying a planar DNA origami structure with the iron transport protein transferrin (Tf) is demonstrated. A variable number of Tf molecules are coupled to the origami structure using a DNA-directed, site-selective labeling technique to retain ligand functionality. A combination of confocal fluorescence microscopy and quantitative (qPCR) techniques shows up to 22-fold increased cytoplasmic uptake compared to unmodified structures and with an efficiency that correlates to the number of transferrin molecules on the origami surface. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Disentangling the many layers of eukaryotic transcriptional regulation.

PubMed

Lelli, Katherine M; Slattery, Matthew; Mann, Richard S

2012-01-01

Regulation of gene expression in eukaryotes is an extremely complex process. In this review, we break down several critical steps, emphasizing new data and techniques that have expanded current gene regulatory models. We begin at the level of DNA sequence where cis-regulatory modules (CRMs) provide important regulatory information in the form of transcription factor (TF) binding sites. In this respect, CRMs function as instructional platforms for the assembly of gene regulatory complexes. We discuss multiple mechanisms controlling complex assembly, including cooperative DNA binding, combinatorial codes, and CRM architecture. The second section of this review places CRM assembly in the context of nucleosomes and condensed chromatin. We discuss how DNA accessibility and histone modifications contribute to TF function. Lastly, new advances in chromosomal mapping techniques have provided increased understanding of intra- and interchromosomal interactions. We discuss how these topological maps influence gene regulatory models.

Regulation of LPS-induced tissue factor expression in human monocytic THP-1 cells by curcumin

USDA-ARS?s Scientific Manuscript database

Tissue factor (TF) is a transmembrane receptor, which initiates thrombotic episodes associated with various diseases. In addition to membrane-bound TF, we have discovered an alternatively spliced form of human TF mRNA. It was later confirmed that this form of TF mRNA expresses a soluble protein circ...

Multisensor Calibration Procedure for an All Weather Short Range Air Defense System Concept.

DTIC Science & Technology

1983-08-15

are then integrated over the rotation interval tF1 - to 1 - tR, to arrive at the following angular displacement mesasuremnts: tF 1 eAl -f WAldt - K~len...g&dt (73) tol to1 tFlAOR1 tj~ 6p’Idt "( 1 8 0 ° " l1 + 0 12 ) (74) tF1 AVAl f Aldt (75) to’ &VB1 tl(6 to1 In order to integrate Al and B1, Reneral...rotation. TFl, TF2 tF1 , tF2 Upper limit of integration during rotation. THTI2,TT13,TRT21 Elments of BCS to ACS transformation THT23,THT311,THT32 matrix

NREL Pyrheliometer Comparisons: September 26-October 7, 2016 (NPC-2016)

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

Reda, Ibrahim; Dooraghi, Mike; Andreas, Afshin

Accurate measurements of direct normal (beam) solar irradiance from pyrheliometers are important for developing and deploying solar energy conversion systems, improving our understanding of the Earth's energy budget for climate change studies, and for other science and technology applications involving solar flux. Providing these measurements places many demands on the quality system used by the operator of commercially available radiometers. Maintaining accurate radiometer calibrations that are traceable to an international standard is the first step in producing research-quality solar irradiance measurements. National Renewable Energy Laboratory (NREL) pyrheliometer comparisons (NPCs) are held annually at the Solar Radiation Research Laboratory (SRRL) inmore » Golden, Colorado. Open to all pyrheliometer owners and operators, each NPC provides an opportunity to determine the unique World Radiometric Reference transfer factor (WRR-TF) for each participating pyrheliometer. By adjusting all subsequent pyrheliometer measurements by the appropriate WRR-TF, the solar irradiance data are traceable to the WRR. NPC-2016 was September 26 through October 7, 2016. Participants operated 45 absolute cavity radiometers and 27 conventional thermopile-based pyrheliometers to simultaneously measure clear-sky, direct normal solar irradiance during this period.« less

ePIANNO: ePIgenomics ANNOtation tool.

PubMed

Liu, Chia-Hsin; Ho, Bing-Ching; Chen, Chun-Ling; Chang, Ya-Hsuan; Hsu, Yi-Chiung; Li, Yu-Cheng; Yuan, Shin-Sheng; Huang, Yi-Huan; Chang, Chi-Sheng; Li, Ker-Chau; Chen, Hsuan-Yu

2016-01-01

Recently, with the development of next generation sequencing (NGS), the combination of chromatin immunoprecipitation (ChIP) and NGS, namely ChIP-seq, has become a powerful technique to capture potential genomic binding sites of regulatory factors, histone modifications and chromatin accessible regions. For most researchers, additional information including genomic variations on the TF binding site, allele frequency of variation between different populations, variation associated disease, and other neighbour TF binding sites are essential to generate a proper hypothesis or a meaningful conclusion. Many ChIP-seq datasets had been deposited on the public domain to help researchers make new discoveries. However, researches are often intimidated by the complexity of data structure and largeness of data volume. Such information would be more useful if they could be combined or downloaded with ChIP-seq data. To meet such demands, we built a webtool: ePIgenomic ANNOtation tool (ePIANNO, http://epianno.stat.sinica.edu.tw/index.html). ePIANNO is a web server that combines SNP information of populations (1000 Genomes Project) and gene-disease association information of GWAS (NHGRI) with ChIP-seq (hmChIP, ENCODE, and ROADMAP epigenomics) data. ePIANNO has a user-friendly website interface allowing researchers to explore, navigate, and extract data quickly. We use two examples to demonstrate how users could use functions of ePIANNO webserver to explore useful information about TF related genomic variants. Users could use our query functions to search target regions, transcription factors, or annotations. ePIANNO may help users to generate hypothesis or explore potential biological functions for their studies.

Identifying decreased diaphragmatic mobility and diaphragm thickening in interstitial lung disease: the utility of ultrasound imaging

PubMed Central

Santana, Pauliane Vieira; Prina, Elena; Albuquerque, André Luis Pereira; Carvalho, Carlos Roberto Ribeiro; Caruso, Pedro

2016-01-01

Objective: To investigate the applicability of ultrasound imaging of the diaphragm in interstitial lung disease (ILD). Methods: Using ultrasound, we compared ILD patients and healthy volunteers (controls) in terms of diaphragmatic mobility during quiet and deep breathing; diaphragm thickness at functional residual capacity (FRC) and at total lung capacity (TLC); and the thickening fraction (TF, proportional diaphragm thickening from FRC to TLC). We also evaluated correlations between diaphragmatic dysfunction and lung function variables. Results: Between the ILD patients (n = 40) and the controls (n = 16), mean diaphragmatic mobility was comparable during quiet breathing, although it was significantly lower in the patients during deep breathing (4.5 ± 1.7 cm vs. 7.6 ± 1.4 cm; p < 0.01). The patients showed greater diaphragm thickness at FRC (p = 0.05), although, due to lower diaphragm thickness at TLC, they also showed a lower TF (p < 0.01). The FVC as a percentage of the predicted value (FVC%) correlated with diaphragmatic mobility (r = 0.73; p < 0.01), and an FVC% cut-off value of < 60% presented high sensitivity (92%) and specificity (81%) for indentifying decreased diaphragmatic mobility. Conclusions: Using ultrasound, we were able to show that diaphragmatic mobility and the TF were lower in ILD patients than in healthy controls, despite the greater diaphragm thickness at FRC in the former. Diaphragmatic mobility correlated with ILD functional severity, and an FVC% cut-off value of < 60% was found to be highly accurate for indentifying diaphragmatic dysfunction on ultrasound. PMID:27167428

Measurement of microparticle tissue factor activity in clinical samples: A summary of two tissue factor-dependent FXa generation assays.

PubMed

Hisada, Yohei; Alexander, Wyeth; Kasthuri, Raj; Voorhees, Peter; Mobarrez, Fariborz; Taylor, Angela; McNamara, Coleen; Wallen, Hakan; Witkowski, Marco; Key, Nigel S; Rauch, Ursula; Mackman, Nigel

2016-03-01

Thrombosis is a leading cause of morbidity and mortality. Detection of a prothrombotic state using biomarkers would be of great benefit to identify patients at risk of thrombosis that would benefit from thromboprophylaxis. Tissue factor (TF) is a highly procoagulant protein that under normal conditions is not present in the blood. However, increased levels of TF in the blood in the form of microparticles (MPs) (also called extracellular vesicles) are observed under various pathological conditions. In this review, we will discuss studies that have measured MP-TF activity in a variety of diseases using two similar FXa generation assay. One of the most robust signals for MP-TF activity (16-26 fold higher than healthy controls) is observed in pancreatic cancer patients with venous thromboembolism. In this case, the TF+ MPs appear to be derived from the cancer cells. Surprisingly, cirrhosis and acute liver injury are associated with 17-fold and 38-fold increases in MP-TF activity, respectively. Based on mouse models, we speculate that the TF+ MPs are derived from hepatocytes. More modest increases are observed in patients with urinary tract infections (6-fold) and in a human endotoxemia model (9-fold) where monocytes are the likely source of the TF+ MPs. Finally, there is no increase in MP-TF activity in the majority of cardiovascular disease patients. These studies indicate that MP-TF activity may be a useful biomarker to identify patients with particular diseases that have an increased risk of thrombosis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Impact of Dental Fluorosis, Socioeconomic Status and Self-Perception in Adolescents Exposed to a High Level of Fluoride in Water

PubMed Central

Molina-Frechero, Nelly; Nevarez-Rascón, Martina; Nevarez-Rascón, Alfredo; González-González, Rogelio; Irigoyen-Camacho, María Esther; Sánchez-Pérez, Leonor; López-Verdin, Sandra; Bologna-Molina, Ronell

2017-01-01

Objective: To identify adolescents’ self-perception of dental fluorosis from two areas with different socioeconomic levels. Methods: A cross-sectional, descriptive study was conducted with 15-year-old youths by applying a questionnaire designed and validated to assess self-perceptions of dental fluorosis in two areas with different socioeconomic statuses (SESs). Fluorosis was clinically evaluated by applying the Thylstrup and Fejerkov (TF) index on the upper front teeth. Results: A total of 308 adolescents were included in the study. The medium-SES population, which was exposed to 2.5 ppm of fluoride in water, and the low-SES population, which was exposed to 5.1 ppm, presented the following levels of dental fluorosis: TF 2–3 (50%), TF 4–5 (45.6%) and TF 6–7 (4.4%) for medium SES and TF 2–3 (12.3%), TF 4–5 (67.1%) and TF 67 (20.6%) for low SES. A significant association was found between self-perception and dental fluorosis in those with medium and low SESs (p < 0.05). The multiple regression model found differences between TF levels and self-perception, with a 6–7 TF level for concerns about color (OR = 1.6), smile (OR = 1.2) and appearance (OR = 3.36). Conclusions: Self-perceptions of dental fluorosis affect adolescents such that adolescents with a medium SES have more negative perceptions than those with a low SES. Such perceptions increase as the TF index increases. PMID:28085102

Rapid screening of transferrin-binders in the flowers of Bauhinia blakeana Dunn by on-line high-performance liquid chromatography-diode-array detector-electrospray ionization-ion-trap-time-of-flight-mass spectrometry-transferrin-fluorescence detection system.

PubMed

Liu, Meixian; Dong, Jing; Lin, Zongtao; Niu, Yanyan; Zhang, Xiaotian; Jiang, Haixiu; Guo, Ning; Li, Wei; Wang, Hong; Chen, Shizhong

2016-06-10

Transferrin (Transferrin, TRF, TF) has drawn increasing attention in cancer therapy due to its potential applications in drug delivery. TF receptor, highly expressed in tumor cells, recognizes and transports Fe(3+)-TF into cells to release iron into cytoplasm. Thus, discovering TF-binding compounds has become an active research area and is of great importance for target therapy. In this study, an on-line analysis method was established for screening TF-binding compounds from the flowers of Bauhinia blakeana Dunn using a high-performance liquid chromatography-diode-array detector-multi-stage mass spectrometry-transferrin-fluorescence detector (HPLC-DAD-MS(n)-TF-FLD) method. As a result, 33 of 80 identified or tentatively characterized compounds in the sample were TF-binding active. Twenty-five flavonol glycosides and eight phenolic acids were identified as TF-binders. Twelve of these active compounds together with six standard compounds were used to study the dose-response effects and structure-activity relationships of flavonoids and phenolic acids. The method was validated by vitexin with a good linearity in the range of concentrations used in the study. The limit of detection for vitexin was 0.1596 nmol. Our study indicated that the established method is simple, rapid and sensitive for screening TF-binding active compounds in the extract of Bauhinia blakeana Dunn, and therefore is important for discovering potential anti-cancer ingredients from complex samples for TF related drug delivery. Copyright © 2016 Elsevier B.V. All rights reserved.

Theaflavin-3,3'-digallate, a component of black tea: an inducer of oxidative stress and apoptosis.

PubMed

Schuck, Alyssa G; Ausubel, Miriam B; Zuckerbraun, Harriet L; Babich, Harvey

2008-04-01

Treatment of human oral squamous carcinoma HSC-2 cells and normal GN46 fibroblasts with theaflavin-3,3'-digallate (TF-3), a polyphenol in black tea, showed a concentration and time dependent inhibition of growth, with the tumor cells more sensitive than the fibroblasts. In buffer and in cell culture medium, TF-3 generated reactive oxygen species, with lower levels detected in buffer amended with catalase and superoxide dismutase, indicating the generation of hydrogen peroxide and superoxide, respectively, and suggesting that TF-3 may be an inducer of oxidative stress. The toxicity of TF-3 was decreased in the presence of catalase, pyruvate, and divalent cobalt, all scavengers of reactive oxygen species, but was potentiated in the presence of diethyldithiocarbamate, an inhibitor of superoxide dismutase. The intracellular level of glutathione in HSC-2 cells was lessened after a 4-h exposure to 250 and 500 microM TF-3. However, for GN46 fibroblasts, a 4-h exposure to 250 microM TF-3 stimulated, but to 500 microM TF-3 lessened, intracellular glutathione. Treatment of the cells with the glutathione depleters, 1,3-bis(2-chloroethyl)-N-nitrosourea, 1-chloro-2,4-dinitrobenzene, and d,l-buthionine-[S,R]-sulfoximine potentiated the toxicity of TF-3. Induction of apoptotic cell death in HSC-2 cells treated with TF-3 was noted by apoptotic cell morphologies, by TUNEL staining, by PARP cleavage, and by elevated activity of caspase-3. Apoptosis was not noted in GN46 fibroblasts treated with TF-3.

RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.

PubMed

Novichkov, Pavel S; Kazakov, Alexey E; Ravcheev, Dmitry A; Leyn, Semen A; Kovaleva, Galina Y; Sutormin, Roman A; Kazanov, Marat D; Riehl, William; Arkin, Adam P; Dubchak, Inna; Rodionov, Dmitry A

2013-11-01

Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, whose lifestyles and natural environments are substantially different, possess highly diverged transcriptional regulatory networks. The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches). RegPrecise (http://regprecise.lbl.gov) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics. We significantly expanded a reference collection of manually curated regulons we introduced earlier. RegPrecise 3.0 provides access to inferred regulatory interactions organized by phylogenetic, structural and functional properties. Taxonomy-specific collections include 781 TF regulogs inferred in more than 160 genomes representing 14 taxonomic groups of Bacteria. TF-specific collections include regulogs for a selected subset of 40 TFs reconstructed across more than 30 taxonomic lineages. Novel collections of regulons operated by RNA regulatory elements (riboswitches) include near 400 regulogs inferred in 24 bacterial lineages. RegPrecise 3.0 provides four classifications of the reference regulons implemented as controlled vocabularies: 55 TF protein families; 43 RNA motif families; ~150 biological processes or metabolic pathways; and ~200 effectors or environmental signals. Genome-wide visualization of regulatory networks and metabolic pathways covered by the reference regulons are available for all studied genomes. A separate section of RegPrecise 3.0 contains draft regulatory networks in 640 genomes obtained by an conservative propagation of the reference regulons to closely related genomes. RegPrecise 3.0 gives access to the transcriptional regulons reconstructed in bacterial genomes. Analytical capabilities include exploration of: regulon content, structure and function; TF binding site motifs; conservation and variations in genome-wide regulatory networks across all taxonomic groups of Bacteria. RegPrecise 3.0 was selected as a core resource on transcriptional regulation of the Department of Energy Systems Biology Knowledgebase, an emerging software and data environment designed to enable researchers to collaboratively generate, test and share new hypotheses about gene and protein functions, perform large-scale analyses, and model interactions in microbes, plants, and their communities.

Effects of the Fruit Extract of Tribulus terrestris on Skin Inflammation in Mice with Oxazolone-Induced Atopic Dermatitis through Regulation of Calcium Channels, Orai-1 and TRPV3, and Mast Cell Activation

PubMed Central

Kang, Seok Yong; Jung, Hyo Won; Nam, Joo Hyun; Kim, Woo Kyung; Kang, Jong-Seong; Kim, Young-Ho; Cho, Cheong-Weon; Cho, Chong Woon

2017-01-01

Ethnopharmacological Relevance In this study, we investigated the effects of Tribulus terrestris fruit (Leguminosae, Tribuli Fructus, TF) extract on oxazolone-induced atopic dermatitis in mice. Materials and Methods TF extract was prepared with 30% ethanol as solvent. The 1% TF extract with or without 0.1% HC was applied to the back skin daily for 24 days. Results 1% TF extract with 0.1% HC improved AD symptoms and reduced TEWL and symptom scores in AD mice. 1% TF extract with 0.1% HC inhibited skin inflammation through decrease in inflammatory cells infiltration as well as inhibition of Orai-1 expression in skin tissues. TF extract inhibited Orai-1 activity in Orai-1-STIM1 cooverexpressing HEK293T cells but increased TRPV3 activity in TRPV3-overexpressing HEK293T cells. TF extract decreased β-hexosaminidase release in RBL-2H3 cells. Conclusions The present study demonstrates that the topical application of TF extract improves skin inflammation in AD mice, and the mechanism for this effect appears to be related to the modulation of calcium channels and mast cell activation. This outcome suggests that the combination of TF and steroids could be a more effective and safe approach for AD treatment. PMID:29348776

A Randomized Implementation Study of Trauma-Focused Cognitive Behavioral Therapy for Adjudicated Teens in Residential Treatment Facilities.

PubMed

Cohen, Judith A; Mannarino, Anthony P; Jankowski, Kay; Rosenberg, Stanley; Kodya, Suzanne; Wolford, George L

2016-05-01

Adjudicated youth in residential treatment facilities (RTFs) have high rates of trauma exposure and post-traumatic stress disorder (PTSD). This study evaluated strategies for implementing trauma-focused cognitive behavioral therapy (TF-CBT) in RTF. Therapists (N = 129) treating adjudicated youth were randomized by RTF program (N = 18) to receive one of the two TF-CBT implementation strategies: (1) web-based TF-CBT training + consultation (W) or (2) W + 2 day live TF-CBT workshop + twice monthly phone consultation (W + L). Youth trauma screening and PTSD symptoms were assessed via online dashboard data entry using the University of California at Los Angeles PTSD Reaction Index. Youth depressive symptoms were assessed with the Mood and Feelings Questionnaire-Short Version. Outcomes were therapist screening; TF-CBT engagement, completion, and fidelity; and youth improvement in PTSD and depressive symptoms. The W + L condition resulted in significantly more therapists conducting trauma screening (p = .0005), completing treatment (p = .03), and completing TF-CBT with fidelity (p = .001) than the W condition. Therapist licensure significantly impacted several outcomes. Adjudicated RTF youth receiving TF-CBT across conditions experienced statistically and clinically significant improvement in PTSD (p = .001) and depressive (p = .018) symptoms. W + L is generally superior to W for implementing TF-CBT in RTF. TF-CBT is effective for improving trauma-related symptoms in adjudicated RTF youth. Implementation barriers are discussed. © The Author(s) 2016.

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

PubMed Central

Schmidt, Florian; Gasparoni, Nina; Gasparoni, Gilles; Gianmoena, Kathrin; Cadenas, Cristina; Polansky, Julia K.; Ebert, Peter; Nordström, Karl; Barann, Matthias; Sinha, Anupam; Fröhler, Sebastian; Xiong, Jieyi; Dehghani Amirabad, Azim; Behjati Ardakani, Fatemeh; Hutter, Barbara; Zipprich, Gideon; Felder, Bärbel; Eils, Jürgen; Brors, Benedikt; Chen, Wei; Hengstler, Jan G.; Hamann, Alf; Lengauer, Thomas; Rosenstiel, Philip; Walter, Jörn; Schulz, Marcel H.

2017-01-01

The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively. PMID:27899623

Medical treatment of orthotopic glioblastoma with transferrin-conjugated nanoparticles encapsulating zoledronic acid.

PubMed

Porru, Manuela; Zappavigna, Silvia; Salzano, Giuseppina; Luce, Amalia; Stoppacciaro, Antonella; Balestrieri, Maria Luisa; Artuso, Simona; Lusa, Sara; De Rosa, Giuseppe; Leonetti, Carlo; Caraglia, Michele

2014-11-15

Glioblastomas are highly aggressive adult brain tumors with poor clinical outcome. In the central nervous system (CNS) the blood-brain barrier (BBB) is the most important limiting factor for both development of new drugs and drug delivery. Here, we propose a new strategy to treat glioblastoma based on transferrin (Tf)-targeted self-assembled nanoparticles (NPs) incorporating zoledronic acid (ZOL) (NPs-ZOL-Tf). NPs-ZOL-Tf have been assessed on the glioblastoma cell line U373MG-LUC that showed a refractoriness in vitro to temozolomide (TMZ) and fotemustine (FTM). NPs-ZOL-Tf treatment resulted in higher in vitro cytotoxic activity than free ZOL. However, the potentiation of anti-proliferative activity of NPs-ZOL-Tf was superimposable to that one induced by NPs-ZOL (not armed with Tf). On the other hand, NPs-ZOL-Tf showed a higher antitumor efficacy if compared with that one caused by NPs-ZOL in immunosuppressed mice intramuscularly bearing U373MG-LUC xenografts, inducing a significant tumor weight inhibition (TWI). The experiments performed on mice with intracranial U373MG-LUC xenografts confirmed the efficacy of NPs-ZOL-Tf. These effects were paralleled by a higher intratumour localization of fluorescently-labeled-NPs-Tf both in intramuscular and intracranial xenografts. In conclusion, our results demonstrate that the encapsulation of ZOL increases the antitumor efficacy of this drug in glioblastoma through the acquisition of ability to cross the BBB.

High-level secretion of tissue factor-rich extracellular vesicles from ovarian cancer cells mediated by filamin-A and protease-activated receptors.

PubMed

Koizume, Shiro; Ito, Shin; Yoshioka, Yusuke; Kanayama, Tomohiko; Nakamura, Yoshiyasu; Yoshihara, Mitsuyo; Yamada, Roppei; Ochiya, Takahiro; Ruf, Wolfram; Miyagi, Etsuko; Hirahara, Fumiki; Miyagi, Yohei

2016-01-01

Thromboembolic events occur frequently in ovarian cancer patients. Tissue factor (TF) is often overexpressed in tumours, including ovarian clear-cell carcinoma (CCC), a subtype with a generally poor prognosis. TF-coagulation factor VII (fVII) complexes on the cell surface activate downstream coagulation mechanisms. Moreover, cancer cells secrete extracellular vesicles (EVs), which act as vehicles for TF. We therefore examined the characteristics of EVs produced by ovarian cancer cells of various histological subtypes. CCC cells secreted high levels of TF within EVs, while the high-TF expressing breast cancer cell line MDA-MB-231 shed fewer TF-positive EVs. We also found that CCC tumours with hypoxic tissue areas synthesised TF and fVII in vivo, rendering the blood of xenograft mice bearing these tumours hypercoagulable compared with mice bearing MDA-MB-231 tumours. Incorporation of TF into EVs and secretion of EVs from CCC cells exposed to hypoxia were both dependent on the actin-binding protein, filamin-A (filA). Furthermore, production of these EVs was dependent on different protease-activated receptors (PARs) on the cell surface. These results show that CCC cells could produce large numbers of TF-positive EVs dependent upon filA and PARs. This phenomenon may be the mechanism underlying the increased incidence of venous thromboembolism in ovarian cancer patients.

Phenology and spatial distribution of native and exotic Tetropium longhorned beetles (Coleoptera: Cerambycidae).

PubMed

Rhainds, Marc; Heard, Stephen B; Sweeney, Jon D; Silk, Peter; Flaherty, Leah

2010-12-01

The co-existence of two closely related Tetropium species in eastern Canada, invasive T. fuscum and native T. cinnamopterum (TF and TC, respectively), provides a model system to investigate seasonal and spatial demographic parameters of biological invasions at the interspecific level. In this study, we take advantage of the similar semiochemical communication of TF and TC to evaluate the abundance of adults of the two species concurrently using grids of traps baited with pheromone and host volatiles in stands of spruce. Adult TF emerged on average 2 wk before TC both in the field and under controlled laboratory conditions. This observation, combined with the early reproduction of emergent females, implies that the smaller (younger) larvae of native TC may be at increased risk of intra-guild predation by TF. The high spatial association between male and female TF in dense, aggregated populations suggests that the rate of mate encounter is depressed in sparse populations toward the edge of the invasive range. The higher level of spatial aggregation for TF than TC, particularly at high population density, suggests a higher propensity of adult TF to congregate at "landmarks." Considering the broader range of host conditions, earlier seasonal emergence, and presumably more effective mate encounter for TF than TC, the exotic TF may be a superior competitor with the potential to displace or reduce the abundance of TC. © 2010 Entomological Society of America

Targeting tissue factor as a novel therapeutic oncotarget for eradication of cancer stem cells isolated from tumor cell lines, tumor xenografts and patients of breast, lung and ovarian cancer.

PubMed

Hu, Zhiwei; Xu, Jie; Cheng, Jijun; McMichael, Elizabeth; Yu, Lianbo; Carson, William E

2017-01-03

Targeting cancer stem cell (CSC) represents a promising therapeutic approach as it can potentially fight cancer at its root. The challenge is to identify a surface therapeutic oncotarget on CSC. Tissue factor (TF) is known as a common yet specific surface target for cancer cells and tumor neovasculature in several solid cancers. However, it is unknown if TF is expressed by CSCs. Here we demonstrate that TF is constitutively expressed on CD133 positive (CD133+) or CD24-CD44+ CSCs isolated from human cancer cell lines, tumor xenografts from mice and breast tumor tissues from patients. TF-targeted agents, i.e., a factor VII (fVII)-conjugated photosensitizer (fVII-PS for targeted photodynamic therapy) and fVII-IgG1Fc (Immunoconjugate or ICON for immunotherapy), can eradicate CSC via the induction of apoptosis and necrosis and via antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity, respectively. In conclusion, these results demonstrate that TF is a novel surface therapeutic oncotarget for CSC, in addition to cancer cell TF and tumor angiogenic vascular endothelial TF. Moreover, this research highlights that TF-targeting therapeutics can effectively eradicate CSCs, without drug resistance, isolated from breast, lung and ovarian cancer with potential to translate into other most commonly diagnosed solid cancer, in which TF is also highly expressed.

A Randomized Implementation Study of Trauma-Focused Cognitive Behavioral Therapy for Adjudicated Teens in Residential Treatment Facilities

PubMed Central

Cohen, Judith A.; Mannarino, Anthony P.; Jankowski, Kay; Rosenberg, Stanley; Kodya, Suzanne; Wolford, George L.

2016-01-01

Adjudicated youth in residential treatment facilities (RTFs) have high rates of trauma exposure and post-traumatic stress disorder (PTSD). This study evaluated strategies for implementing trauma-focused cognitive behavioral therapy (TF-CBT) in RTF. Therapists (N = 129) treating adjudicated youth were randomized by RTF program (N = 18) to receive one of the two TF-CBT implementation strategies: (1) web-based TF-CBT training + consultation (W) or (2) W + 2 day live TF-CBT workshop + twice monthly phone consultation (W + L). Youth trauma screening and PTSD symptoms were assessed via online dashboard data entry using the University of California at Los Angeles PTSD Reaction Index. Youth depressive symptoms were assessed with the Mood and Feelings Questionnaire–Short Version. Outcomes were therapist screening; TF-CBT engagement, completion, and fidelity; and youth improvement in PTSD and depressive symptoms. The W + L condition resulted in significantly more therapists conducting trauma screening (p = .0005), completing treatment (p = .03), and completing TF-CBT with fidelity (p = .001) than the W condition. Therapist licensure significantly impacted several outcomes. Adjudicated RTF youth receiving TF-CBT across conditions experienced statistically and clinically significant improvement in PTSD (p = .001) and depressive (p = .018) symptoms. W + L is generally superior to W for implementing TF-CBT in RTF. TF-CBT is effective for improving trauma-related symptoms in adjudicated RTF youth. Implementation barriers are discussed. PMID:26747845

Medical treatment of orthotopic glioblastoma with transferrin-conjugated nanoparticles encapsulating zoledronic acid

PubMed Central

Porru, Manuela; Zappavigna, Silvia; Salzano, Giuseppina; Luce, Amalia; Stoppacciaro, Antonella; Balestrieri, Maria Luisa; Artuso, Simona; Lusa, Sara; De Rosa, Giuseppe; Leonetti, Carlo; Caraglia, Michele

2014-01-01

Glioblastomas are highly aggressive adult brain tumors with poor clinical outcome. In the central nervous system (CNS) the blood-brain barrier (BBB) is the most important limiting factor for both development of new drugs and drug delivery. Here, we propose a new strategy to treat glioblastoma based on transferrin (Tf)-targeted self-assembled nanoparticles (NPs) incorporating zoledronic acid (ZOL) (NPs-ZOL-Tf). NPs-ZOL-Tf have been assessed on the glioblastoma cell line U373MG-LUC that showed a refractoriness in vitro to temozolomide (TMZ) and fotemustine (FTM). NPs-ZOL-Tf treatment resulted in higher in vitro cytotoxic activity than free ZOL. However, the potentiation of anti-proliferative activity of NPs-ZOL-Tf was superimposable to that one induced by NPs-ZOL (not armed with Tf). On the other hand, NPs-ZOL-Tf showed a higher antitumor efficacy if compared with that one caused by NPs-ZOL in immunosuppressed mice intramuscularly bearing U373MG-LUC xenografts, inducing a significant tumor weight inhibition (TWI). The experiments performed on mice with intracranial U373MG-LUC xenografts confirmed the efficacy of NPs-ZOL-Tf. These effects were paralleled by a higher intratumour localization of fluorescently-labeled-NPs-Tf both in intramuscular and intracranial xenografts. In conclusion, our results demonstrate that the encapsulation of ZOL increases the antitumor efficacy of this drug in glioblastoma through the acquisition of ability to cross the BBB. PMID:25431953

Ovine uterine space restriction alters placental transferrin receptor and fetal iron status during late pregnancy

PubMed Central

Sun, Mary Y.; Habeck, Jason M.; Meyer, Katie M.; Koch, Jill M.; Ramadoss, Jayanth; Blohowiak, Sharon E.; Magness, Ronald R.; Kling, Pamela J.

2013-01-01

Background Fetal growth restriction is reported to be associated with impaired placental iron transport. Transferrin receptor (TfR) is a major placental iron transporter in humans, but is unstudied in sheep. TfR is regulated by both iron and nitric oxide (NO), the molecule produced by endothelial NOS (eNOS). We hypothesized that limited placental development downregulates both placental TfR and eNOS expression, thereby lowering fetal tissue iron. Methods An ovine surgical uterine space restriction (USR) model, combined with multifetal gestation, tested the extremes of uterine and placental adaptation. Blood, tissues, and placentomes from non-space restricted (NSR) singletons were compared to USR fetuses at 120 or 130 days of gestation (GD). Results When expressed proportionate to fetal weight, liver iron content did not differ while renal iron was higher in USR vs. NSR fetuses. Renal TfR protein expression did not differ, but placental TfR expression was lower in USR fetuses at GD130. Placental levels of TfR correlated to eNOS. TfR was localized throughout the placentome, including the hemophagous zone, implicating a role for TfR in ovine placental iron transport. Conclusion In conclusion, fetal iron was regulated in an organ-specific fashion. In USR fetuses, NO-mediated placental adaptations may prevent the normal upregulation of placental TfR at GD130. PMID:23202722

A microfluidic method for synthesis of transferrin-lipid nanoparticles loaded with siRNA LOR-1284 for therapy of acute myeloid leukemia

PubMed Central

Yang, Zhaogang; Yu, Bo; Zhu, Jing; Huang, Xiaomeng; Xie, Jing; Xu, Songlin; Yang, Xiaojuan; Wang, Xinmei; Yung, Bryant C.; Lee, L. James; Lee, Robert J.; Teng, Lesheng

2015-01-01

siRNA LOR-1284 targets the R2 subunit of ribonucleotide reductase (RRM2) and has shown promise in cancer therapy. In this study, transferrin (Tf) conjugated lipid nanoparticles (Tf-NP-LOR-1284) were synthesized by microfluidic hydrodynamic focusing (MHF) and evaluated for targeted delivery of LOR-1284 siRNA to acute myeloid leukemia (AML) cells. In vitro study showed that Tf-NP-LOR-1284 can protect LOR-1284 from serum nuclease degradation. Selective uptake of Tf-NP-LOR-1284 was observed in MV4–11 cells. In addition, qRT-PCR and Western blot results revealed that Tf-NP-LOR-1284 was more effective than free LOR-1284 in reducing the R2 mRNA and protein levels. Tf-NP-LOR-1284 showed prolonged circulation time and increased AUC after i.v. administration relative to free LOR-1284. Furthermore, Tf-NP-LOR-1284 facilitated increased accumulation at the tumor site along with decreased R2 mRNA and protein expression in a murine xenograft model. These results suggest that Tf-conjugated NPs prepared by MHF provide a suitable platform for efficient and specific thereapeutic delivery of LOR-1284 to AML. PMID:25003978

Pediatric tinea faciei in southern Spain: a 30-year survey.

PubMed

del Boz, Javier; Crespo, Vicente; de Troya, Magdalena

2012-01-01

Tinea faciei (TF) is a common clinical form of tinea in children that is frequently misdiagnosed and treated with corticosteroids. No large case series of TF focusing on children have been published. The aim of this study was to analyze the main epidemiologic, clinical, and microbiologic features of TF in children over a period of 30 years and compare these features with those of other tineas. We undertook a retrospective study of 818 cases of tinea in children at a referral hospital in southern Spain, diagnosed between 1977 and 2006, concentrating for this study on TF. Of the 73 cases of TF diagnosed, 50.7% were in girls. Most children (46.6%) were 4 to 9 years old. At the time of diagnosis, 29.2% of the cases had been treated with topical steroids. The most frequently isolated dermatophyte was Trichophyton mentagrophytes, which was isolated significantly more frequently in TF than in the other tineas. Cases of TF in children were not extremely unusual, emphasizing that TF must be considered in children with inflammatory facial eruptions. This consideration and the more-frequent use of mycologic tests can help achieve the correct diagnosis, when present. © 2011 Wiley Periodicals, Inc.

Thiophenone Attenuates Enteropathogenic Escherichia coli O103:H2 Virulence by Interfering with AI-2 Signaling.

PubMed

Witsø, Ingun Lund; Valen Rukke, Håkon; Benneche, Tore; Aamdal Scheie, Anne

2016-01-01

Interference with bacterial quorum sensing communication provides an anti-virulence strategy to control pathogenic bacteria. Here, using the Enteropathogenic E. coli (EPEC) O103:H2, we showed for the first time that thiophenone TF101 reduced expression of lsrB; the gene encoding the AI-2 receptor. Combined results of transcriptional and phenotypic analyses suggested that TF101 interfere with AI-2 signalling, possibly by competing with AI-2 for binding to LsrB. This is supported by in silico docking prediction of thiophenone TF101 in the LsrB pocket. Transcriptional analyses furthermore showed that thiophenone TF101 interfered with expression of the virulence genes eae and fimH. In addition, TF101 reduced AI-2 induced E. coli adhesion to colorectal adenocarcinoma cells. TF101, on the other hand, did not affect epinephrine or norepinephrine enhanced E. coli adhesion. Overall, our results showed that thiophenone TF101 interfered with virulence expression in E. coli O103:H2, suggestedly by interfering with AI-2 mediated quorum sensing. We thus conclude that thiophenone TF101 might represent a promising future anti-virulence agent in the fight against pathogenic E. coli.

Thiophenone Attenuates Enteropathogenic Escherichia coli O103:H2 Virulence by Interfering with AI-2 Signaling

PubMed Central

Valen Rukke, Håkon; Benneche, Tore; Aamdal Scheie, Anne

2016-01-01

Interference with bacterial quorum sensing communication provides an anti-virulence strategy to control pathogenic bacteria. Here, using the Enteropathogenic E. coli (EPEC) O103:H2, we showed for the first time that thiophenone TF101 reduced expression of lsrB; the gene encoding the AI-2 receptor. Combined results of transcriptional and phenotypic analyses suggested that TF101 interfere with AI-2 signalling, possibly by competing with AI-2 for binding to LsrB. This is supported by in silico docking prediction of thiophenone TF101 in the LsrB pocket. Transcriptional analyses furthermore showed that thiophenone TF101 interfered with expression of the virulence genes eae and fimH. In addition, TF101 reduced AI-2 induced E. coli adhesion to colorectal adenocarcinoma cells. TF101, on the other hand, did not affect epinephrine or norepinephrine enhanced E. coli adhesion. Overall, our results showed that thiophenone TF101 interfered with virulence expression in E. coli O103:H2, suggestedly by interfering with AI-2 mediated quorum sensing. We thus conclude that thiophenone TF101 might represent a promising future anti-virulence agent in the fight against pathogenic E. coli. PMID:27309855

TF1, the bacteriophage SPO1-encoded type II DNA-binding protein, is essential for viral multiplication.

PubMed

Sayre, M H; Geiduschek, E P

1988-09-01

The lytic Bacillus subtilis bacteriophage SPO1 encodes an abundant, 99-amino-acid type II DNA-binding protein, transcription factor 1 (TF1). TF1 is special in this family of procaryotic chromatin-forming proteins in its preference for hydroxymethyluracil-containing DNA, such as SPO1 DNA, and in binding with high affinity to specific sites in the SPO1 chromosome. We constructed recessive null alleles of the TF1 gene and introduced them into SPO1 chromosomes. Segregation analysis with partially diploid phage heterozygous for TF1 showed that phage bearing only these null alleles was inviable. Deletion of the nine C-proximal amino acids of TF1 prohibited phage multiplication in vivo and abolished its site-specific DNA-binding activity in vitro.

STAT1:DNA sequence-dependent binding modulation by phosphorylation, protein:protein interactions and small-molecule inhibition

PubMed Central

Bonham, Andrew J.; Wenta, Nikola; Osslund, Leah M.; Prussin, Aaron J.; Vinkemeier, Uwe; Reich, Norbert O.

2013-01-01

The DNA-binding specificity and affinity of the dimeric human transcription factor (TF) STAT1, were assessed by total internal reflectance fluorescence protein-binding microarrays (TIRF-PBM) to evaluate the effects of protein phosphorylation, higher-order polymerization and small-molecule inhibition. Active, phosphorylated STAT1 showed binding preferences consistent with prior characterization, whereas unphosphorylated STAT1 showed a weak-binding preference for one-half of the GAS consensus site, consistent with recent models of STAT1 structure and function in response to phosphorylation. This altered-binding preference was further tested by use of the inhibitor LLL3, which we show to disrupt STAT1 binding in a sequence-dependent fashion. To determine if this sequence-dependence is specific to STAT1 and not a general feature of human TF biology, the TF Myc/Max was analysed and tested with the inhibitor Mycro3. Myc/Max inhibition by Mycro3 is sequence independent, suggesting that the sequence-dependent inhibition of STAT1 may be specific to this system and a useful target for future inhibitor design. PMID:23180800

Iodine-131-labeled, transferrin-capped polypyrrole nanoparticles for tumor-targeted synergistic photothermal-radioisotope therapy.

PubMed

Song, Xuejiao; Liang, Chao; Feng, Liangzhu; Yang, Kai; Liu, Zhuang

2017-08-22

Combining different therapeutic functions within single tumor-targeted nanoscale delivery systems is promising to overcome the limitations of conventional cancer therapies. Herein, transferrin that recognizes transferrin receptors up-regulated on tumor cells is pre-labeled with iodine-131 ( 131 I) and then utilized as the stabilizer in the fabrication of polypyrrole (PPy) nanoparticles. The obtained transferrin-capped PPy@Tf- 131 I nanoparticles could be used for tumor-targeted radioisotope therapy (RIT) and photothermal therapy (PTT), by employing beta-emission from 131 I and the intrinsic high near-infrared (NIR) absorbance of PPy, respectively. Owing to the transferrin-mediated tumor targeting, PPy@Tf- 131 I nanoparticles exhibit obviously enhanced in vitro cancer cell binding and in vivo tumor uptake compared to its non-targeting counterpart. The combined RIT and PTT based on PPy@Tf- 131 I nanoparticles is then conducted, achieving a remarkable synergistic therapeutic effect. This work thus demonstrates a rather simple one-step approach to fabricate tumor-targeting nanoparticles based on protein-capped conjugated polymers, promising for combination cancer therapy with great efficacy and high safety.

Mapping transcription factor interactome networks using HaloTag protein arrays.

PubMed

Yazaki, Junshi; Galli, Mary; Kim, Alice Y; Nito, Kazumasa; Aleman, Fernando; Chang, Katherine N; Carvunis, Anne-Ruxandra; Quan, Rosa; Nguyen, Hien; Song, Liang; Alvarez, José M; Huang, Shao-Shan Carol; Chen, Huaming; Ramachandran, Niroshan; Altmann, Stefan; Gutiérrez, Rodrigo A; Hill, David E; Schroeder, Julian I; Chory, Joanne; LaBaer, Joshua; Vidal, Marc; Braun, Pascal; Ecker, Joseph R

2016-07-19

Protein microarrays enable investigation of diverse biochemical properties for thousands of proteins in a single experiment, an unparalleled capacity. Using a high-density system called HaloTag nucleic acid programmable protein array (HaloTag-NAPPA), we created high-density protein arrays comprising 12,000 Arabidopsis ORFs. We used these arrays to query protein-protein interactions for a set of 38 transcription factors and transcriptional regulators (TFs) that function in diverse plant hormone regulatory pathways. The resulting transcription factor interactome network, TF-NAPPA, contains thousands of novel interactions. Validation in a benchmarked in vitro pull-down assay revealed that a random subset of TF-NAPPA validated at the same rate of 64% as a positive reference set of literature-curated interactions. Moreover, using a bimolecular fluorescence complementation (BiFC) assay, we confirmed in planta several interactions of biological interest and determined the interaction localizations for seven pairs. The application of HaloTag-NAPPA technology to plant hormone signaling pathways allowed the identification of many novel transcription factor-protein interactions and led to the development of a proteome-wide plant hormone TF interactome network.

Double-stranded RNA transcribed from vector-based oligodeoxynucleotide acts as transcription factor decoy

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

Xiao, Xiao; Gang, Yi; Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi’an 710038, Shaanxi Province

2015-02-06

Highlights: • A shRNA vector based transcription factor decoy, VB-ODN, was designed. • VB-ODN for NF-κB inhibited cell viability in HEK293 cells. • VB-ODN inhibited expression of downstream genes of target transcription factors. • VB-ODN may enhance nuclear entry ratio for its feasibility of virus production. - Abstract: In this study, we designed a short hairpin RNA vector-based oligodeoxynucleotide (VB-ODN) carrying transcription factor (TF) consensus sequence which could function as a decoy to block TF activity. Specifically, VB-ODN for Nuclear factor-κB (NF-κB) could inhibit cell viability and decrease downstream gene expression in HEK293 cells without affecting expression of NF-κB itself.more » The specific binding between VB-ODN produced double-stranded RNA and NF-κB was evidenced by electrophoretic mobility shift assay. Moreover, similar VB-ODNs designed for three other TFs also inhibit their downstream gene expression but not that of themselves. Our study provides a new design of decoy for blocking TF activity.« less

Polydopamine-based functional composite particles for tumor cell targeting and dual-mode cellular imaging.

PubMed

Zhou, Yalei; Zhou, Jie; Wang, Feng; Yang, Haifeng

2018-05-01

Particles which bear tumor cell targeting and multimode imaging capabilities are promising in tumor diagnosis and cancer therapy. A simple and versatile method to fabricate gold/polydopamine-Methylene Blue@Bovine Serum Albumin-glutaraldehyde-Transferrin composite particles (Au/PDA-MB@BSA-GA-Tf NPs) for tumor cell targeting and fluorescence (FL) / surface-enhanced Raman scattering (SERS) dual-modal imaging were reported in this work. Polydopamine (PDA) spheres played an important role in gold ion reduction, gold nanoparticle (Au NPs) binding and methylene blue (MB) adsorption, MB were employed as both fluorescence label and Raman reporter. In addition, glutaraldehyde (GA) crosslinked bovine serum albumin (BSA) in the outer layer of Au/PDA-MB nanoparticles can prevent MB from dissociation and leakage. The composite nanoparticles were further conjugated with transferrin (Tf) to target transferrin receptor (TfR)-overexpressed cancer cells. The targeting ability as well as the intracellular location of the probe was investigated through SERS mapping and fluorescence imaging. Their excellent biocompatibility was demonstrated by low cytotoxicity against breast cancer cell (4T1 cell). Copyright © 2018 Elsevier B.V. All rights reserved.

Transcription factor-based biosensors enlightened by the analyte

PubMed Central

Fernandez-López, Raul; Ruiz, Raul; de la Cruz, Fernando; Moncalián, Gabriel

2015-01-01

Whole cell biosensors (WCBs) have multiple applications for environmental monitoring, detecting a wide range of pollutants. WCBs depend critically on the sensitivity and specificity of the transcription factor (TF) used to detect the analyte. We describe the mechanism of regulation and the structural and biochemical properties of TF families that are used, or could be used, for the development of environmental WCBs. Focusing on the chemical nature of the analyte, we review TFs that respond to aromatic compounds (XylS-AraC, XylR-NtrC, and LysR), metal ions (MerR, ArsR, DtxR, Fur, and NikR) or antibiotics (TetR and MarR). Analyzing the structural domains involved in DNA recognition, we highlight the similitudes in the DNA binding domains (DBDs) of these TF families. Opposite to DBDs, the wide range of analytes detected by TFs results in a diversity of structures at the effector binding domain. The modular architecture of TFs opens the possibility of engineering TFs with hybrid DNA and effector specificities. Yet, the lack of a crisp correlation between structural domains and specific functions makes this a challenging task. PMID:26191047

Air core poloidal magnetic field system for a toroidal plasma producing device

DOEpatents

Marcus, Frederick B.

1978-01-01

A poloidal magnetics system for a plasma producing device of toroidal configuration is provided that reduces both the total volt-seconds requirement and the magnitude of the field change at the toroidal field coils. The system utilizes an air core transformer wound between the toroidal field (TF) coils and the major axis outside the TF coils. Electric current in the primary windings of this transformer is distributed and the magnetic flux returned by air core windings wrapped outside the toroidal field coils. A shield winding that is closely coupled to the plasma carries a current equal and opposite to the plasma current. This winding provides the shielding function and in addition serves in a fashion similar to a driven conducting shell to provide the equilibrium vertical field for the plasma. The shield winding is in series with a power supply and a decoupling coil located outside the TF coil at the primary winding locations. The present invention requires much less energy than the usual air core transformer and is capable of substantially shielding the toroidal field coils from poloidal field flux.

Transcription factor-based biosensors enlightened by the analyte.

PubMed

Fernandez-López, Raul; Ruiz, Raul; de la Cruz, Fernando; Moncalián, Gabriel

2015-01-01

Whole cell biosensors (WCBs) have multiple applications for environmental monitoring, detecting a wide range of pollutants. WCBs depend critically on the sensitivity and specificity of the transcription factor (TF) used to detect the analyte. We describe the mechanism of regulation and the structural and biochemical properties of TF families that are used, or could be used, for the development of environmental WCBs. Focusing on the chemical nature of the analyte, we review TFs that respond to aromatic compounds (XylS-AraC, XylR-NtrC, and LysR), metal ions (MerR, ArsR, DtxR, Fur, and NikR) or antibiotics (TetR and MarR). Analyzing the structural domains involved in DNA recognition, we highlight the similitudes in the DNA binding domains (DBDs) of these TF families. Opposite to DBDs, the wide range of analytes detected by TFs results in a diversity of structures at the effector binding domain. The modular architecture of TFs opens the possibility of engineering TFs with hybrid DNA and effector specificities. Yet, the lack of a crisp correlation between structural domains and specific functions makes this a challenging task.

Synthesizing Substituted 2-Amino-2-Chromenes Catalyzed by Tertiaryamine-Functionalized Polyacrylonitrile Fiber for Students to Investigate Multicomponent Reactions and Heterogeneous Catalysis

ERIC Educational Resources Information Center

Xie, Yujia; Liu, Xiaoxing; Tao, Minli

2016-01-01

A multistep experiment for a synthesis laboratory course that incorporates topics in organic synthesis, chemical analysis, and instrumental analysis was developed. Students prepared a tertiaryamine-functionalized polyacrylonitrile fiber (PAN[subscript T]F), and it was subsequently utilized as an immobilized catalyst in a three-component…

Finding biomarkers in non-model species: literature mining of transcription factors involved in bovine embryo development

PubMed Central

2012-01-01

Background Since processes in well-known model organisms have specific features different from those in Bos taurus, the organism under study, a good way to describe gene regulation in ruminant embryos would be a species-specific consideration of closely related species to cattle, sheep and pig. However, as highlighted by a recent report, gene dictionaries in pig are smaller than in cattle, bringing a risk to reduce the gene resources to be mined (and so for sheep dictionaries). Bioinformatics approaches that allow an integration of available information on gene function in model organisms, taking into account their specificity, are thus needed. Besides these closely related and biologically relevant species, there is indeed much more knowledge of (i) trophoblast proliferation and differentiation or (ii) embryogenesis in human and mouse species, which provides opportunities for reconstructing proliferation and/or differentiation processes in other mammalian embryos, including ruminants. The necessary knowledge can be obtained partly from (i) stem cell or cancer research to supply useful information on molecular agents or molecular interactions at work in cell proliferation and (ii) mouse embryogenesis to supply useful information on embryo differentiation. However, the total number of publications for all these topics and species is great and their manual processing would be tedious and time consuming. This is why we used text mining for automated text analysis and automated knowledge extraction. To evaluate the quality of this “mining”, we took advantage of studies that reported gene expression profiles during the elongation of bovine embryos and defined a list of transcription factors (or TF, n = 64) that we used as biological “gold standard”. When successful, the “mining” approach would identify them all, as well as novel ones. Methods To gain knowledge on molecular-genetic regulations in a non model organism, we offer an approach based on literature-mining and score arrangement of data from model organisms. This approach was applied to identify novel transcription factors during bovine blastocyst elongation, a process that is not observed in rodents and primates. As a result, searching through human and mouse corpuses, we identified numerous bovine homologs, among which 11 to 14% of transcription factors including the gold standard TF as well as novel TF potentially important to gene regulation in ruminant embryo development. The scripts of the workflow are written in Perl and available on demand. They require data input coming from all various databases for any kind of biological issue once the data has been prepared according to keywords for the studied topic and species; we can provide data sample to illustrate the use and functionality of the workflow. Results To do so, we created a workflow that allowed the pipeline processing of literature data and biological data, extracted from Web of Science (WoS) or PubMed but also from Gene Expression Omnibus (GEO), Gene Ontology (GO), Uniprot, HomoloGene, TcoF-DB and TFe (TF encyclopedia). First, the human and mouse homologs of the bovine proteins were selected, filtered by text corpora and arranged by score functions. The score functions were based on the gene name frequencies in corpora. Then, transcription factors were identified using TcoF-DB and double-checked using TFe to characterise TF groups and families. Thus, among a search space of 18,670 bovine homologs, 489 were identified as transcription factors. Among them, 243 were absent from the high-throughput data available at the time of the study. They thus stand so far for putative TF acting during bovine embryo elongation, but might be retrieved from a recent RNA sequencing dataset (Mamo et al. , 2012). Beyond the 246 TF that appeared expressed in bovine elongating tissues, we restricted our interpretation to those occurring within a list of 50 top-ranked genes. Among the transcription factors identified therein, half belonged to the gold standard (ASCL2, c-FOS, ETS2, GATA3, HAND1) and half did not (ESR1, HES1, ID2, NANOG, PHB2, TP53, STAT3). Conclusions A workflow providing search for transcription factors acting in bovine elongation was developed. The model assumed that proteins sharing the same protein domains in closely related species had the same protein functionalities, even if they were differently regulated among species or involved in somewhat different pathways. Under this assumption, we merged the information on different mammalian species from different databases (literature and biology) and proposed 489 TF as potential participants of embryo proliferation and differentiation, with (i) a recall of 95% with regard to a biological gold standard defined in 2011 and (ii) an extension of more than 3 times the gold standard of TF detected so far in elongating tissues. The working capacity of the workflow was supported by the manual expertise of the biologists on the results. The workflow can serve as a new kind of bioinformatics tool to work on fused data sources and can thus be useful in studies of a wide range of biological processes. PMID:22931563

Identification of transcription factors potential related to brown planthopper resistance in rice via microarray expression profiling

PubMed Central

2012-01-01

Background Brown planthopper (BPH), Nilaparvata lugens Stål, is one of the most destructive insect pests of rice. The molecular responses of plants to sucking insects resemble responses to pathogen infection. However, the molecular mechanism of BPH-resistance in rice remains unclear. Transcription factors (TF) are up-stream regulators of various genes that bind to specific DNA sequences, thereby controlling the transcription from DNA to mRNA. They are key regulators for transcriptional expression in biological processes, and are probably involved in the BPH-induced pathways in resistant rice varieties. Results We conducted a microarray experiment to analyze TF genes related to BPH resistance in a Sri Lankan rice cultivar, Rathu Heenati (RHT). We compared the expression profiles of TF genes in RHT with those of the susceptible rice cultivar Taichun Native 1 (TN1). We detected 2038 TF genes showing differential expression signals between the two rice varieties. Of these, 442 TF genes were probably related to BPH-induced resistance in RHT and TN1, and 229 may be related to constitutive resistance only in RHT. These genes showed a fold change (FC) of more than 2.0 (P<0.05). Among the 442 TF genes related to BPH-induced resistance, most of them were readily induced in TN1 than in RHT by BPH feeding, for instance, 154 TF genes were up-regulated in TN1, but only 31 TF genes were up-regulated in RHT at 24 hours after BPH infestation; 2–4 times more TF genes were induced in TN1 than in RHT by BPH. At an FC threshold of >10, there were 37 induced TF genes and 26 constitutive resistance TF genes. Of these, 13 were probably involved in BPH-induced resistance, and 8 in constitutive resistance to BPH in RHT. Conclusions We explored the molecular mechanism of resistance to BPH in rice by comparing expressions of TF genes between RHT and TN1. We speculate that the level of gene repression, especially for early TF genes, plays an important role in the defense response. The fundamental point of the resistance strategy is that plants protect themselves by reducing their metabolic level to inhibit feeding by BPH and prevent damage from water and nutrient loss. We have selected 21 TF genes related to BPH resistance for further analyses to understand the molecular responses to BPH feeding in rice. PMID:23228240

Identification of transcription factors potential related to brown planthopper resistance in rice via microarray expression profiling.

PubMed

Wang, Yubing; Guo, Huimin; Li, Haichao; Zhang, Hao; Miao, Xuexia

2012-12-10

Brown planthopper (BPH), Nilaparvata lugens Stål, is one of the most destructive insect pests of rice. The molecular responses of plants to sucking insects resemble responses to pathogen infection. However, the molecular mechanism of BPH-resistance in rice remains unclear. Transcription factors (TF) are up-stream regulators of various genes that bind to specific DNA sequences, thereby controlling the transcription from DNA to mRNA. They are key regulators for transcriptional expression in biological processes, and are probably involved in the BPH-induced pathways in resistant rice varieties. We conducted a microarray experiment to analyze TF genes related to BPH resistance in a Sri Lankan rice cultivar, Rathu Heenati (RHT). We compared the expression profiles of TF genes in RHT with those of the susceptible rice cultivar Taichun Native 1 (TN1). We detected 2038 TF genes showing differential expression signals between the two rice varieties. Of these, 442 TF genes were probably related to BPH-induced resistance in RHT and TN1, and 229 may be related to constitutive resistance only in RHT. These genes showed a fold change (FC) of more than 2.0 (P<0.05). Among the 442 TF genes related to BPH-induced resistance, most of them were readily induced in TN1 than in RHT by BPH feeding, for instance, 154 TF genes were up-regulated in TN1, but only 31 TF genes were up-regulated in RHT at 24 hours after BPH infestation; 2-4 times more TF genes were induced in TN1 than in RHT by BPH. At an FC threshold of >10, there were 37 induced TF genes and 26 constitutive resistance TF genes. Of these, 13 were probably involved in BPH-induced resistance, and 8 in constitutive resistance to BPH in RHT. We explored the molecular mechanism of resistance to BPH in rice by comparing expressions of TF genes between RHT and TN1. We speculate that the level of gene repression, especially for early TF genes, plays an important role in the defense response. The fundamental point of the resistance strategy is that plants protect themselves by reducing their metabolic level to inhibit feeding by BPH and prevent damage from water and nutrient loss. We have selected 21 TF genes related to BPH resistance for further analyses to understand the molecular responses to BPH feeding in rice.

Transfrontal and Transsphenoidal Approaches to Pediatric Craniopharyngioma: A National Perspective.

PubMed

Lin, Yimo; Hansen, Daniel; Sayama, Christina M; Pan, I-Wen; Lam, Sandi

2017-01-01

This study compared transsphenoidal (TS) and transfrontal (TF) approaches to craniopharyngioma utilizing a national database. The Kids' Inpatient Database (2003, 2006, and 2009) was surveyed for patients with a diagnosis of craniopharyngioma who underwent a subset of surgical interventions to compare TS and TF surgery. Demographics, hospital variables, and complications/comorbidities were analyzed with multivariate regression. 314 admissions (TS = 104, TF = 210) were identified. The mean age was 14.8 (TS) versus 9.8 (TF) years (p < 0.001). The mean number of diagnoses was 4.6 (TS) versus 6.2 (TF) (p < 0.001). Diabetes insipidus was associated with 38% (TS) and 69% (TF). Cerebrospinal fluid (CSF) leak affected 19% TS and 4% TF resections. Other complications and comorbidities included postoperative stroke (2% TS vs. 5% TF), panhypopituitarism (5 vs. 8%), death (0 vs. 1%), cranial nerve deficits (1 vs. 6%), thrombotic events (7 vs. 17%), and seizures (0 vs. 12%). 98% of patients were discharged home after a mean 6-day length of stay (LOS) after TS, whereas 90% of TF patients had a LOS of 12 days. TS cases were more likely to be privately insured (68%) and from higher income brackets (61%) than TF ones (56 and 2%, respectively) (p < 0.05). In multivariate regression models adjusting for age, sex, race, number of diagnoses, surgical approach, hospital volume, and insurance type, the TS approach was associated with an increased incidence of CSF leak (OR 10, p < 0.001). More documented diagnoses (OR 16-60, p < 0.01) and TF approach (OR 2.6, p < 0.01) were associated with an increased incidence of other complications and comorbidities. Age younger than 10 (β-coefficient 2.3, p = 0.01), more diagnoses (β-coefficient 1.2, p < 0.001), and TF approach (β- coefficient 3.0, p < 0.01) were associated with increased LOS. A higher number of diagnoses were associated with nonhome discharge destinations (β-coefficient 1.29, p < 0.001). TS surgery was associated with an increased incidence of CSF leak but shorter LOS; TF surgery was associated with an increased incidence of other complications. Patients undergoing TS surgery were more likely to have private insurance and a higher family income bracket. © 2017 S. Karger AG, Basel.

Single Mutations in the VP2 300 Loop Region of the Three-Fold Spike of the Carnivore Parvovirus Capsid Can Determine Host Range.

PubMed

Allison, Andrew B; Organtini, Lindsey J; Zhang, Sheng; Hafenstein, Susan L; Holmes, Edward C; Parrish, Colin R

2016-01-15

Sylvatic carnivores, such as raccoons, have recently been recognized as important hosts in the evolution of canine parvovirus (CPV), a pandemic pathogen of domestic dogs. Although viruses from raccoons do not efficiently bind the dog transferrin receptor (TfR) or infect dog cells, a single mutation changing an aspartic acid to a glycine at capsid (VP2) position 300 in the prototype raccoon CPV allows dog cell infection. Because VP2 position 300 exhibits extensive amino acid variation among the carnivore parvoviruses, we further investigated its role in determining host range by analyzing its diversity and evolution in nature and by creating a comprehensive set of VP2 position 300 mutants in infectious clones. Notably, some position 300 residues rendered CPV noninfectious for dog, but not cat or fox, cells. Changes of adjacent residues (residues 299 and 301) were also observed often after cell culture passage in different hosts, and some of the mutations mimicked changes seen in viruses recovered from natural infections of alternative hosts, suggesting that compensatory mutations were selected to accommodate the new residue at position 300. Analysis of the TfRs of carnivore hosts used in the experimental evolution studies demonstrated that their glycosylation patterns varied, including a glycan present only on the domestic dog TfR that dictates susceptibility to parvoviruses. Overall, there were significant differences in the abilities of viruses with alternative position 300 residues to bind TfRs and infect different carnivore hosts, demonstrating that the process of infection is highly host dependent and that VP2 position 300 is a key determinant of host range. Although the emergence and pandemic spread of canine parvovirus (CPV) are well documented, the carnivore hosts and evolutionary pathways involved in its emergence remain enigmatic. We recently demonstrated that a region in the capsid structure of CPV, centered around VP2 position 300, varies after transfer to alternative carnivore hosts and may allow infection of previously nonsusceptible hosts in vitro. Here we show that VP2 position 300 is the most variable residue in the parvovirus capsid in nature, suggesting that it is a critical determinant in the cross-species transfer of viruses between different carnivores due to its interactions with the transferrin receptor to mediate infection. To this end, we demonstrated that there are substantial differences in receptor binding and infectivity of various VP2 position 300 mutants for different carnivore species and that single mutations in this region can influence whether a host is susceptible or refractory to virus infection. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Single Mutations in the VP2 300 Loop Region of the Three-Fold Spike of the Carnivore Parvovirus Capsid Can Determine Host Range

PubMed Central

Organtini, Lindsey J.; Zhang, Sheng; Hafenstein, Susan L.; Holmes, Edward C.

2015-01-01

ABSTRACT Sylvatic carnivores, such as raccoons, have recently been recognized as important hosts in the evolution of canine parvovirus (CPV), a pandemic pathogen of domestic dogs. Although viruses from raccoons do not efficiently bind the dog transferrin receptor (TfR) or infect dog cells, a single mutation changing an aspartic acid to a glycine at capsid (VP2) position 300 in the prototype raccoon CPV allows dog cell infection. Because VP2 position 300 exhibits extensive amino acid variation among the carnivore parvoviruses, we further investigated its role in determining host range by analyzing its diversity and evolution in nature and by creating a comprehensive set of VP2 position 300 mutants in infectious clones. Notably, some position 300 residues rendered CPV noninfectious for dog, but not cat or fox, cells. Changes of adjacent residues (residues 299 and 301) were also observed often after cell culture passage in different hosts, and some of the mutations mimicked changes seen in viruses recovered from natural infections of alternative hosts, suggesting that compensatory mutations were selected to accommodate the new residue at position 300. Analysis of the TfRs of carnivore hosts used in the experimental evolution studies demonstrated that their glycosylation patterns varied, including a glycan present only on the domestic dog TfR that dictates susceptibility to parvoviruses. Overall, there were significant differences in the abilities of viruses with alternative position 300 residues to bind TfRs and infect different carnivore hosts, demonstrating that the process of infection is highly host dependent and that VP2 position 300 is a key determinant of host range. IMPORTANCE Although the emergence and pandemic spread of canine parvovirus (CPV) are well documented, the carnivore hosts and evolutionary pathways involved in its emergence remain enigmatic. We recently demonstrated that a region in the capsid structure of CPV, centered around VP2 position 300, varies after transfer to alternative carnivore hosts and may allow infection of previously nonsusceptible hosts in vitro. Here we show that VP2 position 300 is the most variable residue in the parvovirus capsid in nature, suggesting that it is a critical determinant in the cross-species transfer of viruses between different carnivores due to its interactions with the transferrin receptor to mediate infection. To this end, we demonstrated that there are substantial differences in receptor binding and infectivity of various VP2 position 300 mutants for different carnivore species and that single mutations in this region can influence whether a host is susceptible or refractory to virus infection. PMID:26512077

Tissue factor and Toll-like receptor (TLR)4 in hyperglycaemia-hyperinsulinaemia. Effects in healthy subjects, and type 1 and type 2 diabetes mellitus.

PubMed

Singh, Anamika; Boden, Guenther; Rao, A Koneti

2015-04-01

Diabetes mellitus (DM) patients have an increased incidence of cardiovascular events. Blood tissue factor-procoagulant activity (TF-PCA), the initiating mechanism for blood coagulation, is elevated in DM. We have shown that hyperglycaemia (HG), hyperinsulinaemia (HI) and combined HG+HI (induced using 24-hour infusion clamps) increases TF-PCA in healthy and type 2 DM (T2DM) subjects, but not in type 1 DM (T1DM) subjects. The mechanisms for this are unknown. DM patients have elevated plasma lipopolysaccharide (LPS), a toll-like receptor (TLR) 4 ligand. We postulated that TLR4 plays a role in modulating TF levels. We studied the effect of HG+HI on TLR4 and TF-PCA in vivo during 24-hour HG+HI infusion clamps in healthy subjects, and T1DM and T2DM subjects, and in vitro in blood. In vivo, in healthy subjects, 24-hour HG + HI infusion increased TLR4 six-fold, which correlated with TF-PCA (r= 0.91, p<0.0001). T2DM patients showed smaller increases in both. In T1DM subjects, TLR4 declined (50%, p<0.05) and correlated with TF-PCA (r=0.55; p<0.05). In vitro, HG (200 mg/dl added glucose) and HI (1-100 nM added insulin) increased TF-PCA in healthy subjects (~2-fold, 2-4 hours). Insulin inhibited by ~30% LPS-induced increase in TF-PCA and high glucose reversed it. TLR4 levels paralleled TF-PCA (r=0.71, p<0.0001); HG and HI increased TLR4 and insulin inhibited LPS-induced TLR4 increase. This is first evidence that even in healthy subjects, HG of short duration increases TLR4 and TF-PCA, key players in inflammation and thrombosis. TLR4-TF interplay is strikingly different in non-diabetic, T1DM and T2DM subjects.

Disruption of sex-hormone levels and steroidogenic-related gene expression on Mongolia Racerunner (Eremias argus) after exposure to triadimefon and its enantiomers.

PubMed

Li, Jitong; Chang, Jing; Li, Wei; Guo, Baoyuan; Li, Jianzhong; Wang, Huili

2017-03-01

Triadimefon (TF) is a widely used chiral fungicide with one chiral centre and two enantiomers (TF 1 and TF 2 ). However, little is reported about the ecological toxicity of reptiles on an enantioselective level. TF is a potential endocrine disruptor that may interfere with sex steroid hormones, such as testosterone (T) and 17beta-estradiol (E 2 ). In our study, the lizards Mongolia Racerunner (Eremias argus) were orally exposed to TF and its enantiomers for 21 days. Plasma sex steroid hormones and steroidogenic-related genes, including 17-beta-hydroxysteroid (hsd17β), cytochrome P450 enzymes (cyp19 and cyp17), and steroid hormone receptors (erα and Ar) were evaluated. After exposure, the plasma testosterone level in the 100 mg/kg bw group was elevated, while the oestradiol level was reduced. This phenomenon may be caused by the transformation of cyp19, which may inhibit the conversion of testosterone to oestradiol and affect sexual behaviour. In addition, the two enantiomers have different effects on hormone levels, which testified to the previously reported biotoxic dissimilarity between TF 1 and TF 2 in organisms. Furthermore, the cyp19 mRNA level in liver and gonad of the TF 2 and TF group (100 mg/kg bw ) were significantly down-regulated, while the cyp17 and hsd17β mRNA levels were up-regulated. The expression of erα and Ar mRNA levels were up-regulated in males but not in females, which may indicate that TF has sex differences on these two genes. As seen from the above results, TF and its enantiomers may have endocrine-disrupting effects on lizards (E. argus) by acting sensitively on sex steroid hormones and steroidogenic-related genes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy

PubMed Central

Cheng, Qiong; Kazemian, Majid; Pham, Hannah; Blatti, Charles; Celniker, Susan E.; Wolfe, Scot A.; Brodsky, Michael H.; Sinha, Saurabh

2013-01-01

ChIP-based genome-wide assays of transcription factor (TF) occupancy have emerged as a powerful, high-throughput method to understand transcriptional regulation, especially on a global scale. This has led to great interest in the underlying biochemical mechanisms that direct TF-DNA binding, with the ultimate goal of computationally predicting a TF's occupancy profile in any cellular condition. In this study, we examined the influence of various potential determinants of TF-DNA binding on a much larger scale than previously undertaken. We used a thermodynamics-based model of TF-DNA binding, called “STAP,” to analyze 45 TF-ChIP data sets from Drosophila embryonic development. We built a cross-validation framework that compares a baseline model, based on the ChIP'ed (“primary”) TF's motif, to more complex models where binding by secondary TFs is hypothesized to influence the primary TF's occupancy. Candidates interacting TFs were chosen based on RNA-SEQ expression data from the time point of the ChIP experiment. We found widespread evidence of both cooperative and antagonistic effects by secondary TFs, and explicitly quantified these effects. We were able to identify multiple classes of interactions, including (1) long-range interactions between primary and secondary motifs (separated by ≤150 bp), suggestive of indirect effects such as chromatin remodeling, (2) short-range interactions with specific inter-site spacing biases, suggestive of direct physical interactions, and (3) overlapping binding sites suggesting competitive binding. Furthermore, by factoring out the previously reported strong correlation between TF occupancy and DNA accessibility, we were able to categorize the effects into those that are likely to be mediated by the secondary TF's effect on local accessibility and those that utilize accessibility-independent mechanisms. Finally, we conducted in vitro pull-down assays to test model-based predictions of short-range cooperative interactions, and found that seven of the eight TF pairs tested physically interact and that some of these interactions mediate cooperative binding to DNA. PMID:23935523

Tissue Factor and Toll Like Receptor (TLR)4 in Hyperglycemia-Hyperinsulinemia: Effects in Healthy Subjects, and Type 1 and Type 2 Diabetes Mellitus

PubMed Central

Singh, Anamika; Boden, Guenther; Rao, A. Koneti

2015-01-01

SUMMARY Background Diabetes mellitus (DM) patients have increased cardiovascular events. Blood tissue factor-procoagulant activity (TF-PCA), the initiating mechanism for blood coagulation, is elevated in DM. We have shown that hyperglycemia (HG), hyperinsulinemia (HI) and combined HG+HI (induced using 24 hr infusion clamps) increases TF-PCA in healthy and T2DM subjects, but not in T1DM subjects. The mechanisms for this are unknown. DM patients have elevated plasma lipopolysaccharide (LPS), a toll-like receptor (TLR) 4 ligand. We postulated that TLR4 plays a role in modulating TF levels. Objectives and Methods We studied the effect of HG+HI on TLR4 and TF-PCA in vivo during 24 hr HG+HI infusion clamps in healthy subjects, and T1DM and T2DM subjects, and in vitro in blood. Results In vivo, in healthy subjects, 24 hr HG + HI infusion increased TLR4 6-fold, which correlated with TF-PCA (r= 0.91, p<0.0001). T2DM patients showed smaller increases in both. In T1DM subjects, TLR4 declined (50%, p<0.05) and correlated with TF-PCA (r=0.55; p<0.05). In vitro, HG (200 mg/dl added glucose) and HI (1-100 nM added insulin) increased TF-PCA in healthy subjects (~2-fold, 2-4 hr). Insulin inhibited by ~30% LPS-induced increase in TF-PCA and high glucose reversed it. TLR4 levels paralleled TF-PCA (r=0.71, p<0.0001); HG and HI increased TLR4 and insulin inhibited LPS-induced TLR4 increase. Conclusions This is first evidence that even in healthy subjects, HG of short duration increases TLR4 and TF-PCA, key players in inflammation and thrombosis. TLR4-TF interplay is strikingly different in non-diabetic, T1DM and T2DM subjects. PMID:25653143

Twenty-four hour intraocular pressure monitoring with the SENSIMED Triggerfish contact lens: effect of body posture during sleep.

PubMed

Beltran-Agulló, Laura; Buys, Yvonne M; Jahan, Farzana; Shapiro, Colin M; Flanagan, John G; Cheng, Jason; Trope, Graham E

2017-10-01

To determine the difference in relative intraocular pressure (IOP) measured by the SENSIMED Triggerfish (TF) contact lens in flat compared with 30° head-up sleeping positions in patients with progressive primary open-angle glaucoma or normotensive glaucoma, based on recent or recurrent disc haemorrhage. Prospective, randomised, cross-over, open-label comparative study. IOP was monitored for 24 hours using TF on two separate sessions. Patients were randomly assigned to sleep flat one night and 30° head-up the other. Outputs in arbitrary units were obtained. Sleep and wake periods were defined as 22:00-6:00 and 8:00-22:00, respectively. Mean TF values during sleep and wake periods and wake-sleep and sleep-wake slopes were calculated for each session. TF output signals were compared between positions. Twelve subjects completed the study. Significant mean positive slopes were noted during the sleep period for both positions (p<0.01). No significant differences in the TF mean values were observed between positions (p=0.51). Six (54%) subjects had mean TF values significantly higher during the flat supine session, while four (36%) subjects had higher values during the head-up session. A significant increase in Goldmann IOP (p=0.001) and TF (p=0.02) measurements were observed after 24 hours of TF wear ('drift phenomenon'). Sleep position affects IOP as measured by TF in some patients with progressive glaucoma. The upward drift in TF output detected in >50% of the subjects requires further investigation to establish whether the increased output values over time are an artefact induced by the TF or a real change in IOP. NCT01351779. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Tissue Factor Coagulant Activity is Regulated by the Plasma Membrane Microenvironment.

PubMed

Yu, Yuanjie; Böing, Anita N; Hau, Chi M; Hajji, Najat; Ruf, Wolfram; Sturk, Auguste; Nieuwland, Rienk

2018-06-01

 Tissue factor (TF) can be present in a non-coagulant and coagulant form. Whether the coagulant activity is affected by the plasma membrane microenvironment is unexplored.  This article studies the presence and coagulant activity of human TF in plasma membrane micro-domains.  Plasma membranes were isolated from human MIA PaCa2 cells, MDA-MB-231 cells and human vascular smooth muscle cells by Percoll gradient ultracentrifugation after cell disruption. Plasma membranes were fractionated by OptiPrep gradient ultracentrifugation, and the presence of TF, flotillin, caveolin, clathrin, protein disulphide isomerase (PDI), TF pathway inhibitor (TFPI) and phosphatidylserine (PS) were determined.  Plasma membranes contain two detergent-resistant membrane (DRM) compartments differing in density and biochemical composition. High-density DRMs (DRM-H) have a density ( ρ ) of 1.15 to 1.20 g/mL and contain clathrin, whereas low-density DRMs (DRM-L) have a density between 1.09 and 1.13 g/mL and do not contain clathrin. Both DRMs contain TF, flotillin and caveolin. PDI is detectable in DRM-H, TFPI is not detectable in either DMR-H or DRM-L and PS is detectable in DRM-L. The DRM-H-associated TF (> 95% of the TF antigen) lacks detectable coagulant activity, whereas the DRM-L-associated TF triggers coagulation. This coagulant activity is inhibited by lactadherin and thus PS-dependent, but seemed insensitive to 16F16, an inhibitor of PDI.  Non-coagulant and coagulant TF are present within different types of DRMs in the plasma membrane, and the composition of these DRMs may affect the TF coagulant activity. Schattauer GmbH Stuttgart.

Role of monocyte-lineage cells in prostate cancer cell invasion and tissue factor expression.

PubMed

Lindholm, Paul F; Lu, Yi; Adley, Brian P; Vladislav, Tudor; Jovanovic, Borko; Sivapurapu, Neela; Yang, Ximing J; Kajdacsy-Balla, André

2010-11-01

Tissue factor (TF) is a cell surface glycoprotein intricately related to blood coagulation and inflammation. This study was performed to investigate the role of monocyte-lineage cells in prostate cancer cell TF expression and cell invasion. Prostate cancer cell invasion was tested with and without added peripheral blood monocytes or human monocyte-lineage cell lines. TF neutralizing antibodies were used to determine the TF requirement for prostate cancer cell invasion activity. Immunohistochemistry was performed to identify prostate tissue CD68 positive monocyte-derived cells and prostate epithelial TF expression. Co-culture of PC-3, DU145, and LNCaP cells with isolated human monocytes significantly stimulated prostate cancer cell invasion activity. TF expression was greater in highly invasive prostate cancer cells and was induced in PC-3, DU145, and LNCaP cells by co-culture with U-937 cells, but not with THP-1 cells. TF neutralizing antibodies inhibited PC-3 cell invasion in co-cultures with monocyte-lineage U-937 or THP-1 cells. Prostate cancer tissues contained more CD68 positive cells in the stroma and epithelium (145 ± 53/mm(2)) than benign prostate (108 ± 31/mm(2)). Samples from advanced stage prostate cancer tended to contain more CD68 positive cells when compared with lower stage lesions. Prostatic adenocarcinoma demonstrated significantly increased TF expression compared with benign prostatic epithelium. This study shows that co-culture with monocyte-lineage cells induced prostate cancer cell invasion activity. PC-3 invasion and TF expression was induced in co-culture with U-937 cells and partially inhibited with TF neutralizing antibodies.

The role of serum transferrin receptor in the diagnosis of iron deficiency.

PubMed

Remacha, A F; Sarda, M P; Parellada, M; Ubeda, J; Manteiga, R

1998-11-01

Iron deficiency anemia (IDA) is often associated with inflammatory disorders. The most conventional parameters of iron metabolism are therefore affected, making the evaluation of iron status difficult. Serum transferrin receptor (sTfR) levels are raised in iron deficiency but are not influenced by inflammatory changes. The aim of this study was to investigate the role of sTfR in differentiating IDA with inflammatory features. A diagnostic study of sTfR measured by immunoassay was carried out in IDA and anemia of chronic disorders (ACD). The cut-off points of sTfR and the ratio of sTfR/serum ferritin, which were obtained after comparing IDA and ACD, were applied to a group of 64 patients with mixed iron patterns (MIX) (16 with ACD and 48 with IDA). The best cut-off point of sTfR between IDA and ACD was 4.7 mg/L. Applying this cut-off to the MIX group, an efficiency of 87% was obtained (sensitivity 92% and specificity 81%). This level of sTfR correctly classified 53 out of 64 cases of the MIX group (83%). Using the ratio of sTfRx 100/serum ferritin, the best cut-off point was 8 (efficiency 100%), which correctly classified 62 out of 64 cases of the MIX group (97%). This study demonstrates that sTfR in conjunction with other iron parameters is very useful in iron deficiency evaluation, especially in hospital practice. Iron treatment should be considered in patients with mixed patterns of iron status, in which the diagnosis of IDA versus ACD is difficult, when the levels of sTfR exceed the cut-off point.

A single-nucleotide polymorphism in transferrin is associated with soluble transferrin receptor in Chinese adolescents.

PubMed

Piao, Wei; Wang, Li; Zhang, Ting; Wang, Zhen; Shangguan, Shaofang; Sun, Jing; Huo, Junsheng

2017-01-01

Associations between genetic variants in the hepcidin regulation pathway and iron status have been reported in previous studies. Most of these studies were conducted in populations of European descent and relatively few studies have been conducted in Chinese populations. In this study, we evaluated associations between single-nucleotide polymorphisms (SNPs) in the hepcidin regulation pathway, serum ferritin (SF) and soluble transferrin receptor (sTfR) in Chinese adolescents. In total, 692 students from rural boarding schools were selected from six cities in China. The participants were divided into case and control groups according to criteria for SF and sTfR. Furthermore, 33 SNPs in TMPRSS6, TF, TFR2, BMP2, BMP4, HJV, CYBRD1, HFE, IL6, PCSK7, HAMP, KIAA1468, and SRPRB were selected. Associations between the genetic variants and SF or sTfR were detected. For SF, rs4820268 in TMPRSS6 was associated with an SF <25 ng/mL status. Carriers of the G/G genotype of rs4820268 exhibited significantly lower SF levels than A allele carriers did (p=0.047). For sTfR, rs1880669 in TF, rs4901474 in BMP4, and rs7536827 in HJV were significantly associated with an sTfR >=4.4 mg/L status. However, in general linear model analysis, after adjustment for age, sex, and location, only rs1880669 exhibited a stable association with higher sTfR levels (p=0.032). We found rs4820268, in TMPRSS6 that was associated with a low SF level, as previously reported, and a new association between 1880669 in TF and sTfR.

Transferrin receptor 1 upregulation in primary tumor and downregulation in benign kidney is associated with progression and mortality in renal cell carcinoma patients

PubMed Central

Greene, Christopher J.; Attwood, Kristopher; Sharma, Nitika J.; Gross, Kenneth W.; Smith, Gary J.; Xu, Bo; Kauffman, Eric C.

2017-01-01

The central dysregulated pathway of clear cell (cc) renal cell carcinoma (RCC), the von Hippel Lindau/hypoxia inducible factor-α axis, is a key regulator of intracellular iron levels, however the role of iron uptake in human RCC tumorigenesis and progression remains unknown. We conducted a thorough, large-scale investigation of the expression and prognostic significance of the primary iron uptake protein, transferrin receptor 1 (TfR1/CD71/TFRC), in RCC patients. TfR1 immunohistochemistry was performed in over 1500 cores from 574 renal cell tumor patient tissues (primary tumors, matched benign kidneys, metastases) and non-neoplastic tissues from 36 different body sites. TfR1 levels in RCC tumors, particularly ccRCC, were significantly associated with adverse clinical prognostic features (anemia, lower body mass index, smoking), worse tumor pathology (size, stage, grade, multifocality, sarcomatoid dedifferentiation) and worse survival outcomes, including after adjustments for tumor pathology. Highest TfR1 tissue levels in the non-gravid body were detected in benign renal tubule epithelium. Opposite to TfR1 changes in the primary tumor, TfR1 levels in benign kidney dropped during tumor progression and were inversely associated with worse survival outcomes, independent of tumor pathology. Quantitative measurement of TfR1 subcellular localization in cell lines demonstrated mixed cytoplasmic and membranous expression with increased TfR1 in clusters in ccRCC versus benign renal cell lines. Results of this study support an important role for TfR1 in RCC progression and identify TfR1 as a novel RCC biomarker and therapeutic target. PMID:29291011

Overexpression of OsTF1L, a rice HD-Zip transcription factor, promotes lignin biosynthesis and stomatal closure that improves drought tolerance.

PubMed

Bang, Seung Woon; Lee, Dong-Keun; Jung, Harin; Chung, Pil Joong; Kim, Youn Shic; Choi, Yang Do; Suh, Joo-Won; Kim, Ju-Kon

2018-05-21

Drought stress seriously impacts on plant development and productivity. Improvement of drought tolerance without yield penalty is a great challenge in crop biotechnology. Here, we report that the rice (Oryza sativa) homeodomain-leucine zipper transcription factor gene, OsTF1L (Oryza sativa transcription factor 1-like), is a key regulator of drought tolerance mechanisms. Overexpression of the OsTF1L in rice significantly increased drought tolerance at the vegetative stages of growth and promoted both effective photosynthesis and a reduction in the water loss rate under drought conditions. Importantly, the OsTF1L overexpressing plants showed a higher drought tolerance at the reproductive stage of growth with a higher grain yield than non-transgenic controls under field-drought conditions. Genome-wide analysis of OsTF1L overexpression plants revealed up-regulation of drought-inducible, stomatal movement and lignin biosynthetic genes. Overexpression of OsTF1L promoted accumulation of lignin in shoots, whereas the RNAi lines showed opposite patterns of lignin accumulation. OsTF1L is mainly expressed in outer cell layers including the epidermis, and the vasculature of the shoots, which coincides with areas of lignification. In addition, OsTF1L overexpression enhances stomatal closure under drought conditions resulted in drought tolerance. More importantly, OsTF1L directly bound to the promoters of lignin biosynthesis and drought-related genes involving poxN/PRX38, Nodulin protein, DHHC4, CASPL5B1 and AAA-type ATPase. Collectively, our results provide a new insight into the role of OsTF1L in enhancing drought tolerance through lignin biosynthesis and stomatal closure in rice. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

The impact of theaflavins on systemic-and microcirculation alterations: The murine and randomized feasibility trials.

PubMed

Saito, Akiko; Nakazato, Risa; Suhara, Yoshitomo; Shibata, Masahiro; Fukui, Toshiki; Ishii, Takeshi; Asanuma, Toshimichi; Mochizuki, Kazuo; Nakayama, Tsutomu; Osakabe, Naomi

2016-06-01

Theaflavins are polyphenols found in black tea; their physiological activities were not well investigated. The present study in rats evaluated the influence of theaflavins on circulation. In addition, an intervention pilot study examined the influence of a theaflavin drink on postprandial hemodynamic change. In an animal study, a single oral dose of theaflavin rich fraction (TF, 10mg/kg) caused transient increase in mean blood pressure (MBP) and heart rate (HR). TF also elevated cremastric blood flow significantly, and the magnitude of this effect was in this order: theaflavin 3'-O-gallate (TF2B) >theaflavin-3-O-gallate (TF2A) >theaflavin (TF1)=theaflavin-3, 3'-di-O-gallate (TF3). In addition, these hemodynamic alterations in mammals totally disappeared when pretreated with carvedilol as an adrenaline blocker. We also treated 10-mg/kg/day TF to the rats for 2 weeks. At the end of the ingestion period, MBP was reduced significantly, and aortic eNOS level was elevated by the repeated ingestion of TF compared with distilled water. In the intervention trial, blood pressure of the volunteers was increased significantly 2 and 4h after ingestion of the TF drink (45mg/drink) compared with before treatment. A significant difference was observed in FMD between the placebo and theaflavin groups 4h after ingestion. These results suggested that theaflavin has potent activity to alter hemodynamics in both murine and healthy subjects. Further studies is needed to elucidate the details; however, the results of animal study suggested that the possible involvement of sympathetic nervous system in the hemodynamic changes caused by TF. Copyright © 2016 Elsevier Inc. All rights reserved.

Inversion of substrate stereoselectivity of horse liver alcohol dehydrogenase by substitutions of Ser-48 and Phe-93.

PubMed

Kim, Keehyuk; Plapp, Bryce V

2017-10-01

The substrate specificities of alcohol dehydrogenases (ADH) are of continuing interest for understanding the physiological functions of these enzymes. Ser-48 and Phe-93 have been identified as important residues in the substrate binding sites of ADHs, but more comprehensive structural and kinetic studies are required. The S48T substitution in horse ADH1E has small effects on kinetic constants and catalytic efficiency (V/K m ) with ethanol, but decreases activity with benzyl alcohol and affinity for 2,2,2-trifluoroethanol (TFE) and 2,3,4,5,6-pentafluorobenzyl alcohol (PFB). Nevertheless, atomic resolution crystal structures of the S48T enzyme complexed with NAD + and TFE or PFB are very similar to the structures for the wild-type enzyme. (The S48A substitution greatly diminishes catalytic activity.) The F93A substitution significantly decreases catalytic efficiency (V/K m ) for ethanol and acetaldehyde while increasing activity for larger secondary alcohols and the enantioselectivity for the R-isomer relative to the S-isomer of 2-alcohols. The doubly substituted S48T/F93A enzyme has kinetic constants for primary and secondary alcohols similar to those for the F93A enzyme, but the effect of the S48T substitution is to decrease V/K m for (S)-2-alcohols without changing V/K m for (R)-2-alcohols. Thus, the S48T/F93A substitutions invert the enantioselectivity for alcohol oxidation, increasing the R/S ratio by 10, 590, and 200-fold for 2-butanol, 2-octanol, and sec-phenethyl alcohol, respectively. Transient kinetic studies and simulations of the ordered bi bi mechanism for the oxidation of the 2-butanols by the S48T/F93A ADH show that the rate of hydride transfer is increased about 7-fold for both isomers (relative to wild-type enzyme) and that the inversion of enantioselectivity is due to more productive binding for (R)-2-butanol than for (S)-2-butanol in the ternary complex. Molecular modeling suggests that both of the sec-phenethyl alcohols could bind to the enzyme and that dynamics must affect the rates of catalysis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

WISE TF: A MID-INFRARED, 3.4 {mu}m EXTENSION OF THE TULLY-FISHER RELATION USING WISE PHOTOMETRY

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

Lagattuta, David J.; Mould, Jeremy R.; Staveley-Smith, Lister

2013-07-10

We present a mid-infrared Tully-Fisher (TF) relation using photometry from the 3.4 {mu}m W1 band of the Wide-field Infrared Survey Explorer (WISE) satellite. The WISE TF relation is formed from 568 galaxies taken from the all-sky 2MASS Tully-Fisher (2MTF) galaxy catalog, spanning a range of environments including field, group, and cluster galaxies. This constitutes the largest mid-infrared TF relation constructed to date. After applying a number of corrections to galaxy magnitudes and line widths, we measure a master TF relation given by M{sub corr} = -22.24 - 10.05[log (W{sub corr}) - 2.5], with an average dispersion of {sigma}{sub WISE} =more » 0.686 mag. There is some tension between WISE TF and a preliminary 3.6 {mu}m relation, which has a shallower slope and almost no intrinsic dispersion. However, our results agree well with a more recent relation constructed from a large sample of cluster galaxies. We additionally compare WISE TF to the near-infrared 2MTF template relations, finding a good agreement between the TF parameters and total dispersions of WISE TF and the 2MTF K-band template. This fact, coupled with typical galaxy colors of (K - W1) {approx} 0, suggests that these two bands are tracing similar stellar populations, including the older, centrally-located stars in the galactic bulge which can (for galaxies with a prominent bulge) dominate the light profile.« less

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.

PubMed

Schmidt, Florian; Gasparoni, Nina; Gasparoni, Gilles; Gianmoena, Kathrin; Cadenas, Cristina; Polansky, Julia K; Ebert, Peter; Nordström, Karl; Barann, Matthias; Sinha, Anupam; Fröhler, Sebastian; Xiong, Jieyi; Dehghani Amirabad, Azim; Behjati Ardakani, Fatemeh; Hutter, Barbara; Zipprich, Gideon; Felder, Bärbel; Eils, Jürgen; Brors, Benedikt; Chen, Wei; Hengstler, Jan G; Hamann, Alf; Lengauer, Thomas; Rosenstiel, Philip; Walter, Jörn; Schulz, Marcel H

2017-01-09

The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Molecular dynamics shows that ion pairing and counterion anchoring control the properties of triflate micelles: a comparison with triflate at the air/water interface.

PubMed

Lima, Filipe S; Chaimovich, Hernan; Cuccovia, Iolanda M; Horinek, Dominik

2014-02-11

Micellar properties of dodecyltrimethylammonium triflate (DTA-triflate, DTATf) are very different from those of DTA-bromide (DTAB). DTATf aggregates show high aggregation numbers (Nagg), low degree of counterion dissociation (α), disk-like shape, high packing, ordering, and low hydration. These micellar properties and the low surface tension of NaTf aqueous solutions point to a high affinity of Tf(-) to the micellar and air/water interfaces. Although the micellar properties of DTATf are well defined, the source of the Tf(-) effect upon the DTA aggregates is unclear. Molecular dynamics (MD) simulations of Tf(-) (and Br(-)) at the air/water interface and as counterion of a DTA aggregate were performed to clarify the nature of Tf(-) preferences for these interfaces. The effect of NaTf or NaBr on surface tension calculated from MD simulations agreed with the reported experimental values. From the MD simulations a high affinity of Tf(-) toward the interface, which occurred in a specific orientation, was calculated. The micellar properties calculated from the MD simulations for DTATf and DTAB were consistent with experimental data: in MD simulations, the DTATf aggregate was more ordered, packed, and dehydrated than the DTAB aggregate. The Tf(-)/alkyltrimethylammonium interaction energies, calculated from the MD simulations, suggested ion pair formation at the micellar interface, stabilized by the preferential orientation of the adsorbed Tf(-) at the micellar interface.

Photoaffinity labeling of the TF1-ATPase from the thermophilic bacterium PS3 with 3'-O-(4-benzoyl)benzoyl ADP.

PubMed

Bar-Zvi, D; Yoshida, M; Shavit, N

1985-05-31

3'-O-(4-Benzoyl)benzoyl ADP (BzADP) was used as a photoaffinity label for covalent binding of adenine nucleotide analogs to the nucleotide binding site(s) of the thermophilic bacterium PS3 ATPase (TF1). As with the CF1-ATPase (Bar-Zvi, D. and Shavit, N. (1984) Biochim. Biophys. Acta 765, 340-356) noncovalently bound BzADP is a reversible inhibitor of the TF1-ATPase. BzADP changes the kinetics of ATP hydrolysis from noncooperative to cooperative in the same way as ADP does, but, in contrast to the effect on the CF1-ATPase, it has no effect on the Vmax. In the absence of Mg2+ 1 mol BzADP binds noncovalently to TF1, while with Mg2+ 3 mol are bound. Photoactivation of BzADP results in the covalent binding of the analog to the nucleotide binding site(s) on TF1 and correlates with the inactivation of the ATPase. Complete inactivation of the TF1-ATPase occurs after covalent binding of 2 mol BzADP/mol TF1. Photoinactivation of TF1 by BzADP is prevented if excess of either ADP or ATP is present during irradiation. Analysis by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate of the Bz[3H]ADP-labeled TF1-ATPase shows that all the radioactivity is incorporated into the beta subunit.

Enhanced washout of 99mTc-tetrofosmin in hypertrophic cardiomyopathy: quantitative comparisons with regional 123I-BMIPP uptake and wall thickness determined by MRI.

PubMed

Thet-Thet-Lwin; Takeda, Tohoru; Wu, Jin; Fumikura, Yuko; Iida, Keiji; Kawano, Satoru; Yamaguchi, Iwao; Itai, Yuji

2003-07-01

The diagnostic value of technetium-99m tetrofosmin (TF) washout in hypertrophic cardiomyopathy (HCM) was examined by investigating its relation to the metabolic abnormality depicted by iodine-123 beta-methyl- p-iodophenylpentadecanoic acid (BMIPP) uptake and the left ventricular (LV) myocardial wall thickness as measured by magnetic resonance imaging (MRI). TF washout was evaluated in 31 patients with HCM and 23 normal control subjects using 30-min (early) and 3-h (delayed) TF single-photon emission tomography images. The LV myocardial wall was divided into 19 segments and the percentage TF washout, regional BMIPP uptake and LV wall thickness were measured in each segment. Mean TF washout in the patients with HCM was significantly faster than that in normal control subjects (23.7+/-5.7 vs 13.4+/-4.1, P<0.0001). In the patients with HCM, TF washout showed an excellent correlation with MRI wall thickness ( r=0.82, P<0.0001) and a good inverse correlation with regional BMIPP uptake ( r=-0.72, P<0.0001). In addition, a good linear correlation was observed between TF uptake and MRI wall thickness in the 19 regional segments. In conclusion, the degree of TF washout corresponds well with the severity of myocardial wall thickness and the degree of metabolic abnormality in patients with HCM. These results suggest that enhanced TF washout might provide additional clinical information regarding metabolic alterations in HCM.

Autologous Chondrocyte Implantation for Bipolar Chondral Lesions in the Tibiofemoral Compartment.

PubMed

Ogura, Takahiro; Bryant, Tim; Mosier, Brian A; Minas, Tom

2018-05-01

Treating bipolar chondral lesions in the tibiofemoral (TF) compartment with cartilage repair procedures is challenging, and a suitable treatment remains unclear. To evaluate clinical outcomes after autologous chondrocyte implantation (ACI) for the treatment of bipolar chondral lesions in the TF compartment. Case series; Level of evidence, 4. We evaluated 57 patients who underwent ACI for the treatment of symptomatic bipolar chondral lesions in the TF compartment by a single surgeon between October 1995 and June 2014. One patient did not return for follow-up. Thus, 56 patients (58 knees) were included with a minimum of 2 years' follow-up. A mean of 3.1 lesions per knee were treated, representing a mean total surface area of 16.1 cm 2 (range, 3.2-44.5 cm 2 ) per knee. Bipolar lesions were present in the medial compartment (32 knees) and in the lateral compartment (26 knees). Patients were evaluated with the modified Cincinnati Knee Rating Scale, visual analog scale for pain, Western Ontario and McMaster Universities Osteoarthritis Index, and Short Form-36. Patients also answered questions regarding self-rated knee function and satisfaction with the procedure. Standard radiographs were evaluated with the Kellgren-Lawrence grading system. The survival rate was 80% at 5 years and 76% at 10 years. A significantly better survival rate was found in patients with the use of a collagen membrane than periosteum (97% vs 61% at 5 years, respectively; P = .0014). Of 46 knees with retained grafts, all functional scores significantly improved postoperatively, with a very high satisfaction rate (91%) at a mean of 8.3 ± 5.1 years (range, 2-20 years) after ACI. At last follow-up, 24 of 46 successful knees were radiographically assessed (mean, 5.5 ± 4.0 years [range, 2.0-18.7 years]) and showed no significant osteoarthritis progression ( P = .3173). Outcomes for 12 patients were considered as failures at a mean of 4.1 years. Of these, 9 patients were converted to partial or total knee arthroplasty at a mean of 4.4 years. Two patients underwent revision ACI at 5 and 17 months. The other 1 patient did not require revision surgery. Our study showed that ACI for the treatment of bipolar chondral lesions in the TF compartment provided successful clinical outcomes in patients with retained grafts and possibly prevented or delayed osteoarthritis progression at midterm to long-term follow-up. A collagen membrane is more encouraging than periosteum for bipolar lesions in the TF compartment. While addressing the predisposing factors affecting cartilage repair, ACI could be an adequate salvage procedure for bipolar chondral lesions in the TF compartment for the relatively young arthritic patient who wishes to avoid arthroplasty.

A balance between TFPI and thrombin-mediated platelet activation is required for murine embryonic development

PubMed Central

Ellery, Paul E. R.; Maroney, Susan A.; Cooley, Brian C.; Luyendyk, James P.; Zogg, Mark; Weiler, Hartmut

2015-01-01

Tissue factor pathway inhibitor (TFPI) is a critical anticoagulant protein present in endothelium and platelets. Mice lacking TFPI (Tfpi−/−) die in utero from disseminated intravascular coagulation. They are rescued by concomitant tissue factor (TF) deficiency, demonstrating that TFPI modulates TF function in vivo. Recent studies have found TFPI inhibits prothrombinase activity during the initiation of coagulation and limits platelet accumulation during thrombus formation, implicating TFPI in modulating platelet procoagulant activity. To examine whether altered platelet function would compensate for the lack of TFPI and rescue TFPI-null embryonic lethality, Tfpi+/− mice lacking the platelet thrombin receptor, protease activated receptor 4 (PAR4; Par4−/−), or its coreceptor, PAR3, were mated. PAR3 deficiency did not rescue Tfpi−/− embryos, but >40% of expected Tfpi−/−:Par4−/− offspring survived to adulthood. Adult Tfpi−/−:Par4−/− mice did not exhibit overt thrombosis. However, they had focal sterile inflammation with fibrin(ogen) deposition in the liver and elevated plasma thrombin-antithrombin complexes, indicating activation of coagulation at baseline. Tfpi−/−:Par4−/− mice have platelet and fibrin accumulation similar to Par4−/− mice following venous electrolytic injury but were more susceptible than Par4−/− mice to TF-induced pulmonary embolism. In addition, ∼30% of the Tfpi−/−:Par4−/− mice were born with short tails. Tfpi−/−:Par4−/− mice are the first adult mice described that lack TFPI with unaltered TF. They demonstrate that TFPI physiologically modulates thrombin-dependent platelet activation in a manner that is required for successful embryonic development and identify a role for TFPI in dampening intravascular procoagulant stimuli that lead to thrombin generation, even in the absence of thrombin-mediated platelet activation. PMID:25954015

Locality of correlation in density functional theory.

PubMed

Burke, Kieron; Cancio, Antonio; Gould, Tim; Pittalis, Stefano

2016-08-07

The Hohenberg-Kohn density functional was long ago shown to reduce to the Thomas-Fermi (TF) approximation in the non-relativistic semiclassical (or large-Z) limit for all matter, i.e., the kinetic energy becomes local. Exchange also becomes local in this limit. Numerical data on the correlation energy of atoms support the conjecture that this is also true for correlation, but much less relevant to atoms. We illustrate how expansions around a large particle number are equivalent to local density approximations and their strong relevance to density functional approximations. Analyzing highly accurate atomic correlation energies, we show that EC → -AC ZlnZ + BCZ as Z → ∞, where Z is the atomic number, AC is known, and we estimate BC to be about 37 mhartree. The local density approximation yields AC exactly, but a very incorrect value for BC, showing that the local approximation is less relevant for the correlation alone. This limit is a benchmark for the non-empirical construction of density functional approximations. We conjecture that, beyond atoms, the leading correction to the local density approximation in the large-Z limit generally takes this form, but with BC a functional of the TF density for the system. The implications for the construction of approximate density functionals are discussed.

Serum transferrin receptor status of healthy adult Arabs.

PubMed

Knox-Macaulay, Huxley; Gravell, David; Elender, Frances

2007-01-01

Several studies have provided reference ranges for the concentration of serum transferrin receptor (sTfR) in various white populations, but there is a dearth of relevant reference sTfR data in non-whites. The aim of this investigation was to establish sTfR reference ranges and mean values for a healthy non-white Arab population that could be used also for Arabs worldwide. sTfR and serum ferritin concentrations were estimated by immunoassays and blood counts were determined by conventional methods. Analysis of the data of 114 volunteer Arab blood donors (91 male, 23 female) revealed a higher mean sTfR concentration in males of 22.6+/-8.1 nmol/L (range 10.9-38.7 nmol/L) compared to that in females of 18.7+/-4.4 nmol/L (range 10.7-25.8 nmol/L, p=0.001). There was no significant correlation of sTfR concentration with age, serum ferritin level, or blood haemoglobin level, but a strong inverse correlation was demonstrated with mean cell volume and mean cell haemoglobin of red cells. Iron-replete volunteer subjects with alpha-thalassaemia trait appear to have relatively high mean sTfR concentration. We recommend the use of gender-dependent sTfR reference values for Arabs.

A microfluidic method to synthesize transferrin-lipid nanoparticles loaded with siRNA LOR-1284 for therapy of acute myeloid leukemia

NASA Astrophysics Data System (ADS)

Yang, Zhaogang; Yu, Bo; Zhu, Jing; Huang, Xiaomeng; Xie, Jing; Xu, Songlin; Yang, Xiaojuan; Wang, Xinmei; Yung, Bryant C.; Lee, L. James; Lee, Robert J.; Teng, Lesheng

2014-07-01

The siRNA LOR-1284 targets the R2 subunit of ribonucleotide reductase (RRM2) and has shown promise in cancer therapy. In this study, transferrin (Tf) conjugated lipid nanoparticles (Tf-NP-LOR-1284) were synthesized by microfluidic hydrodynamic focusing (MHF) and evaluated for the targeted delivery of LOR-1284 siRNA into acute myeloid leukemia (AML) cells. The in vitro study showed that Tf-NP-LOR-1284 can protect LOR-1284 from serum nuclease degradation. Selective uptake of Tf-NP-LOR-1284 was observed in MV4-11 cells. In addition, qRT-PCR and Western blot results revealed that Tf-NP-LOR-1284 was more effective than the free LOR-1284 in reducing the R2 mRNA and protein levels. The Tf-NP-LOR-1284 showed prolonged circulation time and increased AUC after i.v. administration relative to the free LOR-1284. Furthermore, Tf-NP-LOR-1284 facilitated increased accumulation at the tumor site along with the decreased R2 mRNA and protein expression in a murine xenograft model. These results suggest that Tf-conjugated NPs prepared by MHF provide a suitable platform for efficient and specific therapeutic delivery of LOR-1284 into AML cells.

Trigger Factor and DnaK possess overlapping substrate pools and binding specificities.

PubMed

Deuerling, Elke; Patzelt, Holger; Vorderwülbecke, Sonja; Rauch, Thomas; Kramer, Günter; Schaffitzel, Elke; Mogk, Axel; Schulze-Specking, Agnes; Langen, Hanno; Bukau, Bernd

2003-03-01

Ribosome-associated Trigger Factor (TF) and the DnaK chaperone system assist the folding of newly synthesized proteins in Escherichia coli. Here, we show that DnaK and TF share a common substrate pool in vivo. In TF-deficient cells, deltatig, depleted for DnaK and DnaJ the amount of aggregated proteins increases with increasing temperature, amounting to 10% of total soluble protein (approximately 340 protein species) at 37 degrees C. A similar population of proteins aggregated in DnaK depleted tig+ cells, albeit to a much lower extent. Ninety-four aggregated proteins isolated from DnaK- and DnaJ-depleted deltatig cells were identified by mass spectrometry and found to include essential cytosolic proteins. Four potential in vivo substrates were screened for chaperone binding sites using peptide libraries. Although TF and DnaK recognize different binding motifs, 77% of TF binding peptides also associated with DnaK. In the case of the nascent polypeptides TF and DnaK competed for binding, however, with competitive advantage for TF. In vivo, the loss of TF is compensated by the induction of the heat shock response and thus enhanced levels of DnaK. In summary, our results demonstrate that the co-operation of the two mechanistically distinct chaperones in protein folding is based on their overlap in substrate specificities.