Role of plastidic pyruvate dehydrogenase complex (pl. PDC) in chloroplast metabolism of spinach

International Nuclear Information System (INIS)

Schulze-Siebert, D.; Homeyer, U.; Schultz, G.

1986-01-01

Labeling experiments of chloroplasts in the light ( 14 CO 2 , 2- 14 C-pyruvate etc.) revealed that pl. PDC is predominantly involved in the synthesis of branched chain amino acids and pl. isoprenoids (carotenes, PQ, α-T). In this context, pl. phosphoglycerate mutase as missing link in the C 3 → C 2 metabolism of chloroplasts was identified by latency experiments. This indicates a direct pathway from Calvin cycle to pl. PDC. Using protoplasts, maximal rates in pl. PDC metabolism were obtained. On the other hand, mitochondrial PDC in protoplasts is mainly involved in fatty acid synthesis by known mechanism. Additionally, cytosolic-ER-isoprenoids were formed (e.g. sterols). When 14 CO 2 was simultaneously applied with unlabeled acetate to protoplasts in the light an isotopic dilution of fatty acids were found but not of pl. isoprenoids. This may indicate an partially channeling of pl. PDC and mevalonate pathway for pl. isoprenoid synthesis. Inhibitory studies with DCMU point in the same direction

PDC IC WELD FAILURE EVALUATION AND RESOLUTION

Energy Technology Data Exchange (ETDEWEB)

Korinko, P.; Howard, S.; Maxwell, D.; Fiscus, J.

2012-04-16

During final preparations for start of the PDCF Inner Can (IC) qualification effort, welding was performed on an automated weld system known as the PICN. During the initial weld, using a pedigree canister and plug, a weld defect was observed. The defect resulted in a hole in the sidewall of the canister, and it was observed that the plug sidewall had not been consumed. This was a new type of failure not seen during development and production of legacy Bagless Transfer Cans (FB-Line/Hanford). Therefore, a team was assembled to determine the root cause and to determine if the process could be improved. After several brain storming sessions (MS and T, R and D Engineering, PDC Project), an evaluation matrix was established to direct this effort. The matrix identified numerous activities that could be taken and then prioritized those activities. This effort was limited by both time and resources (the number of canisters and plugs available for testing was limited). A discovery process was initiated to evaluate the Vendor's IC fabrication process relative to legacy processes. There were no significant findings, however, some information regarding forging/anneal processes could not be obtained. Evaluations were conducted to compare mechanical properties of the PDC canisters relative to the legacy canisters. Some differences were identified, but mechanical properties were determined to be consistent with legacy materials. A number of process changes were also evaluated. A heat treatment procedure was established that could reduce the magnetic characteristics to levels similar to the legacy materials. An in-situ arc annealing process was developed that resulted in improved weld characteristics for test articles. Also several tack welds configurations were addressed, it was found that increasing the number of tack welds (and changing the sequence) resulted in decreased can to plug gaps and a more stable weld for test articles. Incorporating all of the process

Investigation of PDC bit failure base on stick-slip vibration analysis of drilling string system plus drill bit

Science.gov (United States)

Huang, Zhiqiang; Xie, Dou; Xie, Bing; Zhang, Wenlin; Zhang, Fuxiao; He, Lei

2018-03-01

The undesired stick-slip vibration is the main source of PDC bit failure, such as tooth fracture and tooth loss. So, the study of PDC bit failure base on stick-slip vibration analysis is crucial to prolonging the service life of PDC bit and improving ROP (rate of penetration). For this purpose, a piecewise-smooth torsional model with 4-DOF (degree of freedom) of drilling string system plus PDC bit is proposed to simulate non-impact drilling. In this model, both the friction and cutting behaviors of PDC bit are innovatively introduced. The results reveal that PDC bit is easier to fail than other drilling tools due to the severer stick-slip vibration. Moreover, reducing WOB (weight on bit) and improving driving torque can effectively mitigate the stick-slip vibration of PDC bit. Therefore, PDC bit failure can be alleviated by optimizing drilling parameters. In addition, a new 4-DOF torsional model is established to simulate torsional impact drilling and the effect of torsional impact on PDC bit's stick-slip vibration is analyzed by use of an engineering example. It can be concluded that torsional impact can mitigate stick-slip vibration, prolonging the service life of PDC bit and improving drilling efficiency, which is consistent with the field experiment results.

Does PDC Belong in Facilities Management?

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Dessoff, Alan

2012-01-01

Whether planning, design, and construction (PDC) of buildings should be part of facilities management, with its traditional operations and maintenance functions, or separated from it, has been a divisive question on many campuses for a long time. Now, although it is not happening everywhere, facilities managers at a number of institutions, public…

Hydrogenolysis of α-methylbenzyl alcohol to ethylbenzene over Pd/C catalyst

Science.gov (United States)

Feng, J.; Zhong, Y. H.; Dai, S. H.

2018-01-01

The hydrogenolysis of α-methylbenzyl alcohol (MBA) to ethylbenzene (EB) over Pd/C catalyst was studied. The XRD and TEM results show that Pd nanoparticles are well dispersed on the carbon support with good crystallinity. There is no 1-cyclohexylethanol or ethylcyclohexane in the products, indicating that Pd/C is excellent for inhibiting the hydrogenation of the aromatic ring. Alcohol solvents are beneficial to increase the catalytic activity because of their strong polarity and good solubility.

The bit's the thing : PDC bits are the sparkly new best friend of drillers everywhere

Energy Technology Data Exchange (ETDEWEB)

Cook, D.

2008-09-15

Polycrystalline diamond compact (PDC) cutters were introduced to the oil and gas industry in 1972. The drill bit technology has made significant advances since its introduction, and the PDC bits are now more widely used than conventional roller cone bits. This article discussed new PDC drill bits designed to have rates of penetration (ROP) of over 1000 feet an hour, run distances of up to 22,000 feet, and have cumulative depths of 180,000 feet. A diamond volume management (DVM) system is used to place the diamond where it is needed for specific applications. Designed by Precise Drilling Component Ltd, the bits are accompanied by thermo stable cutters developed to increase the stability of the PDC bits. Precise Drilling Component is now supplying the drilling equipment to major international oil companies. The company has also developed new abrasion-resistant cutters and improved hydraulics that have increased durability and stability, as well as lower drilling costs. The PDC cutters are able to remove rock more efficiently than the grinding and gouging actions of roller bits, which translates into faster penetration rates and longer bit lives. PDC bits are increasingly being used in steam assisted gravity drainage (SAGD) operations as the tungsten carbide matrix used for the PDC bits is able to withstand the abrasive sands encountered in oil sands wellbores. It was concluded that the PDC drill bits will continue to be optimized for use in harsh oil sands conditions. New optimization features and analytical models for improving drilling efficiency were also outlined. 4 figs.

Conformational dynamics and ligand binding in the multi-domain protein PDC109.

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Hyun Jin Kim

2010-02-01

Full Text Available PDC109 is a modular multi-domain protein with two fibronectin type II (Fn2 repeats joined by a linker. It plays a major role in bull sperm binding to the oviductal epithelium through its interactions with phosphorylcholines (PhCs, a head group of sperm cell membrane lipids. The crystal structure of the PDC109-PhC complex shows that each PhC binds to the corresponding Fn2 domain, while the two domains are on the same face of the protein. Long timescale explicit solvent molecular dynamics (MD simulations of PDC109, in the presence and absence of PhC, suggest that PhC binding strongly correlates with the relative orientation of choline-phospholipid binding sites of the two Fn2 domains; unless the two domains tightly bind PhCs, they tend to change their relative orientation by deforming the flexible linker. The effective PDC109-PhC association constant of 28 M(-1, estimated from their potential of mean force is consistent with the experimental result. Principal component analysis of the long timescale MD simulations was compared to the significantly less expensive normal mode analysis of minimized structures. The comparison indicates that difference between relative domain motions of PDC109 with bound and unbound PhC is captured by the first principal component in the principal component analysis as well as the three lowest normal modes in the normal mode analysis. The present study illustrates the use of detailed MD simulations to clarify the energetics of specific ligand-domain interactions revealed by a static crystallographic model, as well as their influence on relative domain motions in a multi-domain protein.

Ethanol electrooxidation on Pt/C and Pd/C catalysts promoted with oxide

Energy Technology Data Exchange (ETDEWEB)

Xu, Changwei [Department of Chemistry and Institute of Nanochemistry, Jinan University, Guangzhou 510632 (China); State Key Laboratory of Optoelectronic Materials and Technologies, School of Physics and Engineering, Sun Yat-Sen University, Guangzhou 510275 (China); Shen, Pei kang [State Key Laboratory of Optoelectronic Materials and Technologies, School of Physics and Engineering, Sun Yat-Sen University, Guangzhou 510275 (China); Liu, Yingliang [Department of Chemistry and Institute of Nanochemistry, Jinan University, Guangzhou 510632 (China)

2007-02-10

This research aims to investigate Pd-based catalysts as a replacement for Pt-based catalysts for ethanol electrooxidation in alkaline media. The results show that Pd/C has a higher catalytic activity and better steady-state behaviour for ethanol oxidation than that of Pt/C. The effect of the addition of CeO{sub 2} and NiO to the Pt/C and Pd/C electrocatalysts on ethanol oxidation is also studied in alkaline media. The electrocatalysts with a weight ratio of noble metal (Pt, Pd) to CeO{sub 2} of 2:1 and a noble metal to NiO ration 6:1 show the highest catalytic activity for ethanol oxidation. The oxide promoted Pt/C and Pd/C electrocatalysts show a higher activity than the commercial E-TEK PtRu/C electrocatalyst for ethanol oxidation in alkaline media. (author)

PDC bit selection to drill the Brazilian pre-salt heterogeneous carbonates; Selecao de broca PDC para a perfuracao dos carbonatos heterogeneos do pre-sal brasileiro

Energy Technology Data Exchange (ETDEWEB)

Lima, Araken Dumont Ramos; Tocantins, Joao Pedro Tourinho [Schlumberger, Rio de Janeiro, RJ (Brazil)

2012-07-01

The well drilling operation to access the oil reserves of the Brazilian pre-salt find their highest challenge in the rock reservoir, which is formed from organic limestone and other sediments, and it can have different heterogeneous features that are hostile to drilling. Those features such as the silica nodules increase the rock formation strength and abrasiveness that together with the PDC bit vibrations generated during the rock cutting reduce the life of the cutting structure to a few meters. Because of these conditions, the development of more stable bits, with very low lateral and torsional vibration levels and with more strength PDC, has been one oil industry challenges to drill the pre-salt limestone with silica. This paper aims to present a dynamic comparative analysis between three PDC bits, called BR1, BR2 and BR3, of different generations, selected to drill a well design in a limestone heterogeneous and homogeneous (without silica nodules). This analysis was performed with dynamic three dimensional finite elements software, which considers the interaction between the bit cutter structure and the rock to be drilled, used to design bits, reamers and BHA (Bottom Hole Assembly). (author)

Co-C and Pd-C Eutectic Fixed Points for Radiation Thermometry and Thermocouple Thermometry

Science.gov (United States)

Wang, L.

2017-12-01

Two Co-C and Pd-C eutectic fixed point cells for both radiation thermometry and thermocouple thermometry were constructed at NMC. This paper describes details of the cell design, materials used, and fabrication of the cells. The melting curves of the Co-C and Pd-C cells were measured with a reference radiation thermometer realized in both a single-zone furnace and a three-zone furnace in order to investigate furnace effect. The transition temperatures in terms of ITS-90 were determined to be 1324.18 {°}C and 1491.61 {°}C with the corresponding combined standard uncertainty of 0.44 {°}C and 0.31 {°}C for Co-C and Pd-C, respectively, taking into account of the differences of two different types of furnaces used. The determined ITS-90 temperatures are also compared with that of INRIM cells obtained using the same reference radiation thermometer and the same furnaces with the same settings during a previous bilateral comparison exercise (Battuello et al. in Int J Thermophys 35:535-546, 2014). The agreements are within k=1 uncertainty for Co-C cell and k = 2 uncertainty for Pd-C cell. Shapes of the plateaus of NMC cells and INRIM cells are compared too and furnace effects are analyzed as well. The melting curves of the Co-C and Pd-C cells realized in the single-zone furnace are also measured by a Pt/Pd thermocouple, and the preliminary results are presented as well.

Silicon-containing polymer-derived ceramic nanocomposites (PDC-NCs): preparative approaches and properties.

Science.gov (United States)

Ionescu, Emanuel; Kleebe, Hans-Joachim; Riedel, Ralf

2012-08-07

Composites consist by definition of at least two materials (Gibbsian phases) with rather different properties. They exhibit a heterogeneous microstructure and possess improved properties with respect to their components. Furthermore, the design of their microstructure allows for tailoring their overall properties. In the last decades, intense work was performed on the synthesis of nanocomposites, which have the feature that at least one of their components is nanoscaled. However, the microstructure-property relationship of nanocomposite materials is still a challenging topic. This tutorial review paper deals with a special class of nanocomposites, i.e. polymer-derived ceramic nanocomposites (PDC-NCs), which have been shown to be promising materials for various structural and functional applications. Within this context, different preparative approaches for PDC-NCs as well as some of their properties will be presented and discussed. Furthermore, recent results concerning the relationship between the nano/microstructure of PDC-NCs and their properties will be highlighted.

Mediterranean glucose-6-phosphate dehydrogenase (G6PDC563T) mutation among jordanian females with acute hemolytic crisis

International Nuclear Information System (INIS)

Jabbar, A.A.; Kanakiri, N.; Kamil, M.; Rimawi, H.S.A.

2010-01-01

To evaluate the G6PDC563T Mediterranean mutation among Jordanian females who were admitted to Princess Rahma Teaching Hospital (PRTH) with/or previous history of favism. Study Design: A descriptive study. Place and Duration of Study: Jordanian University of Science and Technology and PRTH, from October 2003 to October 2004. Methodology: After obtaining approval from the Ethics Committee of Jordanian University of Science and Technology, a total of 32 females were included in this study. Samples from 15 healthy individual females were used as a negative control. Blood samples from these patients were collected and analyzed by allele-specific polymerase chain reaction (AS-PCR) to determine the G6PDC563T mutation. Results: Twenty one out of 32 patients were found to be G6PDC563T Mediterranean mutation (65.6%) positive. Three out of 21 patients were homozygous and remaining 18 were heterozygous for G6PDC563T Mediterranean mutation. Eleven (34.4%) out of 32 patients were found to be negative for G6PDC563T mutation indicating the presence of other G6PD mutations in the study sample. Conclusion: G6PDC563T Mediterranean mutation accounted for 65.6% of the study sample with favism in the North of Jordan. There is likely to be another G6PD deficiency variant implicated in acute hemolytic crisis (favism). (author)

The In-Situ One-Step Synthesis of a PDC Macromolecular Pro-Drug and the Fabrication of a Novel Core-Shell Micell.

Science.gov (United States)

Yu, Cui-Yun; Yang, Sa; Li, Zhi-Ping; Huang, Can; Ning, Qian; Huang, Wen; Yang, Wen-Tong; He, Dongxiu; Sun, Lichun

2016-01-01

The development of slow release nano-sized carriers for efficient antineoplastic drug delivery with a biocompatible and biodegradable pectin-based macromolecular pro-drug for tumor therapy has been reported in this study. Pectin-doxorubicin conjugates (PDC), a macromolecular pro-drug, were prepared via an amide condensation reaction, and a novel amphiphilic core-shell micell based on a PDC macromolecular pro-drug (PDC-M) was self-assembled in situ, with pectin as the hydrophilic shell and doxorubicin (DOX) as the hydrophobic core. Then the chemical structure of the PDC macromolecular pro-drug was identified by both Fourier transform infrared spectroscopy (FTIR) and nuclear magnetic resonance spectroscopy ((1)H-NMR), and proved that doxorubicin combined well with the pectin and formed macromolecular pro-drug. The PDC-M were observed to have an unregularly spherical shape and were uniform in size by scanning electron microscopy (SEM). The average particle size of PDC-M, further measured by a Zetasizer nanoparticle analyzer (Nano ZS, Malvern Instruments), was about 140 nm. The encapsulation efficiency and drug loading were 57.82% ± 3.7% (n = 3) and 23.852% ±2.3% (n = 3), respectively. The in vitro drug release behaviors of the resulting PDC-M were studied in a simulated tumor environment (pH 5.0), blood (pH 7.4) and a lysosome media (pH 6.8), and showed a prolonged slow release profile. Assays for antiproliferative effects and flow cytometry of the resulting PDC-M in HepG2 cell lines demonstrated greater properties of delayed and slow release as compared to free DOX. A cell viability study against endothelial cells further revealed that the resulting PDC-M possesses excellent cell compatibilities and low cytotoxicities in comparison with that of the free DOX. Hemolysis activity was investigated in rabbits, and the results also demonstrated that the PDC-M has greater compatibility in comparison with free DOX. This shows that the resulting PDC-M can ameliorate the

Molecular identification and characterization of the pyruvate decarboxylase gene family associated with latex regeneration and stress response in rubber tree.

Science.gov (United States)

Long, Xiangyu; He, Bin; Wang, Chuang; Fang, Yongjun; Qi, Jiyan; Tang, Chaorong

2015-02-01

In plants, ethanolic fermentation occurs not only under anaerobic conditions but also under aerobic conditions, and involves carbohydrate and energy metabolism. Pyruvate decarboxylase (PDC) is the first and the key enzyme of ethanolic fermentation, which branches off the main glycolytic pathway at pyruvate. Here, four PDC genes were isolated and identified in a rubber tree, and the protein sequences they encode are very similar. The expression patterns of HbPDC4 correlated well with tapping-simulated rubber productivity in virgin rubber trees, indicating it plays an important role in regulating glycometabolism during latex regeneration. HbPDC1, HbPDC2 and HbPDC3 had striking expressional responses in leaves and bark to drought, low temperature and high temperature stresses, indicating that the HbPDC genes are involve in self-protection and defense in response to various abiotic and biotic stresses during rubber tree growth and development. To understand ethanolic fermentation in rubber trees, it will be necessary to perform an in-depth study of the regulatory pathways controlling the HbPDCs in the future. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Cloning of affecting pyruvate decarboxylase gene in the production bioethanol of agricultural waste in the E.coli bacteria

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Masome Zeinali

2016-09-01

Full Text Available Introduction: Ethanol made by a biomass is one of the useful strategies in terms of economic and environmental and as a clean and safe energy to replace fossil fuels considered and examined. Materials and methods: In this study, key enzyme in the production of ethanol (Pyruvate decarboxylase from Zymomonas mobilis bacteria was isolated and cloned at E. coli bacteria by freeze and thaw method. For gene cloning, we used specific primers of pdc and PCR reaction and then pdc gene isolated and pET 28a plasmid double digested with (Sal I and Xho I enzymes. Digestion Products were ligated by T4 DNA ligase in 16 °C for 16 hours. Results: Results of bacteria culture showed that a few colonies containing pET 28a plasmid could grow. Result of colony pcr of pdc gene with specific primers revealed 1700 bp bands in 1% agarose gel electrophoresis. The results of PCR with T7 promotor forward primer and pdc revers primer have proved the accurate direction of integration of pdc gene into plasmid and revealed 1885 bp band. Double digestion of recombinant plasmid with SalI and XhoI enzymes revealed same bands. Finally, RT showed the expected band of 1700 bp that implies the desired gene expression in the samples. Discussion and conclusion: Due to the increased production of ethanol via pyruvate decarboxylase gene cloning in expression plasmids with a strong promoter upstream of the cloning site can conclude that, pyruvate decarboxylase cloning as a key gene would be useful and according to beneficial properties of E. coli bacteria, transfering the gene to bacteria appears to be reasonable.

Design of PDC Controllers by Matrix Reversibility for Synchronization of Yin and Yang Chaotic Takagi-Sugeno Fuzzy Henon Maps

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Chun-Yen Ho

2012-01-01

Full Text Available This paper investigates the synchronization of Yin and Yang chaotic T-S fuzzy Henon maps via PDC controllers. Based on the Chinese philosophy, Yin is the decreasing, negative, historical, or feminine principle in nature, while Yang is the increasing, positive, contemporary, or masculine principle in nature. Yin and Yang are two fundamental opposites in Chinese philosophy. The Henon map is an invertible map; so the Henon maps with increasing and decreasing argument can be called the Yang and Yin Henon maps, respectively. Chaos synchronization of Yin and Yang T-S fuzzy Henon maps is achieved by PDC controllers. The design of PDC controllers is based on the linear invertible matrix theory. The T-S fuzzy model of Yin and Yang Henon maps and the design of PDC controllers are novel, and the simulation results show that the approach is effective.

Analysis of bit-rock interaction during stick-slip vibrations using PDC cutting force model

Energy Technology Data Exchange (ETDEWEB)

Patil, P.A.; Teodoriu, C. [Technische Univ. Clausthal, Clausthal-Zellerfeld (Germany). ITE

2013-08-01

Drillstring vibration is one of the limiting factors maximizing the drilling performance and also causes premature failure of drillstring components. Polycrystalline diamond compact (PDC) bit enhances the overall drilling performance giving the best rate of penetrations with less cost per foot but the PDC bits are more susceptible to the stick slip phenomena which results in high fluctuations of bit rotational speed. Based on the torsional drillstring model developed using Matlab/Simulink for analyzing the parametric influence on stick-slip vibrations due to drilling parameters and drillstring properties, the study of relations between weight on bit, torque on bit, bit speed, rate of penetration and friction coefficient have been analyzed. While drilling with the PDC bits, the bit-rock interaction has been characterized by cutting forces and the frictional forces. The torque on bit and the weight on bit have both the cutting component and the frictional component when resolved in horizontal and vertical direction. The paper considers that the bit is undergoing stick-slip vibrations while analyzing the bit-rock interaction of the PDC bit. The Matlab/Simulink bit-rock interaction model has been developed which gives the average cutting torque, T{sub c}, and friction torque, T{sub f}, values on cutters as well as corresponding average weight transferred by the cutting face, W{sub c}, and the wear flat face, W{sub f}, of the cutters value due to friction.

Bi-modified Pd/C catalyst via irreversible adsorption and its catalytic activity for ethanol oxidation in alkaline medium

International Nuclear Information System (INIS)

Cai, Jindi; Huang, Yiyin; Guo, Yonglang

2013-01-01

Highlights: • Pd-Bi/C catalysts were easily prepared by irreversible adsorption of Bi on Pd/C surface. • The adsorption of Bi increases the oxygen-containing species obviously on Pd-Bi/C surface. • Only a little amount of Bi on Pd-Bi/C can play a significant role in ethanol oxidation reaction (EOR). • Current density of EOR on Pd-Bi/C (20:1) is 2.4 times higher than that on Pd/C. • Anti-poisoning ability and durability of Pd-Bi/C (20:1) is greatly enhanced. -- Abstract: A facile approach to promote ethanol electro-oxidation on Pd-based catalysts is presented by the modification of Bi on Pd/C catalyst via irreversible adsorption. X-ray diffraction (XRD), transmission electron microscope (TEM) and X-ray photoelectron spectroscopy (XPS) measurements show that the modification of Bi has no significant effect on the Pd morphology and particle size distribution. Bi(III) and Pd(0) are the dominant forms in Pd-Bi/C catalyst. Electrochemical tests show that the modification of the appropriate amount of Bi on Pd/C catalyst can remarkably enhance activity toward ethanol oxidation reaction (EOR) up to about 2.4 times higher compared to Pd/C catalyst. The Pd-Bi/C (20:1) catalyst exhibits excellent stability and enhances CO tolerance. The enhanced electrochemical performance of Pd-Bi/C catalyst is attributed to the electronic effect and the bifunctional mechanism. The high exchange current density and the low apparent activation energy on Pd-Bi/C (20:1) catalyst reveal its faster kinetics and higher intrinsic activity compared to Pd/C catalyst

Glycerol electro-oxidation in alkaline medium using Pd/C and PdSn/C electrocatalysts prepared by electron beam irradiation

International Nuclear Information System (INIS)

Geraldes, Adriana Napoleao; Silva, Dionisio Fortunato da; Pino, Eddy Segura; Spinace, Estevan Vitorio; Oliveira Neto, Almir; Linardi, Marcelo; Santos, Mauro Coelhos dos

2013-01-01

Carbon-supported metal nanoparticles were prepared for fuel cell applications by radiation-induced reduction of metal ions precursors. Pd/C and PdSn/C electrocatalysts (Pd:Sn atomic ratio 90:10), prepared by using electron beam irradiation, were tested for glycerol electro-oxidation in single alkaline direct glycerol fuel cell (ADGFC). EDX analysis showed that the Pd:Sn atomic ratio is very similar to the nominal one. X-ray diffractograms of PdSn/C electrocatalyst showed the presence of Pd (fcc) phase. Cyclic voltammetry (CV) indicated that Pd/C and PdSn/C electrocatalysts have good activity for glycerol electro-oxidation, at room temperature. Experiments with single ADGFC were carried out from 60 to 90 deg C, using Pd/C and PdSn/C electrocatalysts and glycerol 2.0 mol.L -1 , as fuel. The best performance was obtained at 85 deg C, for both electrocatalysts. The Pd/C and PdSn/C electrocatalysts showed similar performance (34 mW cm -2 ), at 85 deg C. (author)

Practice of knowledge management in Prototype and Plant Development Center (PDC)

International Nuclear Information System (INIS)

Mohamad Safuan Sulaiman; Rapieh Aminuddin; Rosli Darmawan; Mohd Ashhar Khalid

2007-01-01

As reflecting the evolvement and movement of world economy direction, Malaysia move one step a head towards knowledge based economy (K-Economy). The movement indirectly changes the Malaysian Nuclear Agency (Nuclear Malaysia) environment to contribute to the K-Economy in the field of science and technology. Therefore, the practice of knowledge management is slowly introduced to the Nuclear Malaysia community to support the K-Economy. This paper describes the detail of the practice of knowledge management at macro and micro level in an organization. The Prototype and Plant Development Center(PDC) under the Technical Support Division, Technical Service Program has been chosen to be the case study in implementing the practice of knowledge management in Nuclear Malaysia. The main objective of this paper is to introduce the right practice of Knowledge management in an organization and PDC as among the first case for this purpose. (Author)

Technical advance: Generation of human pDC equivalents from primary monocytes using Flt3-L and their functional validation under hypoxia.

Science.gov (United States)

Sekar, Divya; Brüne, Bernhard; Weigert, Andreas

2010-08-01

The division of labor between DC subsets is evolutionarily well-defined. mDC are efficient in antigen presentation, whereas pDC act as rheostats of the immune system. They activate NK cells, cause bystander activation of mDC, and interact with T cells to induce tolerance. This ambiguity positions pDC at the center of inflammatory diseases, such as cancer, arthritis, and autoimmune diseases. The ability to generate human mDC ex vivo made it possible to engineer them to suit therapy needs. Unfortunately, a similar, easily accessible system to generate human pDC is not available. We describe a method to generate human pDC equivalents ex vivo, termed mo-pDC from peripheral blood monocytes using Flt3-L. mo-pDC showed a characteristic pDC profile, such as high CD123 and BDCA4, but low CD86 and TLR4 surface expression and a low capacity to induce autologous lymphocyte proliferation and to phagocytose apoptotic debris in comparison with mDC. Interestingly, mo-pDC up-regulated the pDC lineage-determining transcription factor E2-2 as well as expression of BDCA2, which is under the transcriptional control of E2-2 but not its inhibitor ID2, during differentiation. mo-pDC produced high levels of IFN-alpha when pretreated overnight with TNF-alpha. Under hypoxia, E2-2 was down-regulated, and ID2 was induced in mo-pDC, whereas surface expression of MHCI, CD86, and BDCA2 was decreased. Furthermore, mo-pDC produced high levels of inflammatory cytokines when differentiated under hypoxia compared with normoxia. Hence, mo-pDC can be used to study differentiation and functions of human pDC under microenvironmental stimuli.

Alkaline Ionic Liquid Modified Pd/C Catalyst as an Efficient Catalyst for Oxidation of 5-Hydroxymethylfurfural

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Zou Bin

2018-01-01

Full Text Available Conversion of HMF into FDCA was carried out by a simple and green process based on alkaline ionic liquid (IL modified Pd/C catalyst (Pd/C-OH−. Alkaline ionic liquids were chosen to optimize Pd/C catalyst for special hydrophilicity and hydrophobicity, redox stability, and unique dissolving abilities for polar compounds. The Pd/C-OH− catalyst was successfully prepared and characterized by SEM, XRD, TG, FT-IR, and CO2-TPD technologies. Loading of alkaline ionic liquid on the surface of Pd/C was 2.54 mmol·g−1. The catalyst showed excellent catalytic activity in the HMF oxidation after optimization of reaction temperature, reaction time, catalyst amount, and solvent. Supported alkaline ionic liquid (IL could be a substitute and promotion for homogeneous base (NaOH. Under optimal reaction conditions, high HMF conversion of 100% and FDCA yield of 82.39% were achieved over Pd/C-OH− catalyst in water at 373 K for 24 h.

Supraspinal and spinal effects of L-trans-PDC, an inhibitor of glutamate transporter, on the micturition reflex in rats.

Science.gov (United States)

Honda, Masashi; Yoshimura, Naoki; Hikita, Katsuya; Hinata, Nobuyuki; Muraoka, Kuniyasu; Saito, Motoaki; Chancellor, Michael B; Takenaka, Atsushi

2013-09-01

Glutamate is a major excitatory transmitter in the central nervous system, controlling lower urinary tract function. Five types of glutamate transporters such as GLAST (EAAT1), GLT-1 (EAAT2), EAAC-1 (EAAT3), EAAT4, and EAAT5 have been cloned so far. In the current study we tested whether L-trans-pyrrolidine-2,4-dicarboxylic acid (L-trans-PDC), a non-selective inhibitor of glutamate transporters that increases endogenous glutamate concentration, can affect the micturition reflex in urethane anesthetized rats. Continuous cystometrograms (CMG, 0.04 ml/min infusion rate) were performed in two groups of urethane-anesthetized rats. A group of 18 rats was used for intrathecal administration of 1-10 µg of L-trans-PDC via an intrathecal catheter. In the second group of 18 rats, 1-10 µg of L-trans-PDC were administered intracerebroventricularly via a catheter inserted into the lateral ventricle. Micturition parameters were recorded and compared before and after drug administration. Intrathecal administration of L-trans-PDC at 1, 3, and 10 µg (n = 6 per dose) increased intercontraction intervals in dose dependent fashion, but did not affect postvoid residual or basal pressure at any doses tested. Intracerebroventricular administration of L-trans-PDC at 1, 3, and 10 µg (n = 6 per dose) also increased intercontraction intervals in dose dependent fashion, but did not affect postvoid residual or basal pressure at any doses tested. The current results show that, in urethane-anesthetized rats, suppression of glutamate transporters by L-trans-PDC has an inhibitory effect on the micturition reflex at supraspinal and spinal sites, possibly via activation of glutamate-mediated inhibitory pathways. Copyright © 2012 Wiley Periodicals, Inc.

Overexpression of the genes PDC1 and ADH1 activates glycerol conversion to ethanol in the thermotolerant yeast Ogataea (Hansenula) polymorpha.

Science.gov (United States)

Kata, Iwona; Semkiv, Marta V; Ruchala, Justyna; Dmytruk, Kostyantyn V; Sibirny, Andriy A

2016-08-01

Conversion of byproduct from biodiesel production glycerol to high-value compounds is of great importance. Ethanol is considered a promising product of glycerol bioconversion. The methylotrophic thermotolerant yeast Ogataea (Hansenula) polymorpha is of great interest for this purpose as the glycerol byproduct contains methanol and heavy metals as contaminants, and this yeast utilizes methanol and is relatively resistant to heavy metals. Besides, O. polymorpha shows robust growth on glycerol and produces ethanol from various carbon sources. The thermotolerance of this yeast is an additional advantage, allowing increased fermentation temperature to 45-48 °C, leading to increased rate of the fermentation process and a fall in the cost of distillation. The wild-type strain of O. polymorpha produces insignificant amounts of ethanol from glycerol (0.8 g/l). Overexpression of PDC1 coding for pyruvate decarboxylase enhanced ethanol production up to 3.1 g/l, whereas simultaneous overexpression of PDC1 and ADH1 (coding for alcohol dehydrogenase) led to further increase in ethanol production from glycerol. Moreover, the increased temperature of fermentation up to 45 °C stimulated the production of ethanol from glycerol used as the only carbon source up to 5.0 g/l, which exceeds the data obtained by methylotrophic yeast strains reported so far. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Diamonds are forever : roller bits once ruled the roost, but PDC drillbits have emerged as oilpatch champions

Energy Technology Data Exchange (ETDEWEB)

Cope, G.

2008-06-15

Polycrystalline diamond compact (PDC) drill bits are used in over 60 per cent of wells currently being drilled. PDC bits use thumb-sized diamond-impregnated cutters fixed into the body of the bit in order to shear the rock. Certain rock formations that contain large amounts of chert or pyrite can destroy PDCs, which are ideally suited for use in offshore wells which have soft, homogenous rock sections. This article discussed recent research programs conducted to analyze the strengths and weaknesses of PDCs and improve their cutting efficiency through the analysis of cutter geometry, material composition, and processing conditions. Researchers have now discovered that diamond chips of 10 microns performed better than chips of 70 microns. Cutters were found to be more durable when cobalt was used as a binder to sinter the diamond chips. PDCs are now being used extensively by the oil sands industry due to their abrasion resistance. Research is ongoing in order to improve the performance of PDC drill bits. 2 figs.

Peripheral Blood CD4 T-Cell and Plasmacytoid Dendritic Cell (pDC) Reactivity to Herpes Simplex Virus 2 and pDC Number Do Not Correlate with the Clinical or Virologic Severity of Recurrent Genital Herpes

Science.gov (United States)

Moss, Nicholas J.; Magaret, Amalia; Laing, Kerry J.; Kask, Angela Shaulov; Wang, Minna; Mark, Karen E.; Schiffer, Joshua T.; Wald, Anna

2012-01-01

Leukocytes participate in the immune control of herpes simplex virus (HSV). Data from HIV coinfections, germ line mutations, and case reports suggest involvement of CD4 T cells and plasmacytoid dendritic cells (pDC). We investigated the relationships between these cells and recurrent genital herpes disease severity in the general population. Circulating CD4 T-cell responses to HSV-2 were measured in specimens from 67 immunocompetent individuals with measured genital lesion and HSV shedding rates. Similarly, pDC number and functional responses to HSV-2 were analyzed in 40 persons. CD4 responses and pDC concentrations and responses ranged as much as 100-fold between persons while displaying moderate within-person consistency over time. No correlations were observed between these immune response parameters and genital HSV-2 severity. Cytomegalovirus (CMV) coinfection was not correlated with differences in HSV-2-specific CD4 T-cell responses. The CD4 T-cell response to HSV-2 was much more polyfunctional than was the response to CMV. These data suggest that other immune cell subsets with alternate phenotypes or anatomical locations may be responsible for genital herpes control in chronically infected individuals. PMID:22761381

Ethanol electro-oxidation in alkaline medium using Pd/c and PdRh/C electrocatalysts prepared by electron beam irradiation

International Nuclear Information System (INIS)

Silva, Dionisio Furtunato da; Geraldes, Adriana Napoleao; Pino, Eddy Segura; Spinace, Estevam Vitorio; Oliveira Neto, Almir; Linardi, Marcelo

2013-01-01

In this study, carbon-supported Pd (Pd/C) and bimetallic PdRh (Pd:Rh 90:10 atomic ratio) (PdRh/C) electrocatalysts were prepared using electron beam irradiation. The morphology and composition of the obtained materials were characterized by Cyclic voltammetry (VC), Chronoamperometry (CA), Energy dispersive X-ray (EDX), X-ray Diffraction (XRD) and Thermo-gravimetric analysis (TGA). The catalytic activities of the electrocatalysts toward the ethanol electro-oxidation were evaluated in alkaline medium in a single alkaline direct ethanol fuel cell (ADEFC), in a range temperature of 50 to 85 deg C. The best performances were obtained at 85 deg C (25 mW.cm -2 ) and 75 deg C (38 mW.cm -2 ) for Pd/C and PdRh/C electrocatalysts, respectively. The XRD of the PdRh/C electrocatalyst showed the presence of Pd-rich (fcc) phase. CV and CA experiments showed that PdRh/C electrocatalyst demonstrated superior activity toward ethanol electro-oxidation at room temperature, compared to Pd/C electrocatalyst. (author)

All-electron ab initio investigation of the electronic states of the PdC molecule

DEFF Research Database (Denmark)

Shim, Irene; Gingerich, Karl A.

2001-01-01

The electronic structure of transition metal containing molecules are extremely complicated and extensive calculations are required for reliable descriptions. In spite of this the results can often be interpreted in simple terms. The electronic structure of PdC is consistent with the molecular or...

Ethanol electro-oxidation in alkaline medium using Pd/c and PdRh/C electrocatalysts prepared by electron beam irradiation

Energy Technology Data Exchange (ETDEWEB)

Silva, Dionisio Furtunato da; Geraldes, Adriana Napoleao; Pino, Eddy Segura; Spinace, Estevam Vitorio; Oliveira Neto, Almir; Linardi, Marcelo, E-mail: dfsilva@ipen.br, E-mail: drinager@ig.com.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

2013-07-01

In this study, carbon-supported Pd (Pd/C) and bimetallic PdRh (Pd:Rh 90:10 atomic ratio) (PdRh/C) electrocatalysts were prepared using electron beam irradiation. The morphology and composition of the obtained materials were characterized by Cyclic voltammetry (VC), Chronoamperometry (CA), Energy dispersive X-ray (EDX), X-ray Diffraction (XRD) and Thermo-gravimetric analysis (TGA). The catalytic activities of the electrocatalysts toward the ethanol electro-oxidation were evaluated in alkaline medium in a single alkaline direct ethanol fuel cell (ADEFC), in a range temperature of 50 to 85 deg C. The best performances were obtained at 85 deg C (25 mW.cm{sup -2}) and 75 deg C (38 mW.cm{sup -2}) for Pd/C and PdRh/C electrocatalysts, respectively. The XRD of the PdRh/C electrocatalyst showed the presence of Pd-rich (fcc) phase. CV and CA experiments showed that PdRh/C electrocatalyst demonstrated superior activity toward ethanol electro-oxidation at room temperature, compared to Pd/C electrocatalyst. (author)

Pd/C Synthesized with Citric Acid: An Efficient Catalyst for Hydrogen Generation from Formic Acid/Sodium Formate

Science.gov (United States)

Wang, Zhi-Li; Yan, Jun-Min; Wang, Hong-Li; Ping, Yun; Jiang, Qing

2012-01-01

A highly efficient hydrogen generation from formic acid/sodium formate aqueous solution catalyzed by in situ synthesized Pd/C with citric acid has been successfully achieved at room temperature. Interestingly, the presence of citric acid during the formation and growth of the Pd nanoparticles on carbon can drastically enhance the catalytic property of the resulted Pd/C, on which the conversion and turnover frequency for decomposition of formic acid/sodium formate system can reach the highest values ever reported of 85% within 160 min and 64 mol H2 mol−1 catalyst h−1, respectively, at room temperature. The present simple, low cost, but highly efficient CO-free hydrogen generation system at room temperature is believed to greatly promote the practical application of formic acid system on fuel cells. PMID:22953041

Stability and Reactivity of Cyclometallated Naphthylamine Complexes in Pd-C Bond Insertion Reactions with Coordinated Alkynylphosphanes

KAUST Repository

Chen, Shuli

2013-09-17

Phenylbis(phenylethynyl)phosphane PhP(C≡CPh)2 coordinates regiospecifically to the α-methyl-chiral ortho-platinated and -palladated naphthylamine units at the positions trans to the nitrogen donors. The P→Pt coordination bond is kinetically inert, whereas the P→Pd bond is labile. Upon heating of these phosphane complexes at 70 °C, one of the C≡C bonds in the coordinated PhP(C≡CPh)2 was activated towards an intermolecular Pd-C bond insertion reaction with an external ortho-palladated naphthylamine ring. No intramolecular insertion reaction occurred. In contrast to its palladium analogue, the ortho-platinated ring is not reactive towards coordinated PhP(C≡CPh)2, although it can promote the Pd-C bond insertion reaction. However, despite the high kinetic stability of the P→Pt coordination, the organoplatinum unit is a noticeably weaker activator than its organopalladium counterpart. The chirality of the reacting ortho-metallated naphthylamine ligand exhibited high stereochemical influence on the formation of the new stereogenic phosphorus center during the course of these C-C bond-formation reactions. The coordination chemistry and the absolute stereochemistry of the dimetallic products were determined by single-crystal X-ray crystallographic analysis. The asymmetric monoinsertion of PhP(C≡CPh)2 coordinated to a cyclometallated N,N-dimethyl naphthyl/benzylamine template into the Pd-C bonds of N,N-dimethylnaphthylamine palladacycles has been demonstrated for the synthesis of a variety of new P-stereogenic homo- or heterodimetallic complexes. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stability and Reactivity of Cyclometallated Naphthylamine Complexes in Pd-C Bond Insertion Reactions with Coordinated Alkynylphosphanes

KAUST Repository

Chen, Shuli; Chiew, Jun Xuan; Pullarkat, Sumod A.; Li, Yongxin; Leung, Pak Hing

2013-01-01

, whereas the P→Pd bond is labile. Upon heating of these phosphane complexes at 70 °C, one of the C≡C bonds in the coordinated PhP(C≡CPh)2 was activated towards an intermolecular Pd-C bond insertion reaction with an external ortho-palladated naphthylamine

Oxide (CeO{sub 2}, NiO, Co{sub 3}O{sub 4} and Mn{sub 3}O{sub 4})-promoted Pd/C electrocatalysts for alcohol electrooxidation in alkaline media

Energy Technology Data Exchange (ETDEWEB)

Xu, Changwei; Tian, Zhiqun; Jiang, San Ping [School of Mechanical and Aerospace Engineering, Nanyang Technological University (Singapore); Shen, Peikang [School of Physics and Engineering, Sun Yat-Sen University, Guangzhou 510275 (China)

2008-01-01

This study investigated Pt/C, Pd/C and oxide (CeO{sub 2}, NiO, Co{sub 3}O{sub 4} and Mn{sub 3}O{sub 4})-promoted Pd/C for electrooxidation reactions of methanol, ethanol, ethylene glycol and glycerol in alkaline media. The results show that Pd/C electrocatalysts alone have low activity and very poor stability for the alcohol electrooxidation. However, addition of oxides like CeO{sub 2}, NiO, Co{sub 3}O{sub 4} and Mn{sub 3}O{sub 4} significantly promotes catalytic activity and stability of the Pd/C electrocatalysts for the alcohol electrooxidation. The Pd-Co{sub 3}O{sub 4} (2:1, w:w)/C shows the highest activity for the electrooxidation of methanol, EG and glycerol while the most active catalyst for the ethanol electrooxidation is Pd-NiO (6:1, w:w)/C. On the other hand, Pd-Mn{sub 3}O{sub 4}/C shows significantly better performance stability than other oxide-promoted Pd/C for the alcohol electrooxidation. The poor stability of the Pd-Co{sub 3}O{sub 4}/C electrocatalysts is most likely related to the limited solubility of cobalt oxides in alkaline solutions. (author)

Stabilization Using a Discrete Fuzzy PDC Control with PID Controllers and Pole Placement: Application to an Experimental Greenhouse

Directory of Open Access Journals (Sweden)

Amine Chouchaine

2011-01-01

Full Text Available This paper proposes a control strategy for complex and nonlinear systems, based on a parallel distributed compensation (PDC controller. A solution is presented to solve a stability problem that arises when dealing with a Takagi-Sugeno discrete system with great numbers of rules. The PDC controller will use a classical controller like a PI, PID, or RST in each rule with a pole placement strategy to avoid causing instability. The fuzzy controller presented combines the multicontrol approach and the performance of the classical controllers to obtain a robust nonlinear control action that can also deal with time-variant systems. The presented method was applied to a small greenhouse to control its inside temperature by variation in ventilation rate inside the process. The results obtained will show the efficiency of the adopted method to control the nonlinear and complex systems.

Methods and materials for the production of L-lactic acid in yeast

Science.gov (United States)

Hause, Ben [Jordan, MN; Rajgarhia, Vineet [Minnetonka, MN; Suominen, Pirkko [Maple Grove, MN

2009-05-19

Recombinant yeast are provided having, in one aspect, multiple exogenous LDH genes integrated into the genome, while leaving native PDC genes intact. In a second aspect, recombinant yeast are provided having an exogenous LDH gene integrated into its genome at the locus of a native PDC gene, with deletion of the native PDC gene. The recombinant yeast are useful in fermentation process for producing lactic acid.

Point Lepreau refurbishment project programmable digital comparator (PDC) replacement for SDS1 and SDS2

International Nuclear Information System (INIS)

Ichiyen, N.M.; Chan, D.; Thompson, P.D.

2003-01-01

NB Power is tentatively planning to conduct an 18-month maintenance outage of the Point Lepreau Generating Station (PLGS) starting in April 2007. The scope of the outage was determined from the outcome of a two year study (Phase 1) involving a detailed condition assessment of the station which examined issues relating to ageing and obsolescence, along with a detailed review of Safety and Licensing issues associated with extended operation. In order to minimize schedule and regulatory risk for the Refurbishment project, pre-project work was initiated in early 2002. This program is called Phase 2 ESA (Early Start Activities). As part of the Phase 1 assessments it was concluded that replacement of the PDCs (Programmable Digital Comparators) for both shutdown systems was required in order to ensure operation of the plant for a further 25-30 years. Critical tasks were identified related to PDC replacement as part of the Phase 2 ESA program. This paper describes the activities that have taken place in the Phase 2 ESA program as well as the plan for future work for the PDC replacement for SDS 1 (Shutdown System Number One) and SDS2 (Shutdown System Number Two). (author)

Development status of the PDC-1 Parabolic Dish Concentrator

Science.gov (United States)

Thostesen, T.; Soczak, I. F.; Pons, R. L.

1982-01-01

The status of development of the 12 m diameter parabolic dish concentrator which is planned for use with the Small Community Solar Thermal Power System. The PDC-1 unit features the use of plastic reflector film bonded to structural plastic gores supported by front-bracing steel ribs. An elevation-over-azimuth mount arrangement is employed, with a conventional wheel-and-track arrangement; outboard trunnions permit the dish to be stored in the face down position, with the added advantage of easy access to the power conversion assembly. The control system is comprised of a central computer (LSI 1123), a manual control panel, a concentrator control unit, two motor controllers, a Sun sensor, and two angular position resolvers. The system is designed for the simultaneous control of several concentrators. The optical testing of reflective panels is described.

[Pr2(pdc3(Hpdc(H2O4]n·n(H3hp·8n(H2O, a One-Dimensional Coordination Polymer Containing PrO6N3 Tri-Capped Trigonal Prisms and PrO8N Mono-Capped Square Anti-Prisms (H2pdc = Pyridine 2,6-Dicarboxylic Acid, C7H5NO4; 3hp = 3-Hydroxy Pyridine, C5H5NO

Directory of Open Access Journals (Sweden)

Shahzad Sharif

2012-08-01

Full Text Available The synthesis, structure and some properties of the one-dimensional coordination polymer, [Pr2(pdc3(Hpdc]n·n(H3hp·8n(H2O, (H2pdc = pyridine 2,6-dicarboxylic acid, C7H5NO4; 3hp = 3-hydroxypyridine, C5H5NO are described. One of the Pr3+ ions is coordinated by two O,N,O-tridentate pdc2− ligands and one tridentate Hpdc− anion to generate a fairly regular PrO6N3 tri-capped trigonal prism, with the N atoms acting as the caps. The second Pr3+ ion is coordinated by one tridentate pdc2− dianion, four water molecules and two monodentate bridging pdc2− ligands to result in a PrO8N coordination polyhedron that approximates to a mono-capped square-anti-prism. The ligands bridge the metal-atom nodes into a chain, which extends in the [100] direction. The H3hp+ cation and uncoordinated water molecules occupy the inter-chain regions and an N–HLO and numerous O–HLO hydrogen bonds consolidate the structure. The H3hp+ species appears to intercalate between pendant pdc rings to consolidate the polymeric structure. Crystal data: 1 (C33H43N5O29Pr2, Mr = 1255.54, triclinic,  (No. 2, Z = 2, a = 13.2567(1 Å, b = 13.6304(2 Å, c = 13.6409(2 Å, α = 89.695(1°, β = 63.049(1°, γ = 86.105(1°, V = 2191.16(5 Å3, R(F = 0.033, wR(F2 = 0.084.

Point Lepreau Refurbishment Project. Programmable digital comparator (PDC) replacement for SDS1 and SDS2 - update 1

International Nuclear Information System (INIS)

Fraser, K.G.; Ichiyen, N.M.; Condor, A.E.; Thompson, P.D.

2005-01-01

NB Power is tentatively planning to conduct an 18-month maintenance outage of the Point Lepreau Generating Station starting in April 2008. The scope of the outage was determined from the outcome of a two year study (Phase 1) involving a detailed condition assessment of the station which examined issues relating to ageing and obsolescence, along with a detailed review of Safety and Licensing issues associated with extended operation. In order to minimize schedule and regulatory risk for the Refurbishment project, pre-project work was initiated in early 2002. This program is called Phase 2 ESA (Early Start Activities). As part of the Phase 1 assessments it was concluded that replacement of the Programmable Digital Comparators for both shutdown systems was required in order to ensure operation of the plant for a further 25-30 years. Critical tasks were identified related to PDC replacement as part of the Phase 2 ESA program. This paper describes the progress of the Phase 2 ESA program as well as the planned future (Phase 2) work for the PDC replacement for both shutdown systems. (author)

The Progress in Localization Initiatives in PDC, BST

International Nuclear Information System (INIS)

Rosli Darmawan; Hasni Hassan; Anwar Abdul Rahman

2011-01-01

Nuclear Malaysia has been established since 1972. It has evolves from laying the foundation for infrastructure and human resources in nuclear technology; research and development in nuclear applications; producing new products and prototypes; and finally, transferring the products and technology to the end users such as the industry and communities. While Nuclear Malaysia has been able to develop various nuclear applications, there are areas which have been left behind. Most of the facilities and instruments for nuclear Research and Development are imported. Although Nuclear Malaysia has been able to operate and maintain the facilities, there are occasions where the foreign experts and components need to be sought for. This dependency on foreign technology has cost Nuclear Malaysia a lot, especially in the maintenance and procurement of new instruments and spare parts. To reduce this dependency, some localization initiatives have been conducted by various groups in Nuclear Malaysia. This paper discusses the recent progress and achievement of localization initiatives undertaken by PDC on the related technology which has reduced the dependency on foreign experts and technology. (author)

Identification of the para-nitrophenol catabolic pathway, and characterization of three enzymes involved in the hydroquinone pathway, in pseudomonas sp. 1-7

Directory of Open Access Journals (Sweden)

Zhang Shuangyu

2012-03-01

Full Text Available Abstract Background para-Nitrophenol (PNP, a priority environmental pollutant, is hazardous to humans and animals. However, the information relating to the PNP degradation pathways and their enzymes remain limited. Results Pseudomonas sp.1-7 was isolated from methyl parathion (MP-polluted activated sludge and was shown to degrade PNP. Two different intermediates, hydroquinone (HQ and 4-nitrocatechol (4-NC were detected in the catabolism of PNP. This indicated that Pseudomonas sp.1-7 degraded PNP by two different pathways, namely the HQ pathway, and the hydroxyquinol (BT pathway (also referred to as the 4-NC pathway. A gene cluster (pdcEDGFCBA was identified in a 10.6 kb DNA fragment of a fosmid library, which cluster encoded the following enzymes involved in PNP degradation: PNP 4-monooxygenase (PdcA, p-benzoquinone (BQ reductase (PdcB, hydroxyquinol (BT 1,2-dioxygenase (PdcC, maleylacetate (MA reductase (PdcF, 4-hydroxymuconic semialdehyde (4-HS dehydrogenase (PdcG, and hydroquinone (HQ 1,2-dioxygenase (PdcDE. Four genes (pdcDEFG were expressed in E. coli and the purified pdcDE, pdcG and pdcF gene products were shown to convert HQ to 4-HS, 4-HS to MA and MA to β-ketoadipate respectively by in vitro activity assays. Conclusions The cloning, sequencing, and characterization of these genes along with the functional PNP degradation studies identified 4-NC, HQ, 4-HS, and MA as intermediates in the degradation pathway of PNP by Pseudomonas sp.1-7. This is the first conclusive report for both 4-NC and HQ- mediated degradation of PNP by one microorganism.

Comparative study of cellular kinetics of reporter probe [{sup 131}I]FIAU in neonatal cardiac myocytes after transfer of HSV1-tk reporter gene with two vectors

Energy Technology Data Exchange (ETDEWEB)

Lan Xiaoli [Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022 (China); Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022 (China)], E-mail: lxl730724@hotmail.com; Yin Xiaohua; Wang Ruihua; Liu Ying [Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022 (China); Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022 (China); Zhang Yongxue [Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022 (China) and Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022 (China)], E-mail: zhyx1229@163.com

2009-02-15

Aim: Reporter gene imaging is a promising approach for noninvasive monitoring of cardiac gene therapy. In this study, HSV1-tk (herpes simplex virus type 1 thymidine kinase) and FIAU (2'-fluoro-2'-deoxy-1-{beta}-D-arabinofuranosyl-5-iodouracil) were used as the reporter gene and probe, respectively. Cellular uptakes of radiolabeled FIAU of neonatal rat cardiac myocytes transferred with HSV1-tk were compared between two vectors, adenovirus and liposome. The aims of this study were to choose the better vector and to provide a theoretical basis for good nuclide images. Methods: Neonatal cardiac myocytes were obtained from rat heart by single collagenase digestion. HSV1-tk inserted into adenovirus vector (recombinant adenovirus type 5, Ad5-tk) and plasmid (pDC316-tk) coated with Lipofectamine 2000 (pDC316-tk/lipoplex) were developed; thus, HSV1-tk could be transferred into neonatal cardiac myocytes. FAU (2'-fluoro-2'-deoxy-1-{beta}-D-arabinofuranosyluracil) was labeled with {sup 131}I, and the product was assessed after purification with reversed-phase Sep-Pak C-18 column. The uptake rates of [{sup 131}I]FIAU in the transferred cardiac myocytes at different times (0.5, 1, 2, 3, 4 and 5 h) were detected. Furthermore, mRNA expression and protein expression of HSV1-tk were detected by semiquantitative reverse-transcriptase polymerase chain reaction and immunocytochemistry. Results: FAU could be labeled with {sup 131}I, and the labeling efficiency and radiochemical purity rates were 53.82{+-}2.05% and 94.85{+-}1.76%, respectively. Time-dependent increase of the accumulation of [{sup 131}I]FIAU was observed in both the Ad5-tk group and the pDC316/lipoplex group, and the highest uptake rate occurred at 5 h, with peak values of 12.55{+-}0.37% and 2.09{+-}0.34%, respectively. Greater uptakes of [{sup 131}I]FIAU in Ad5-tk-infected cells compared with pDC316/lipoplex-transfected ones occurred at all the time points (t=12.978-38.253, P<.01). The exogenous gene

Modulation of phosducin-like protein 3 (PhLP3 levels promotes cytoskeletal remodelling in a MAPK and RhoA-dependent manner.

Directory of Open Access Journals (Sweden)

Nandini V L Hayes

Full Text Available Phosducin-like protein 3 (PhLP3 forms a ternary complex with the ATP-dependent molecular chaperone CCT and its folding client tubulin. In vitro studies suggest PhLP3 plays an inhibitory role in β-tubulin folding while conversely in vivo genetic studies suggest PhLP3 is required for the correct folding of β-tubulin. We have a particular interest in the cytoskeleton, its chaperones and their role in determining cellular phenotypes associated with high level recombinant protein expression from mammalian cell expression systems.As studies into PhLP3 function have been largely carried out in non mammalian systems, we examined the effect of human PhLP3 over-expression and siRNA silencing using a single murine siRNA on both tubulin and actin systems in mammalian Chinese hamster ovary (CHO cell lines. We show that over-expression of PhLP3 promotes an imbalance of α and β tubulin subunits, microtubule disassembly and cell death. In contrast, β-actin levels are not obviously perturbed. On-the-other-hand, RNA silencing of PhLP3 increases RhoA-dependent actin filament formation and focal adhesion formation and promotes a dramatic elongated fibroblast-like change in morphology. This was accompanied by an increase in phosphorylated MAPK which has been associated with promoting focal adhesion assembly and maturation. Transient overexpression of PhLP3 in knockdown experiments rescues cells from the morphological change observed during PhLP3 silencing but mitosis is perturbed, probably reflecting a tipping back of the balance of PhLP3 levels towards the overexpression state.Our results support the hypothesis that PhLP3 is important for the maintenance of β-tubulin levels in mammalian cells but also that its modulation can promote actin-based cytoskeletal remodelling by a mechanism linked with MAPK phosphorylation and RhoA-dependent changes. PhLP3 levels in mammalian cells are thus finely poised and represents a novel target for engineering industrially

Superhydrophobic photocatalytic PTFE – Titania coatings deposited by reactive pDC magnetron sputtering from a blended powder target

Energy Technology Data Exchange (ETDEWEB)

Ratova, Marina, E-mail: marina_ratova@hotmail.com; Kelly, Peter J.; West, Glen T.

2017-04-01

The production of photocatalytic coatings with superhydrophobic properties, as opposed to the conventional hydrophilic properties, is desirable for the prevention of adhesion of contaminants to photocatalytic surfaces with subsequent deterioration of photocatalytic properties. In this work polytetrafluoroethylene (PTFE) – TiO{sub 2} composite thin films were deposited using a novel method of reactive pulsed direct current (pDC) magnetron sputtering of a blended PTFE – titanium oxide powder target. The surface characteristics and photocatalytic properties of the deposited composite coatings were studied. The as-deposited coatings were annealed at 523 K in air and analysed with Raman spectroscopy, optical profilometry and scanning electron microscopy. Hydrophobicity was assessed though measurements of water contact angles, and photocatalytic properties were studied via methylene blue dye degradation under UV irradiation. It was found that variations of gas flow and, hence, process pressures allowed deposition of samples combining superhydrophobicity with stable photocatalytic efficiency under UV light irradiation. Reversible wettability behaviour was observed with the alternation of light-dark cycles. - Highlights: • PTFE-TiO{sub 2} coatings were deposited by pDC reactive magnetron sputtering. • Blended powder target was used for coatings deposition. • Deposited coatings combined superhydrophobic and photocatalytic properties. • Under UV irradiation coatings exhibited reversible wettability.

PDC 2016. Proceedings of the 14th Participatory Design Conference - Volume II

DEFF Research Database (Denmark)

Participatory Design in an Era of Participation : Introduction to volume 2 Participatory Design is a diverse collection of principles and practices aimed at making technologies, tools, environments, businesses and social institutions more responsive to human needs. A central tenet of Participatory...... is ‘Participatory Design in an Era of Participation’. Over 25 years after the first PDC in 1990, participation and co-creation have become essential features of design and research into technology. Living in an era of participation prompts critical questions around the goals and practices of involving people....... • In “Expanding the ‘How’ of Participatory Design”, five papers provide insights into techniques and methods that support novel perspectives on how participatory design activities might be practiced or reflected upon. This includes examples that should benefit practitioners and researchers who wish to think...

PDC: A wire chamber cathode read-out on 6-bit fast ADC

Energy Technology Data Exchange (ETDEWEB)

De Giorgi, M; Gasparini, F; Meneguzzo, A T; Pitacco, G [Istituto Nazionale di Fisica Nucleare, Padua (Italy); Padua Univ. (Italy). Ist. di Fisica)

1984-06-01

A read-out for MWPC and drift chamber is presented in which the coordinate along the sense wires is obtained by measuring the centre of gravity (CoG) of the charge induced on cathode strips or pads. The peak value of the signals coming from subsets of 8-pad cathodes are recorded by a parallel sample and hold, strobed by their own OR, and then serially digitized by one 6-bit fast ADC (FADC). The basic module of the system is a peak detector and converter (PDC) built in CAMAC cards, which could be an interesting approach to the analog signal acquisition of large particle detectors. The system has been designed to equip the central detector in an experiment at the CERN LEAR facility. A prototype of a card will be described and the results of some tests will be presented.

Investigations at INRIM on a Pd-C cell manufactured by NPL

Science.gov (United States)

Battuello, M.; Florio, M.; Machin, G.

2011-10-01

One of a set of metal-carbon eutectic cells (a Pd-C cell, 1765 K) manufactured by NPL and used for a previous comparison of temperature scales with NIST has been investigated at INRIM. There it was implemented in two different furnaces, namely a single- and a three-zone, and measured with a standard radiation thermometer operating at 900 nm and 950 nm. Both ITS-90 and thermodynamic melting temperatures of the cell were determined by means of an extrapolation approach. The thermodynamic temperature differs by only -0.31 K from the NIST value whereas the ITS-90 temperature differs by only -0.46 K from the NPL value. The agreements, within the combined expanded uncertainties, are particularly significant, because of the different approach followed at INRIM, namely the extrapolation of multi-fixed-point scales (n = 3 and n = 4), as compared with a direct radiometric method at NIST and an ITS-90 realization traceable to the gold point at NPL.

Mural granulosa cell gene expression associated with oocyte developmental competence

Directory of Open Access Journals (Sweden)

Jiang Jin-Yi

2010-03-01

Full Text Available Abstract Background Ovarian follicle development is a complex process. Paracrine interactions between somatic and germ cells are critical for normal follicular development and oocyte maturation. Studies have suggested that the health and function of the granulosa and cumulus cells may be reflective of the health status of the enclosed oocyte. The objective of the present study is to assess, using an in vivo immature rat model, gene expression profile in granulosa cells, which may be linked to the developmental competence of the oocyte. We hypothesized that expression of specific genes in granulosa cells may be correlated with the developmental competence of the oocyte. Methods Immature rats were injected with eCG and 24 h thereafter with anti-eCG antibody to induce follicular atresia or with pre-immune serum to stimulate follicle development. A high percentage (30-50%, normal developmental competence, NDC of oocytes from eCG/pre-immune serum group developed to term after embryo transfer compared to those from eCG/anti-eCG (0%, poor developmental competence, PDC. Gene expression profiles of mural granulosa cells from the above oocyte-collected follicles were assessed by Affymetrix rat whole genome array. Results The result showed that twelve genes were up-regulated, while one gene was down-regulated more than 1.5 folds in the NDC group compared with those in the PDC group. Gene ontology classification showed that the up-regulated genes included lysyl oxidase (Lox and nerve growth factor receptor associated protein 1 (Ngfrap1, which are important in the regulation of protein-lysine 6-oxidase activity, and in apoptosis induction, respectively. The down-regulated genes included glycoprotein-4-beta galactosyltransferase 2 (Ggbt2, which is involved in the regulation of extracellular matrix organization and biogenesis. Conclusions The data in the present study demonstrate a close association between specific gene expression in mural granulosa cells and

The Simple, Effective Synthesis of Highly Dispersed Pd/C and CoPd/C Heterogeneous Catalysts via Charge-Enhanced Dry Impregnation

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Lawrence D’Souza

2016-05-01

Full Text Available Pd/C and CoPd/C heterogeneous catalysts have been synthesized by adopting Charge Enhanced Dry Impregnation (CEDI. The particles size distribution, their high metal surface-to-bulk ratios, and synthesis feasibility are unmatchable to any known noble metal bimetallic heterogeneous catalyst preparation techniques. Next generation Fuel Cells and Fischer-Tropsch catalytic processes economy will be benefited from the proposed methodology.

Comparative Investigation on the Performance of Modified System Poles and Traditional System Poles Obtained from PDC Data for Diagnosing the Ageing Condition of Transformer Polymer Insulation Materials

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Jiefeng Liu

2018-02-01

Full Text Available The life expectancy of a transformer is largely depended on the service life of transformer polymer insulation materials. Nowadays, several papers have reported that the traditional system poles obtained from polarization and depolarization current (PDC data can be used to assess the condition of transformer insulation systems. However, the traditional system poles technique only provides limited ageing information for transformer polymer insulation. In this paper, the modified system poles obtained from PDC data are proposed to assess the ageing condition of transformer polymer insulation. The aim of the work is to focus on reporting a comparative investigation on the performance of modified system poles and traditional system poles for assessing the ageing condition of a transformer polymer insulation system. In the present work, a series of experiments have been performed under controlled laboratory conditions. The PDC measurement data, degree of polymerization (DP and moisture content of the oil-immersed polymer pressboard specimens were carefully monitored. It is observed that, compared to the relationships between traditional system poles and DP values, there are better correlations between the modified system poles and DP values, because the modified system poles can obtain much more ageing information on transformer polymer insulation. Therefore, the modified system poles proposed in the paper are more suitable for the diagnosis of the ageing condition of transformer polymer insulation.

The experimental study of reporter probe 131I-FIAU in neonatal cardiac myocytes after transfer of herpes simplex virus type 1 thymidine kinase reporter gene by different vectors

International Nuclear Information System (INIS)

Yin Xiaohua; Lan Xiaoli; Wang Ruihua; Liu Ying; Zhang Yongxue

2009-01-01

Objective: Reporter gene imaging is a promising approach for noninvasive monitoring of cardiac gene therapy. In the present study, the recombinant plasmid and adenoviral vector carrying reporter gene. herpes simplex virus type 1 thymidine kinase (HSV1-tk), were constructed and transferred into nee-natal cardiac myocytes, and a series of in vitro studies were carried out on the cells transferred to evaluate the uptake of radiolabeled reporter probe and to compare both vectors for cardiac reporter gene imaging. Methods: Neonatal cardiac myocytes were obtained from rat heart by single collagenase digestion. HSVI-tk. chosen as the reporter gene.was inserted into adenovirus vector (Ad5-tk) and plasmid (pDC316-tk), thus it could be transferred into neonatal cardiac myocytes. Recombinant adenovirus containing enhanced green fluorescent protein (Ad5-EGFP) was used as control. Recombinant plasmid was coated with lipofectamine TM 2000 (pDC316-tk/lipoplex). The specific reporter probe of HSV1-tk, 2'-fluoro-2'-deoxy-l-β-D-arabinofuranosyl-uracil (FAU), was labeled with 131 I by solid phase oxidation with lodogen. Product wag purified on a reverse. phase Sep-Pak C18 column and the radiochemical purity wag then assessed. The accumulation of it in the transferred cardiac myocytes wag detected as uptake rate. Furthermore, mRNA expression of HSV1-tk was detected by semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR), while its protein expression wag located by immunocytochemistry. Results: FAU could be labeled with 131 I and the labeling efficiency was (53.82 ±2.05)%. The radiochemical purity was (94.85 ± 1.76)% after purification, and it kept stable in vitro for at least 24h. Time-dependent increase of the ac- cumulation of 131 I-FIAU was observed in both Ad5-tk group and pDC316-tk/lipoplex group. and the highest uptake rate occurred at 5h, with peak values of (12.55 ± 0.37)% and (2.09 ± 0.34)% respectively. However, it also indicated that greater

Reação de bis-inserção de 1,2-difenilacetileno na ligação Pd-C de ciclometalados Bis insertion reaction of 1,2-diphenylacetilene into Pd-C bond of cyclometallated species

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Sandra Regina Ananias

2003-01-01

Full Text Available The present paper deals with the bis-insertion reactions of 1,2-diphenylacetylene into Pd-C bond of the cyclopalladated complexes [Pd(dmba(µ-NCO]2 (1 and [Pd(dmba(MeCN2](NO3 (2 (dmba = N,N-dimethylbenzylamine, MeCN = acetonitrile. Two new complexes [Pd{PhC=CPh-CPh=CPhC6H4CH2N(CH 32}(NCO] (3 and [Pd{PhC=CPh-CPh=CPhC6H4CH2N(CH 32}(NO3 ] (4 were obtained and characterized by IR and NMR spectroscopy and elemental analysis.

Identification of target genes to control acetate yield during aerobic fermentation with Saccharomyces cerevisiae.

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Curiel, José Antonio; Salvadó, Zoel; Tronchoni, Jordi; Morales, Pilar; Rodrigues, Alda Joao; Quirós, Manuel; Gonzalez, Ramón

2016-09-15

Aerobic fermentation of grape must, leading to respiro-fermentative metabolism of sugars, has been proposed as way of reducing alcohol content in wines. Two factors limit the usefulness of Saccharomyces cerevisiae for this application, the Crabtree effect, and excess volatile acidity under aerobic conditions. This work aimed to explore the impact on ethanol acetate production of different S. cerevisiae strains deleted for genes previously related with the Crabtree phenotype. Recombinant strains were constructed on a wine industrial genetic background, FX10. All yeast strains, including FX10, showed respiro-fermentative metabolism in natural grape must under aerobic conditions, as well as a concomitant reduction in ethanol yield. This indicates that the Crabtree effect is not a major constrain for reaching relevant respiration levels in grape must. Indeed, only minor differences in ethanol yield were observed between the original and some of the recombinant strains. In contrast, some yeast strains showed a relevant reduction of acetic acid production. This was identified as a positive feature for the feasibility of alcohol level reduction by respiration. Reduced acetic acid production was confirmed by a thorough analysis of these and some additional deletion strains (involving genes HXK2, PYK1, REG1, PDE2 and PDC1). Some recombinant yeasts showed altered production of glycerol and pyruvate derived metabolites. REG1 and PDC1 deletion strains showed a strong reduction of acetic acid yield in aerobic fermentations. Since REG1 defective strains may be obtained by non-GMO approaches, these gene modifications show good promise to help reducing ethanol content in wines.

Reference: 34 [Arabidopsis Phenome Database[Archive

Lifescience Database Archive (English)

Full Text Available al gene in different tissues, under normal growth conditions, and when the plants were subjected to anoxia or other environmental...e1 gene of Arabidopsis is required during anoxia but not other environmental stre...ronmental stresses. We also characterize the expression of the aldehyde dehydrogena...ed under oxygen limitation among the PDC1 gene family and that a pdc1 null mutant is comprised in anoxia tolerance but not other envi

Analysis of gene expression and proteomic profiles of clonal genotypes from Theobroma cacao subjected to soil flooding.

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Bertolde, Fabiana Z; Almeida, Alex-Alan F; Pirovani, Carlos P

2014-01-01

Soil flooding causes changes in gene transcription, synthesis and degradation of proteins and cell metabolism. The main objective of this study was to understand the biological events of Theobroma cacao during soil flooding-induced stress, using the analyses of gene expression and activity of key enzymes involved in fermentation, as well as the identification of differentially expressed proteins by mass spectrometry in two contrasting genotypes for flooding tolerance (tolerant - TSA-792 and susceptible - TSH-774). Soil anoxia caused by flooding has led to changes in the expression pattern of genes associated with the biosynthesis of alcohol dehydrogenase (ADH), pyruvate decarboxylase (PDC) and lactate dehydrogenase (LDH) in leaves and roots of the two evaluated genotypes. Significant differences were observed between the enzyme activities of the two genotypes. Leaves and roots of the TSA-792 genotype showed higher ADH activity as compared to the TSH-774 genotype, whereas the activities of PDC and LDH have varied over the 96 h of soil flooding, being higher for TSA-792 genotype, at the initial stage, and TSH-774 genotype, at the final stage. Some of the identified proteins are those typical of the anaerobic metabolism-involved in glycolysis and alcoholic fermentation-and different proteins associated with photosynthesis, protein metabolism and oxidative stress. The ability to maintain glycolysis and induce fermentation was observed to play an important role in anoxia tolerance in cacao and may also serve to distinguish tolerant and susceptible genotypes in relation to this stressor.

Highly efficient transduction of human plasmacytoid dendritic cells without phenotypic and functional maturation

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Plumas Joel

2009-01-01

Full Text Available Abstract Background Gene modified dendritic cells (DC are able to modulate DC functions and induce therapeutic immunity or tolerance in an antigen-specific manner. Among the different DC subsets, plasmacytoid DC (pDC are well known for their ability to recognize and respond to a variety of viruses by secreting high levels of type I interferon. Methods We analyzed here, the transduction efficiency of a pDC cell line, GEN2.2, and of pDC derived from CD34+ progenitors, using lentiviral vectors (LV pseudotyped with different envelope glycoproteins such as the vesicular stomatitis virus envelope (VSVG, the gibbon ape leukaemia virus envelope (GaLV or the feline endogenous virus envelope (RD114. At the same time, we evaluated transgene expression (E-GFP reporter gene under the control of different promoters. Results We found that efficient gene transfer into pDC can be achieved with VSVG-pseudotyped lentiviral vectors (LV under the control of phoshoglycerate kinase (PGK and elongation factor-1 (EF1α promoters (28% to 90% of E-GFP+ cells, respectively in the absence of phenotypic and functional maturation. Surprisingly, promoters (desmin or synthetic C5–12 described as muscle-specific and which drive gene expression in single strand AAV vectors in gene therapy protocols were very highly active in pDC using VSVG-LV. Conclusion Taken together, our results indicate that LV vectors can serve to design pDC-based vaccines in humans, and they are also useful in vitro to evaluate the immunogenicity of the vector preparations, and the specificity and safety of given promoters used in gene therapy protocols.

[Discovery of the target genes inhibited by formic acid in Candida shehatae].

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Cai, Peng; Xiong, Xujie; Xu, Yong; Yong, Qiang; Zhu, Junjun; Shiyuan, Yu

2014-01-04

At transcriptional level, the inhibitory effects of formic acid was investigated on Candida shehatae, a model yeast strain capable of fermenting xylose to ethanol. Thereby, the target genes were regulated by formic acid and the transcript profiles were discovered. On the basis of the transcriptome data of C. shehatae metabolizing glucose and xylose, the genes responsible for ethanol fermentation were chosen as candidates by the combined method of yeast metabolic pathway analysis and manual gene BLAST search. These candidates were then quantitatively detected by RQ-PCR technique to find the regulating genes under gradient doses of formic acid. By quantitative analysis of 42 candidate genes, we finally identified 10 and 5 genes as markedly down-regulated and up-regulated targets by formic acid, respectively. With regard to gene transcripts regulated by formic acid in C. shehatae, the markedly down-regulated genes ranking declines as follows: xylitol dehydrogenase (XYL2), acetyl-CoA synthetase (ACS), ribose-5-phosphate isomerase (RKI), transaldolase (TAL), phosphogluconate dehydrogenase (GND1), transketolase (TKL), glucose-6-phosphate dehydrogenase (ZWF1), xylose reductase (XYL1), pyruvate dehydrogenase (PDH) and pyruvate decarboxylase (PDC); and a declining rank for up-regulated gens as follows: fructose-bisphosphate aldolase (ALD), glucokinase (GLK), malate dehydrogenase (MDH), 6-phosphofructokinase (PFK) and alcohol dehydrogenase (ADH).

A novel method for synthesis of phosphomolybdic acid-modified Pd/C catalysts for oxygen reduction reaction

Science.gov (United States)

Zhu, Mingyuan; Gao, Xiaoling; Luo, Guangqin; Dai, Bin

2013-03-01

This manuscript reports a convenient method for immobilizing phosphomolybdic acid (HPMo) on polyaniline (PAN-) functionalized carbon supports. The obtained HPMo-PAN-C sample is used as the support to prepare a Pd/HPMo-PAN-C catalyst. The samples are characterized by Fourier transform infrared spectroscopy, transmission electron microscopy and X-ray diffraction analysis. The results suggest that HPMo retains its Keggin structure and that the presence of HPMo reduces the average particle size of the Pd nano-particles in the obtained Pd/HPMo-PAN-C catalyst. Electro-chemical measurements in 0.5 M HClO4 solution reveal that the Pd/HPMo-PAN-C catalyst has higher catalytic activity for oxygen reduction reactions than does a Pd/C catalyst prepared using a similar procedure. The stability of the Pd/HPMo-PAN-C catalyst is evaluated by multiple-cycle voltammetry techniques; the mass catalytic activity decreases by only 10% after 100 scanning cycles.

Adaptive mutations in sugar metabolism restore growth on glucose in a pyruvate decarboxylase negative yeast strain

DEFF Research Database (Denmark)

Zhang, Yiming; Liu, Guodong; Engqvist, Martin K. M.

2015-01-01

Background: A Saccharomyces cerevisiae strain carrying deletions in all three pyruvate decarboxylase (PDC) genes (also called Pdc negative yeast) represents a non-ethanol producing platform strain for the production of pyruvate derived biochemicals. However, it cannot grow on glucose as the sole...... DNA sequencing. Among these genetic changes, 4 genes were found to carry point mutations in at least two of the evolved strains: MTH1 encoding a negative regulator of the glucose-sensing signal transduction pathway, HXT2 encoding a hexose transporter, CIT1 encoding a mitochondrial citrate synthase...... further increased the maximum specific growth rate to 0.069 h-1. Conclusions: In this study, possible evolving mechanisms of Pdc negative strains on glucose were investigated by genome sequencing and reverse engineering. The non-synonymous mutations in MTH1 alleviated the glucose repression by repressing...

‘Hummingbird’ Sign in a Patient with Guam Parkinsonism-Dementia Complex

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Tianrong Yeo

2017-09-01

Full Text Available We present a case of a 71-year-old male Chamorro patient from Guam who presented with progressive supranuclear palsy (PSP-Richardson’s syndrome. Considering his strong family history of parkinsonism and a PSP phenotype, he was clinically diagnosed with Guam parkinsonism-dementia complex (PDC. Magnetic resonance imaging (MRI of the brain revealed prominent midbrain atrophy with preserved pontine volume, forming the ‘hummingbird’ sign, which has not been described before in Guam PDC. Molecular analysis of the chromosome 9 open reading frame 72 gene (C9orf72 showed only 6 GGGGCC repeats. We discuss the clinico-pathological similarities and differences between PSP and Guam PDC, and highlight the topography of neuropathological changes seen in Guam PDC to explain the appearance of the ‘hummingbird’ sign on MRI.

Recognition of Aspergillus fumigatus hyphae by human plasmacytoid dendritic cells is mediated by dectin-2 and results in formation of extracellular traps.

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Loures, Flávio V; Röhm, Marc; Lee, Chrono K; Santos, Evelyn; Wang, Jennifer P; Specht, Charles A; Calich, Vera L G; Urban, Constantin F; Levitz, Stuart M

2015-02-01

Plasmacytoid dendritic cells (pDCs) were initially considered as critical for innate immunity to viruses. However, our group has shown that pDCs bind to and inhibit the growth of Aspergillus fumigatus hyphae and that depletion of pDCs renders mice hypersusceptible to experimental aspergillosis. In this study, we examined pDC receptors contributing to hyphal recognition and downstream events in pDCs stimulated by A. fumigatus hyphae. Our data show that Dectin-2, but not Dectin-1, participates in A. fumigatus hyphal recognition, TNF-α and IFN-α release, and antifungal activity. Moreover, Dectin-2 acts in cooperation with the FcRγ chain to trigger signaling responses. In addition, using confocal and electron microscopy we demonstrated that the interaction between pDCs and A. fumigatus induced the formation of pDC extracellular traps (pETs) containing DNA and citrullinated histone H3. These structures closely resembled those of neutrophil extracellular traps (NETs). The microarray analysis of the pDC transcriptome upon A. fumigatus infection also demonstrated up-regulated expression of genes associated with apoptosis as well as type I interferon-induced genes. Thus, human pDCs directly recognize A. fumigatus hyphae via Dectin-2; this interaction results in cytokine release and antifungal activity. Moreover, hyphal stimulation of pDCs triggers a distinct pattern of pDC gene expression and leads to pET formation.

Recognition of Aspergillus fumigatus hyphae by human plasmacytoid dendritic cells is mediated by dectin-2 and results in formation of extracellular traps.

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Flávio V Loures

2015-02-01

Full Text Available Plasmacytoid dendritic cells (pDCs were initially considered as critical for innate immunity to viruses. However, our group has shown that pDCs bind to and inhibit the growth of Aspergillus fumigatus hyphae and that depletion of pDCs renders mice hypersusceptible to experimental aspergillosis. In this study, we examined pDC receptors contributing to hyphal recognition and downstream events in pDCs stimulated by A. fumigatus hyphae. Our data show that Dectin-2, but not Dectin-1, participates in A. fumigatus hyphal recognition, TNF-α and IFN-α release, and antifungal activity. Moreover, Dectin-2 acts in cooperation with the FcRγ chain to trigger signaling responses. In addition, using confocal and electron microscopy we demonstrated that the interaction between pDCs and A. fumigatus induced the formation of pDC extracellular traps (pETs containing DNA and citrullinated histone H3. These structures closely resembled those of neutrophil extracellular traps (NETs. The microarray analysis of the pDC transcriptome upon A. fumigatus infection also demonstrated up-regulated expression of genes associated with apoptosis as well as type I interferon-induced genes. Thus, human pDCs directly recognize A. fumigatus hyphae via Dectin-2; this interaction results in cytokine release and antifungal activity. Moreover, hyphal stimulation of pDCs triggers a distinct pattern of pDC gene expression and leads to pET formation.

Modeling and Fuzzy PDC Control and Its Application to an Oscillatory TLP Structure

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Cheng-Wu Chen

2010-01-01

Full Text Available An analytical solution is derived to describe the wave-induced flow field and surge motion of a deformable platform structure controlled with fuzzy controllers in an oceanic environment. In the controller design procedure, a parallel distributed compensation (PDC scheme is utilized to construct a global fuzzy logic controller by blending all local state feedback controllers. The Lyapunov method is used to carry out stability analysis of a real system structure. The corresponding boundary value problems are then incorporated into scattering and radiation problems. These are analytically solved, based on the separation of variables, to obtain a series of solutions showing the harmonic incident wave motion and surge motion. The dependence of the wave-induced flow field and its resonant frequency on wave characteristics and structural properties including platform width, thickness and mass can thus be drawn with a parametric approach. The wave-induced displacement of the surge motion is determined from these mathematical models. The vibration of the floating structure and mechanical motion caused by the wave force are also discussed analytically based on fuzzy logic theory and the mathematical framework to find the decay in amplitude of the surge motion in the tension leg platform (TLP system. The expected effects of the damping in amplitude of the surge motion due to the control force on the structural response are obvious.

Dendritic cell fate is determined by BCL11A

Science.gov (United States)

Ippolito, Gregory C.; Dekker, Joseph D.; Wang, Yui-Hsi; Lee, Bum-Kyu; Shaffer, Arthur L.; Lin, Jian; Wall, Jason K.; Lee, Baeck-Seung; Staudt, Louis M.; Liu, Yong-Jun; Iyer, Vishwanath R.; Tucker, Haley O.

2014-01-01

The plasmacytoid dendritic cell (pDC) is vital to the coordinated action of innate and adaptive immunity. pDC development has not been unequivocally traced, nor has its transcriptional regulatory network been fully clarified. Here we confirm an essential requirement for the BCL11A transcription factor in fetal pDC development, and demonstrate this lineage-specific requirement in the adult organism. Furthermore, we identify BCL11A gene targets and provide a molecular mechanism for its action in pDC commitment. Embryonic germ-line deletion of Bcl11a revealed an absolute cellular, molecular, and functional absence of pDCs in fetal mice. In adults, deletion of Bcl11a in hematopoietic stem cells resulted in perturbed yet continued generation of progenitors, loss of downstream pDC and B-cell lineages, and persisting myeloid, conventional dendritic, and T-cell lineages. Challenge with virus resulted in a marked reduction of antiviral response in conditionally deleted adults. Genome-wide analyses of BCL11A DNA binding and expression revealed that BCL11A regulates transcription of E2-2 and other pDC differentiation modulators, including ID2 and MTG16. Our results identify BCL11A as an essential, lineage-specific factor that regulates pDC development, supporting a model wherein differentiation into pDCs represents a primed “default” pathway for common dendritic cell progenitors. PMID:24591644

Beneficial effect of feeding a ketogenic diet to mothers on brain development in their progeny with a murine model of pyruvate dehydrogenase complex deficiency.

Science.gov (United States)

Pliss, Lioudmila; Jatania, Urvi; Patel, Mulchand S

2016-06-01

Pyruvate dehydrogenase complex (PDC) deficiency is a major inborn error of oxidative metabolism of pyruvate in the mitochondria causing congenital lactic acidosis and primarily structural and functional abnormalities of the central nervous system. To provide an alternate source of acetyl-CoA derived from ketone bodies to the developing brain, a formula high in fat content is widely employed as a treatment. In the present study we investigated efficacy of a high-fat diet given to mothers during pregnancy and lactation on lessening of the impact of PDC deficiency on brain development in PDC-deficient female progeny. A murine model of systemic PDC deficiency by interrupting the X-linked Pdha1 gene was employed in this study. Maternal consumption of a high-fat diet during pregnancy and lactation had no effect on number of live-birth, body growth, tissue PDC activity levels, as well as the in vitro rates of glucose oxidation and fatty acid biosynthesis by the developing brain of PDC-deficient female offspring during the postnatal age 35 days, as compared to the PDC-deficient progeny born to dams on a chow diet. Interestingly, brain weight was normalized in PDC-deficient progeny of high fat-fed mothers with improvement in impairment in brain structure deficit whereas brain weight was significantly decreased and was associated with greater cerebral structural defects in progeny of chow-fed mothers as compared to control progeny of mothers fed either a chow or high fat diet. The findings provide for the first time experimental support for beneficial effects of a ketogenic diet during the prenatal and early postnatal periods on the brain development of PDC-deficient mammalian progeny.

Increased superoxide accumulation in pyruvate dehydrogenase complex deficient fibroblasts.

Science.gov (United States)

Glushakova, Lyudmyla G; Judge, Sharon; Cruz, Alex; Pourang, Deena; Mathews, Clayton E; Stacpoole, Peter W

2011-11-01

The pyruvate dehydrogenase complex (PDC) oxidizes pyruvate to acetyl CoA and is critically important in maintaining normal cellular energy homeostasis. Loss-of-function mutations in PDC give rise to congenital lactic acidosis and to progressive cellular energy failure. However, the subsequent biochemical consequences of PDC deficiency that may contribute to the clinical manifestations of the disorder are poorly understood. We postulated that altered flux through PDC would disrupt mitochondrial electron transport, resulting in oxidative stress. Compared to cells from 4 healthy subjects, primary cultures of skin fibroblasts from 9 patients with variable mutations in the gene encoding the alpha subunit (E1α) of pyruvate dehydrogenase (PDA1) demonstrated reduced growth and viability. Superoxide (O(2)(.-)) from the Qo site of complex III of the electron transport chain accumulated in these cells and was associated with decreased activity of manganese superoxide dismutase. The expression of uncoupling protein 2 was also decreased in patient cells, but there were no significant changes in the expression of cellular markers of protein or DNA oxidative damage. The expression of hypoxia transcription factor 1 alpha (HIF1α) also increased in PDC deficient fibroblasts. We conclude that PDC deficiency is associated with an increase in O(2)(.-) accumulation coupled to a decrease in mechanisms responsible for its removal. Increased HIF1α expression may contribute to the increase in glycolytic flux and lactate production in PDC deficiency and, by trans-activating pyruvate dehydrogenase kinase, may further suppress residual PDC activity through phosphorylation of the E1α subunit. Copyright © 2011 Elsevier Inc. All rights reserved.

Use of Different Furnaces to Study Repeatability and Reproducibility of Three Pd-C Cells

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Battuello, M.; Florio, M.; Girard, F.

2010-09-01

Three different Pd-C eutectic fixed-point cells were prepared and investigated at INRIM. Several tens of phase transition runs were carried out and recorded with both a Si-based radiation thermometer at 950 nm and a precision InGaAs-based thermometer at 1.6 μm. Two of the cells were of the same design with an inner volume of 12 cm3. The third one was smaller with a useful inner volume of 3.6 cm3. The three cells were filled with palladium powder 4N5 or 4N8 pure and graphite powder 6N pure. The repeatability and stability of the inflection point were investigated over a period of 1 year. The noticeably different external dimensions of the two cells, namely, 110 mm and 40 mm in length, allowed the influence of the longitudinal temperature distribution to be investigated. For this purpose, two different furnaces, a single-zone with SiC heaters and a three-zone with MoSi2 heaters, were used. Different operative conditions, namely, temperature steps, melting rate, longitudinal temperature distributions, and position of cells within the furnace, were tested to investigate the reproducibility of the cells. Effects on the duration and shape of the plateaux were also studied. This article gives details of the measurement setup and analyses of the melting plateaux obtained with the different conditions.

Voltage Oscillations in a Polymer Electrolyte Membrane Fuel Cell with Pd-Pt/C and Pd/C Anodes.

Science.gov (United States)

Nogueira, Jéssica Alves; Varela, Hamilton

2017-10-01

Polymer electrolyte membrane fuel cells (PEMFC) fed with H 2 contaminated with CO may exhibit oscillatory behavior when operated galvanostatically. The self-organization of the anodic overpotential is interesting because it can be accompanied by an increase in the average performance. Herein we report experimental studies of voltage oscillations that emerge in a PEMFC equipped with a Pd/C or PdPt/C anode and fed with H 2 contaminated with CO (100 ppm). We used on-line mass spectrometry to investigate how the mass fragments associated with CO 2 and CO ( m / z 44 and 28, respectively) varied with the voltage oscillations. Overall, we observed that oscillations in the anodic overpotential are in phase with that of the CO and CO 2 signals. This fact is consistent with an autonomous adsorption-oxidation cyclic process. For both anodes, it has been observed that, in general, an increase in current density implies an increase in oscillatory frequency. By using CO stripping, we also discuss how the onset of CO oxidation is related to the maximum overpotential reached during a cycle, whereas the minimum overpotential can be associated with the catalytic activity of the electrode for H 2 oxidation.

Overexpression of pyruvate decarboxylase in the yeast Hansenula polymorpha results in increased ethanol yield in high-temperature fermentation of xylose.

Science.gov (United States)

Ishchuk, Olena P; Voronovsky, Andriy Y; Stasyk, Oleh V; Gayda, Galina Z; Gonchar, Mykhailo V; Abbas, Charles A; Sibirny, Andriy A

2008-11-01

Improvement of xylose fermentation is of great importance to the fuel ethanol industry. The nonconventional thermotolerant yeast Hansenula polymorpha naturally ferments xylose to ethanol at high temperatures (48-50 degrees C). Introduction of a mutation that impairs ethanol reutilization in H. polymorpha led to an increase in ethanol yield from xylose. The native and heterologous (Kluyveromyces lactis) PDC1 genes coding for pyruvate decarboxylase were expressed at high levels in H. polymorpha under the control of the strong constitutive promoter of the glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH). This resulted in increased pyruvate decarboxylase activity and improved ethanol production from xylose. The introduction of multiple copies of the H. polymorpha PDC1 gene driven by the strong constitutive promoter led to a 20-fold increase in pyruvate decarboxylase activity and up to a threefold elevation of ethanol production.

Rewiring Lactococcus lactis for Ethanol Production

DEFF Research Database (Denmark)

Solem, Christian; Dehli, Tore Ibsen; Jensen, Peter Ruhdal

2013-01-01

to redirect the metabolism of LAB model organism Lactococcus lactis toward ethanol production. Codon-optimized Zymomonas mobilis pyruvate decarboxylase (PDC) was introduced and expressed from synthetic promoters in different strain backgrounds. In the wild-type L. lactis strain MG1363 growing on glucose, only...... small amounts of ethanol were obtained after introducing PDC, probably due to a low native alcohol dehydrogenase activity. When the same strains were grown on maltose, ethanol was the major product and lesser amounts of lactate, formate, and acetate were formed. Inactivating the lactate dehydrogenase...... genes ldhX, ldhB, and ldh and introducing codon-optimized Z. mobilis alcohol dehydrogenase (ADHB) in addition to PDC resulted in high-yield ethanol formation when strains were grown on glucose, with only minor amounts of by-products formed. Finally, a strain with ethanol as the sole observed...

Regulation of pyruvate dehydrogenase kinase expression by the farnesoid X receptor

International Nuclear Information System (INIS)

Savkur, Rajesh S.; Bramlett, Kelli S.; Michael, Laura F.; Burris, Thomas P.

2005-01-01

The pyruvate dehydrogenase complex (PDC) functions as an important junction in intermediary metabolism by influencing the utilization of fat versus carbohydrate as a source of fuel. Activation of PDC is achieved by phosphatases, whereas, inactivation is catalyzed by pyruvate dehydrogenase kinases (PDKs). The expression of PDK4 is highly regulated by the glucocorticoid and peroxisome proliferator-activated receptors. We demonstrate that the farnesoid X receptor (FXR; NR1H4), which regulates a variety of genes involved in lipoprotein metabolism, also regulates the expression of PDK4. Treatment of rat hepatoma cells as well as human primary hepatocytes with FXR agonists stimulates the expression of PDK4 to levels comparable to those obtained with glucocorticoids. In addition, treatment of mice with an FXR agonist significantly increased hepatic PDK4 expression, while concomitantly decreasing plasma triglyceride levels. Thus, activation of FXR may suppress glycolysis and enhance oxidation of fatty acids via inactivation of the PDC by increasing PDK4 expression

Starmerella bombicola influences the metabolism of Saccharomyces cerevisiae at pyruvate decarboxylase and alcohol dehydrogenase level during mixed wine fermentation

Science.gov (United States)

2012-01-01

Background The use of a multistarter fermentation process with Saccharomyces cerevisiae and non-Saccharomyces wine yeasts has been proposed to simulate natural must fermentation and to confer greater complexity and specificity to wine. In this context, the combined use of S. cerevisiae and immobilized Starmerella bombicola cells (formerly Candida stellata) was assayed to enhance glycerol concentration, reduce ethanol content and to improve the analytical composition of wine. In order to investigate yeast metabolic interaction during controlled mixed fermentation and to evaluate the influence of S. bombicola on S. cerevisiae, the gene expression and enzymatic activity of two key enzymes of the alcoholic fermentation pathway such as pyruvate decarboxylase (Pdc1) and alcohol dehydrogenase (Adh1) were studied. Results The presence of S. bombicola immobilized cells in a mixed fermentation trial confirmed an increase in fermentation rate, a combined consumption of glucose and fructose, an increase in glycerol and a reduction in the production of ethanol as well as a modification in the fermentation of by products. The alcoholic fermentation of S. cerevisiae was also influenced by S. bombicola immobilized cells. Indeed, Pdc1 activity in mixed fermentation was lower than that exhibited in pure culture while Adh1 activity showed an opposite behavior. The expression of both PDC1 and ADH1 genes was highly induced at the initial phase of fermentation. The expression level of PDC1 at the end of fermentation was much higher in pure culture while ADH1 level was similar in both pure and mixed fermentations. Conclusion In mixed fermentation, S. bombicola immobilized cells greatly affected the fermentation behavior of S. cerevisiae and the analytical composition of wine. The influence of S. bombicola on S. cerevisiae was not limited to a simple additive contribution. Indeed, its presence caused metabolic modifications during S. cerevisiae fermentation causing variation in the gene

Starmerella bombicola influences the metabolism of Saccharomyces cerevisiae at pyruvate decarboxylase and alcohol dehydrogenase level during mixed wine fermentation

Directory of Open Access Journals (Sweden)

Milanovic Vesna

2012-02-01

Full Text Available Abstract Background The use of a multistarter fermentation process with Saccharomyces cerevisiae and non-Saccharomyces wine yeasts has been proposed to simulate natural must fermentation and to confer greater complexity and specificity to wine. In this context, the combined use of S. cerevisiae and immobilized Starmerella bombicola cells (formerly Candida stellata was assayed to enhance glycerol concentration, reduce ethanol content and to improve the analytical composition of wine. In order to investigate yeast metabolic interaction during controlled mixed fermentation and to evaluate the influence of S. bombicola on S. cerevisiae, the gene expression and enzymatic activity of two key enzymes of the alcoholic fermentation pathway such as pyruvate decarboxylase (Pdc1 and alcohol dehydrogenase (Adh1 were studied. Results The presence of S. bombicola immobilized cells in a mixed fermentation trial confirmed an increase in fermentation rate, a combined consumption of glucose and fructose, an increase in glycerol and a reduction in the production of ethanol as well as a modification in the fermentation of by products. The alcoholic fermentation of S. cerevisiae was also influenced by S. bombicola immobilized cells. Indeed, Pdc1 activity in mixed fermentation was lower than that exhibited in pure culture while Adh1 activity showed an opposite behavior. The expression of both PDC1 and ADH1 genes was highly induced at the initial phase of fermentation. The expression level of PDC1 at the end of fermentation was much higher in pure culture while ADH1 level was similar in both pure and mixed fermentations. Conclusion In mixed fermentation, S. bombicola immobilized cells greatly affected the fermentation behavior of S. cerevisiae and the analytical composition of wine. The influence of S. bombicola on S. cerevisiae was not limited to a simple additive contribution. Indeed, its presence caused metabolic modifications during S. cerevisiae fermentation

Extended causal modeling to assess Partial Directed Coherence in multiple time series with significant instantaneous interactions.

Science.gov (United States)

Faes, Luca; Nollo, Giandomenico

2010-11-01

The Partial Directed Coherence (PDC) and its generalized formulation (gPDC) are popular tools for investigating, in the frequency domain, the concept of Granger causality among multivariate (MV) time series. PDC and gPDC are formalized in terms of the coefficients of an MV autoregressive (MVAR) model which describes only the lagged effects among the time series and forsakes instantaneous effects. However, instantaneous effects are known to affect linear parametric modeling, and are likely to occur in experimental time series. In this study, we investigate the impact on the assessment of frequency domain causality of excluding instantaneous effects from the model underlying PDC evaluation. Moreover, we propose the utilization of an extended MVAR model including both instantaneous and lagged effects. This model is used to assess PDC either in accordance with the definition of Granger causality when considering only lagged effects (iPDC), or with an extended form of causality, when we consider both instantaneous and lagged effects (ePDC). The approach is first evaluated on three theoretical examples of MVAR processes, which show that the presence of instantaneous correlations may produce misleading profiles of PDC and gPDC, while ePDC and iPDC derived from the extended model provide here a correct interpretation of extended and lagged causality. It is then applied to representative examples of cardiorespiratory and EEG MV time series. They suggest that ePDC and iPDC are better interpretable than PDC and gPDC in terms of the known cardiovascular and neural physiologies.

Effect of the nanosized TiO2 particles in Pd/C catalysts as cathode materials in direct methanol fuel cells.

Science.gov (United States)

Choi, Mahnsoo; Han, Choonsoo; Kim, In-Tae; Lee, Ji-Jung; Lee, Hong-Ki; Shim, Joongpyo

2011-07-01

Pd-TiO2/C catalysts were prepared by impregnating titanium dioxide (TiO2) on carbon-supported Pd (Pd/C) for use as the catalyst for the oxygen reduction reaction (ORR) in direct methanol fuel cells (DMFCs). Transmission electron microscope (TEM), scanning electron microscope (SEM) and X-ray diffraction (XRD) analyses were carried to confirm the distribution, morphology and structure of Pd and TiO2 on the carbon support. In fuel cell test, we confirmed that the addition of TiO2 nanoparticles make the improved catalytic activity of oxygen reduction. The electrochemical characterization of the Pd-TiO2/C catalyst for the ORR was carried out by cyclic voltammetry (CV) in the voltage window of 0.04 V to 1.2 V with scan rate of 25 mV/s. With the increase in the crystallite size of TiO2, the peak potential for OH(ads) desorption on the surface of Pd particle shifted to higher potential. This implies that TiO2 might affect the adsorption and desorption of oxygen molecules on Pd catalyst. The performance of Pd-TiO2/C as a cathode material was found to be similar to or better performance than that of Pt/C.

Both AtrbohD and AtrbohF are essential for mediating responses to oxygen deficiency in Arabidopsis.

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Liu, Bo; Sun, Lirong; Ma, Liya; Hao, Fu-Shun

2017-06-01

Both AtrbohD and AtrbohF promote the increases in activities of ADH, PDC, LDH, and Ca 2+ levels, and induce the expression of multiple hypoxia response genes, thus improving Arabidopsis adaptation to oxygen deficiency. NADPH oxidase AtrbohD and AtrbohF cooperatively play key roles in regulation of growth and stress signaling in Arabidopsis. However, reports on AtrbohD and AtrbohF functioning together in hypoxia signaling are scarce, and the underlying mechanisms remain elusive. Here, we show that the double null mutant atrbohD/F is more sensitive to oxygen deprivation compared with wild type (WT) and the single mutant atrbohD and atrbohF. Under oxygen deficiency, enhancements of the transcripts of alcohol dehydrogenase 1 (ADH1) and pyruvate decarboxylase 1 (PDC1) and the activities of ADH, PDC and lactate dehydrogenase in WT are clearly reduced in the single mutants, and more strongly reduced in the double mutant. Moreover, increases in the production of ATP, H 2 O 2 and Ca 2+ in WT are significantly arrested in atrbohD, atrbohF, and especially in atrbohD/F. Hypoxia-promoted rise in the expression of some hypoxic responsive genes is also inhibited in atrbohD/F relative to WT, atrbohD and atrbohF. These genes include ethylene response factor 73, lactate dehydrogenase, MYB transcription factor 2, sucrose synthase 1 (SUS1), SUS4, heat stress transcription factor A2 and heat-shock protein 18.2. These results suggest that both AtrbohD and AtrbohF are essential for mediating hypoxia signaling. H 2 O 2 derived from AtrbohD and AtrbohF triggers the Ca 2+ increase and induces the expression of multiple hypoxia response genes, thus improving Arabidopsis tolerance to low-oxygen stress. These findings provide new insights into the mechanisms of AtrbohF in regulating the responses to oxygen deprivation in Arabidopsis.

Selective Hydrogenolysis of Furfural Derivative 2-Methyltetrahydrofuran into Pentanediol Acetate and Pentanol Acetate over Pd/C and Sc(OTf)3 Cocatalytic System.

Science.gov (United States)

Zhang, Kun; Li, Xing-Long; Chen, Shi-Yan; Xu, Hua-Jian; Deng, Jin; Fu, Yao

2018-02-22

It is of great significance to convert platform molecules and their derivatives into high value-added alcohols, which have multitudinous applications. This study concerns systematic conversion of 2-methyltetrahydrofuran (MTHF), which is obtained from furfural, into 1-pentanol acetate (PA) and 1,4-pentanediol acetate (PDA). Reaction parameters, such as the Lewis acid species, reaction temperature, and hydrogen pressure, were investigated in detail. 1 H NMR spectroscopy and reaction dynamics study were also conducted to help clarify the reaction mechanism. Results suggested that cleavage of the primary alcohol acetate was less facile than that of the secondary alcohol acetate, with the main product being PA. A PA yield of 91.8 % (150 °C, 3 MPa H 2 , 30 min) was achieved by using Pd/C and Sc(OTf) 3 as a cocatalytic system and an 82 % yield of PDA was achieved (150 °C, 30 min) by using Sc(OTf) 3 catalyst. Simultaneously, the efficient conversion of acetic esters into alcohols by simple saponification was carried out and led to a good yield. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum key distribution with entangled photon sources

International Nuclear Information System (INIS)

Ma Xiongfeng; Fung, Chi-Hang Fred; Lo, H.-K.

2007-01-01

A parametric down-conversion (PDC) source can be used as either a triggered single-photon source or an entangled-photon source in quantum key distribution (QKD). The triggering PDC QKD has already been studied in the literature. On the other hand, a model and a post-processing protocol for the entanglement PDC QKD are still missing. We fill in this important gap by proposing such a model and a post-processing protocol for the entanglement PDC QKD. Although the PDC model is proposed to study the entanglement-based QKD, we emphasize that our generic model may also be useful for other non-QKD experiments involving a PDC source. Since an entangled PDC source is a basis-independent source, we apply Koashi and Preskill's security analysis to the entanglement PDC QKD. We also investigate the entanglement PDC QKD with two-way classical communications. We find that the recurrence scheme increases the key rate and the Gottesman-Lo protocol helps tolerate higher channel losses. By simulating a recent 144-km open-air PDC experiment, we compare three implementations: entanglement PDC QKD, triggering PDC QKD, and coherent-state QKD. The simulation result suggests that the entanglement PDC QKD can tolerate higher channel losses than the coherent-state QKD. The coherent-state QKD with decoy states is able to achieve highest key rate in the low- and medium-loss regions. By applying the Gottesman-Lo two-way post-processing protocol, the entanglement PDC QKD can tolerate up to 70 dB combined channel losses (35 dB for each channel) provided that the PDC source is placed in between Alice and Bob. After considering statistical fluctuations, the PDC setup can tolerate up to 53 dB channel losses

Improvement of ethanol yield from glycerol via conversion of pyruvate to ethanol in metabolically engineered Saccharomyces cerevisiae.

Science.gov (United States)

Yu, Kyung Ok; Jung, Ju; Ramzi, Ahmad Bazli; Kim, Seung Wook; Park, Chulhwan; Han, Sung Ok

2012-02-01

The conversion of low-priced glycerol to higher value products has been proposed as a way to improve the economic viability of the biofuels industry. In a previous study, the conversion of glycerol to ethanol in a metabolically engineered strain of Saccharomyces cerevisiae was accomplished by minimizing the synthesis of glycerol, the main by-product in ethanol fermentation processing. To further improve ethanol production, overexpression of the native genes involved in conversion of pyruvate to ethanol in S. cerevisiae was successfully accomplished. The overexpression of an alcohol dehydrogenase (adh1) and a pyruvate decarboxylase (pdc1) caused an increase in growth rate and glycerol consumption under fermentative conditions, which led to a slight increase of the final ethanol yield. The overall expression of the adh1 and pdc1 genes in the modified strains, combined with the lack of the fps1 and gpd2 genes, resulted in a 1.4-fold increase (about 5.4 g/L ethanol produced) in fps1Δgpd2Δ (pGcyaDak, pGupCas) (about 4.0 g/L ethanol produced). In summary, it is possible to improve the ethanol yield by overexpression of the genes involved in the conversion of pyruvate to ethanol in engineered S. cerevisiae using glycerol as substrate.

Imaging gene expression in real-time using aptamers

Energy Technology Data Exchange (ETDEWEB)

Shin, Il Chung [Iowa State Univ., Ames, IA (United States)

2011-01-01

Signal transduction pathways are usually activated by external stimuli and are transient. The downstream changes such as transcription of the activated genes are also transient. Real-time detection of promoter activity is useful for understanding changes in gene expression, especially during cell differentiation and in development. A simple and reliable method for viewing gene expression in real time is not yet available. Reporter proteins such as fluorescent proteins and luciferase allow for non-invasive detection of the products of gene expression in living cells. However, current reporter systems do not provide for real-time imaging of promoter activity in living cells. This is because of the long time period after transcription required for fluorescent protein synthesis and maturation. We have developed an RNA reporter system for imaging in real-time to detect changes in promoter activity as they occur. The RNA reporter uses strings of RNA aptamers that constitute IMAGEtags (Intracellular MultiAptamer GEnetic tags), which can be expressed from a promoter of choice. The tobramycin, neomycin and PDC RNA aptamers have been utilized for this system and expressed in yeast from the GAL1 promoter. The IMAGEtag RNA kinetics were quantified by RT-qPCR. In yeast precultured in raffinose containing media the GAL1 promoter responded faster than in yeast precultured in glucose containing media. IMAGEtag RNA has relatively short half-life (5.5 min) in yeast. For imaging, the yeast cells are incubated with their ligands that are labeled with fluorescent dyes. To increase signal to noise, ligands have been separately conjugated with the FRET (Förster resonance energy transfer) pairs, Cy3 and Cy5. With these constructs, the transcribed aptamers can be imaged after activation of the promoter by galactose. FRET was confirmed with three different approaches, which were sensitized emission, acceptor photobleaching and donor lifetime by FLIM (fluorescence lifetime imaging

Imaging gene expression in real-time using aptamers

Energy Technology Data Exchange (ETDEWEB)

Shin, Ilchung [Iowa State Univ., Ames, IA (United States)

2012-01-01

Signal transduction pathways are usually activated by external stimuli and are transient. The downstream changes such as transcription of the activated genes are also transient. Real-time detection of promoter activity is useful for understanding changes in gene expression, especially during cell differentiation and in development. A simple and reliable method for viewing gene expression in real time is not yet available. Reporter proteins such as fluorescent proteins and luciferase allow for non-invasive detection of the products of gene expression in living cells. However, current reporter systems do not provide for real-time imaging of promoter activity in living cells. This is because of the long time period after transcription required for fluorescent protein synthesis and maturation. We have developed an RNA reporter system for imaging in real-time to detect changes in promoter activity as they occur. The RNA reporter uses strings of RNA aptamers that constitute IMAGEtags (Intracellular MultiAptamer GEnetic tags), which can be expressed from a promoter of choice. The tobramycin, neomycin and PDC RNA aptamers have been utilized for this system and expressed in yeast from the GAL1 promoter. The IMAGEtag RNA kinetics were quantified by RT-qPCR. In yeast precultured in raffinose containing media the GAL1 promoter responded faster than in yeast precultured in glucose containing media. IMAGEtag RNA has relatively short half-life (5.5 min) in yeast. For imaging, the yeast cells are incubated with their ligands that are labeled with fluorescent dyes. To increase signal to noise, ligands have been separately conjugated with the FRET (Förster resonance energy transfer) pairs, Cy3 and Cy5. With these constructs, the transcribed aptamers can be imaged after activation of the promoter by galactose. FRET was confirmed with three different approaches, which were sensitized emission, acceptor photobleaching and donor lifetime by FLIM (fluorescence lifetime imaging

Dentoskeletal features associated with unilateral or bilateral palatal displacement of maxillary canines.

Science.gov (United States)

Sacerdoti, Raffaele; Baccetti, Tiziano

2004-12-01

The aim of the present study was to analyze the prevalence and distribution of palatally displaced maxillary canines (PDC) in a large orthodontic population, and to investigate the associations between PDC, craniofacial features, and other dental anomalies such as aplasia or small-sized upper lateral incisors. An initial sample of 5000 subjects was evaluated. The reference values were calculated in a control group of 1000 subjects that was extracted from the initial sample. Chi-squared tests were used for statistical comparisons. The prevalence rate of PDC was 2.4%, with a male-to-female ratio of 1:3. PDC subjects with low angle vertical relationships showed a significantly high prevalence rate (60.2%). Unilateral PDC was significantly associated with aplasia of upper lateral incisors, whereas bilateral PDC was associated with aplasia of third molars. PDC showed reciprocal significant associations with bilateral small-sized upper lateral incisors. None of the three hypotheses offered in support of the "guidance theory" in the etiology of PDC were corroborated by the findings of the present study. The occurrence of other dental anomalies concurrent with PDC, sex differences, and the bilateral expression of PDC, all confirm the genetic component in the etiology of this tooth disturbance.

LDPC coding for QKD at higher photon flux levels based on spatial entanglement of twin beams in PDC

International Nuclear Information System (INIS)

Daneshgaran, Fred; Mondin, Marina; Bari, Inam

2014-01-01

Twin beams generated by Parametric Down Conversion (PDC) exhibit quantum correlations that has been effectively used as a tool for many applications including calibration of single photon detectors. By now, detection of multi-mode spatial correlations is a mature field and in principle, only depends on the transmission and detection efficiency of the devices and the channel. In [2, 4, 5], the authors utilized their know-how on almost perfect selection of modes of pairwise correlated entangled beams and the optimization of the noise reduction to below the shot-noise level, for absolute calibration of Charge Coupled Device (CCD) cameras. The same basic principle is currently being considered by the same authors for possible use in Quantum Key Distribution (QKD) [3, 1]. The main advantage in such an approach would be the ability to work with much higher photon fluxes than that of a single photon regime that is theoretically required for discrete variable QKD applications (in practice, very weak laser pulses with mean photon count below one are used).The natural setup of quantization of CCD detection area and subsequent measurement of the correlation statistic needed to detect the presence of the eavesdropper Eve, leads to a QKD channel model that is a Discrete Memoryless Channel (DMC) with a number of inputs and outputs that can be more than two (i.e., the channel is a multi-level DMC). This paper investigates the use of Low Density Parity Check (LDPC) codes for information reconciliation on the effective parallel channels associated with the multi-level DMC. The performance of such codes are shown to be close to the theoretical limits.

The Use of the Performance Diagnostic Checklist-Human Services to Assess and Improve the Job Performance of Individuals with Intellectual Disabilities.

Science.gov (United States)

Smith, Madison; Wilder, David A

2018-06-01

The Performance Diagnostic Checklist-Human Services (PDC-HS) is an informant-based tool designed to identify the variables responsible for performance problems. To date, the PDC-HS has not been examined with individuals with intellectual disabilities. In the current study, two supervisors with intellectual disabilities completed the PDC-HS to assess the productivity of two supervisees with disabilities who performed a pricing task in a thrift store. The PDC-HS suggested that performance deficits were due to a lack of training; a PDC-HS-indicated intervention was effective to increase accurate pricing. • The PDC-HS is an informant-based tool designed to identify the variables responsible for employee performance problems in human service settings. • The PDC-HS can be completed by some individuals with intellectual disabilities in a supervisory position to identify the variables responsible for problematic job performance among their supervisees. • A PDC-HS indicated intervention was demonstrated to be effective to improve the job performance of individuals with disabilities. • The PDC-HS may be a useful tool to support performance improvement and job maintenance among individuals with intellectual disabilities.

Evaluation of Fluorescent Analogs of Deoxycytidine for Monitoring DNA Transitions from Duplex to Functional Structures

Directory of Open Access Journals (Sweden)

Yogini P. Bhavsar

2011-01-01

Full Text Available Topological variants of single-strand DNA (ssDNA structures, referred to as “functional DNA,” have been detected in regulatory regions of many genes and are thought to affect gene expression. Two fluorescent analogs of deoxycytidine, Pyrrolo-dC (PdC and 1,3-diaza-2-oxophenoxazine (tC∘, can be incorporated into DNA. Here, we describe spectroscopic studies of both analogs to determine fluorescent properties that report on structural transitions from double-strand DNA (dsDNA to ssDNA, a common pathway in the transition to functional DNA structures. We obtained fluorescence-detected circular dichroism (FDCD spectra, steady-state fluorescence spectra, and fluorescence lifetimes of the fluorophores in DNA. Our results show that PdC is advantageous in fluorescence lifetime studies because of a distinct ~2 ns change between paired and unpaired bases. However, tC∘ is a better probe for FDCD experiments that report on the helical structure of DNA surrounding the fluorophore. Both fluorophores provide complementary data to measure DNA structural transitions.

iTRAQ Quantitative Proteomic Analysis of Vitreous from Patients with Retinal Detachment

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Fátima Milhano Santos

2018-04-01

Full Text Available Rhegmatogenous retinal detachment (RRD is a potentially blinding condition characterized by a physical separation between neurosensory retina and retinal pigment epithelium. Quantitative proteomics can help to understand the changes that occur at the cellular level during RRD, providing additional information about the molecular mechanisms underlying its pathogenesis. In the present study, iTRAQ labeling was combined with two-dimensional LC-ESI-MS/MS to find expression changes in the proteome of vitreous from patients with RRD when compared to control samples. A total of 150 proteins were found differentially expressed in the vitreous of patients with RRD, including 96 overexpressed and 54 underexpressed. Several overexpressed proteins, several such as glycolytic enzymes (fructose-bisphosphate aldolase A, gamma-enolase, and phosphoglycerate kinase 1, glucose transporters (GLUT-1, growth factors (metalloproteinase inhibitor 1, and serine protease inhibitors (plasminogen activator inhibitor 1 are regulated by HIF-1, which suggests that HIF-1 signaling pathway can be triggered in response to RRD. Also, the accumulation of photoreceptor proteins, including phosducin, rhodopsin, and s-arrestin, and vimentin in vitreous may indicate that photoreceptor degeneration occurs in RRD. Also, the accumulation of photoreceptor proteins, including phosducin, rhodopsin, and s-arrestin, and vimentin in vitreous may indicate that photoreceptor degeneration occurs in RRD. Nevertheless, the differentially expressed proteins found in this study suggest that different mechanisms are activated after RRD to promote the survival of retinal cells through complex cellular responses.

Enhancement of protocatechuate decarboxylase activity for the effective production of muconate from lignin-related aromatic compounds.

Science.gov (United States)

Sonoki, Tomonori; Morooka, Miyuki; Sakamoto, Kimitoshi; Otsuka, Yuichiro; Nakamura, Masaya; Jellison, Jody; Goodell, Barry

2014-12-20

The decarboxylation reaction of protocatechuate has been described as a bottleneck and a rate-limiting step in cis,cis-muconate (ccMA) bioproduction from renewable feedstocks such as sugar. Because sugars are already in high demand in the development of many bio-based products, our work focuses on improving protocatechuate decarboxylase (Pdc) activity and ccMA production in particular, from lignin-related aromatic compounds. We previously had transformed an Escherichia coli strain using aroY, which had been used as a protocatechuate decarboxylase encoding gene from Klebsiella pneumoniae subsp. pneumoniae A170-40, and inserted other required genes from Pseudomonas putida KT2440, to allow the production of ccMA from vanillin. This recombinant strain produced ccMA from vanillin, however the Pdc reaction step remained a bottleneck during incubation. In the current study, we identify a way to increase protocatechuate decarboxylase activity in E. coli through enzyme production involving both aroY and kpdB; the latter which encodes for the B subunit of 4-hydroxybenzoate decarboxylase. This permits expression of Pdc activity at a level approximately 14-fold greater than the strain with aroY only. The expression level of AroY increased, apparently as a function of the co-expression of AroY and KpdB. Our results also imply that ccMA may inhibit vanillate demethylation, a reaction step that is rate limiting for efficient ccMA production from lignin-related aromatic compounds, so even though ccMA production may be enhanced, other challenges to overcome vanilate demethylation inhibition still remain.

Overexpression of miR-183/-96/-182 triggers neuronal cell fate in Human Retinal Pigment Epithelial (hRPE) cells in culture.

Science.gov (United States)

Davari, Maliheh; Soheili, Zahra-Soheila; Samiei, Shahram; Sharifi, Zohreh; Pirmardan, Ehsan Ranaei

2017-01-29

miR-183 cluster, composed of miR-183/-96/-182 genes, is highly expressed in the adult retina, particularly in photoreceptors. It involves in development, maturation and normal function of neuroretina. Ectopic overexpression of miR-183/-96/-182 genes was performed to assess reprogramming of hRPE cells. They were amplified from genomic DNA and cloned independently or in tandem configuration into pAAV.MCS vector. hRPE cells were then transfected with the recombinant constructs. Real-Time PCR was performed to measure the expression levels of miR-183/-96/-182 and that of several retina-specific neuronal genes such as OTX2, NRL, PDC and DCT. The transfected cells also were immunocytochemically examined for retina-specific neuronal markers, including Rhodopsin, red opsin, CRX, Thy1, CD73, recoverin and PKCα, to determine the cellular fate of the transfected hRPE cells. Data showed that upon miR-183/-96/-182 overexpression in hRPE cultures, the expression of neuronal genes including OTX2, NRL, PDC and DCT was also upregulated. Moreover, miR-183 cluster-treated hRPE cells were immunoreactive for neuronal markers such as Rhodopsin, red opsin, CRX and Thy1. Both transcriptional and translational upregulation of neuronal genes in miR-183 cluster-treated hRPE cells suggests that in vitro overexpression of miR-183 cluster could trigger reprogramming of hRPE cells to retinal neuron fate. Copyright © 2016 Elsevier Inc. All rights reserved.

Dysfunction of Protein Quality Control in Parkinsonism–Dementia Complex of Guam

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Bert M. Verheijen

2018-03-01

Full Text Available Guam parkinsonism–dementia complex (G-PDC is an enigmatic neurodegenerative disease that is endemic to the Pacific island of Guam. G-PDC patients are clinically characterized by progressive cognitive impairment and parkinsonism. Neuropathologically, G-PDC is characterized by abundant neurofibrillary tangles, which are composed of hyperphosphorylated tau, marked deposition of 43-kDa TAR DNA-binding protein, and neuronal loss. Although both genetic and environmental factors have been implicated, the etiology and pathogenesis of G-PDC remain unknown. Recent neuropathological studies have provided new clues about the pathomechanisms involved in G-PDC. For example, deposition of abnormal components of the protein quality control system in brains of G-PDC patients indicates a role for proteostasis imbalance in the disease. This opens up promising avenues for new research on G-PDC and could have important implications for the study of other neurodegenerative disorders.

The switch from fermentation to respiration in Saccharomyces cerevisiae is regulated by the Ert1 transcriptional activator/repressor.

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Gasmi, Najla; Jacques, Pierre-Etienne; Klimova, Natalia; Guo, Xiao; Ricciardi, Alessandra; Robert, François; Turcotte, Bernard

2014-10-01

In the yeast Saccharomyces cerevisiae, fermentation is the major pathway for energy production, even under aerobic conditions. However, when glucose becomes scarce, ethanol produced during fermentation is used as a carbon source, requiring a shift to respiration. This adaptation results in massive reprogramming of gene expression. Increased expression of genes for gluconeogenesis and the glyoxylate cycle is observed upon a shift to ethanol and, conversely, expression of some fermentation genes is reduced. The zinc cluster proteins Cat8, Sip4, and Rds2, as well as Adr1, have been shown to mediate this reprogramming of gene expression. In this study, we have characterized the gene YBR239C encoding a putative zinc cluster protein and it was named ERT1 (ethanol regulated transcription factor 1). ChIP-chip analysis showed that Ert1 binds to a limited number of targets in the presence of glucose. The strongest enrichment was observed at the promoter of PCK1 encoding an important gluconeogenic enzyme. With ethanol as the carbon source, enrichment was observed with many additional genes involved in gluconeogenesis and mitochondrial function. Use of lacZ reporters and quantitative RT-PCR analyses demonstrated that Ert1 regulates expression of its target genes in a manner that is highly redundant with other regulators of gluconeogenesis. Interestingly, in the presence of ethanol, Ert1 is a repressor of PDC1 encoding an important enzyme for fermentation. We also show that Ert1 binds directly to the PCK1 and PDC1 promoters. In summary, Ert1 is a novel factor involved in the regulation of gluconeogenesis as well as a key fermentation gene. Copyright © 2014 by the Genetics Society of America.

Relationship between the maxillary transverse dimension and palatally displaced canines: A cone-beam computed tomographic study.

Science.gov (United States)

Hong, Wei-Hsin; Radfar, Rebecca; Chung, Chun-Hsi

2015-05-01

To examine the relationship between palatally displaced maxillary canines (PDC) and the maxillary transverse dimension using cone-beam computed tomography (CBCT). Thirty-three patients (11 males and 22 females, mean age 18.2 years) with PDC were matched to 66 patients (22 males and 44 females, mean age 18.1 years) without PDC (control) by gender, age, and posterior occlusion. A CBCT image was taken on all the patients prior to any orthodontic treatment. For each patient the maxillary basal bone widths and interdental widths at the maxillary first molars and first and second premolars were measured on axial and coronal sections of CBCT images. In addition, the presence of permanent tooth agenesis and the widths of maxillary incisors were recorded. Similar maxillary transverse dimensions, both skeletally and dentally, were found between the PDC and control groups. In the PDC group, the number of patients with permanent tooth agenesis was six times higher than in the control group. In addition, the maxillary lateral incisors on PDC-affected sides were smaller than those of control group (P transverse dimension, both skeletally and dentally, had no effect on the occurrence of PDC. The higher prevalence of permanent tooth agenesis was found in the PDC group. Moreover, the mean mesiodistal width of maxillary lateral incisors in the PDC group was significantly smaller than in the control group (P < .05).

Recent insights into the implications of metabolism in plasmacytoid dendritic cell innate functions: Potential ways to control these functions [version 1; referees: 1 approved, 2 approved with reservations

Directory of Open Access Journals (Sweden)

Philippe Saas

2017-04-01

Full Text Available There are more and more data concerning the role of cellular metabolism in innate immune cells, such as macrophages or conventional dendritic cells. However, few data are available currently concerning plasmacytoid dendritic cells (PDC, another type of innate immune cells. These cells are the main type I interferon (IFN producing cells, but they also secrete other pro-inflammatory cytokines (e.g., tumor necrosis factor or interleukin [IL]-6 or immunomodulatory factors (e.g., IL-10 or transforming growth factor-β. Through these functions, PDC participate in antimicrobial responses or maintenance of immune tolerance, and have been implicated in the pathophysiology of several autoimmune diseases. Recent data support the idea that the glycolytic pathway (or glycolysis, as well as lipid metabolism (including both cholesterol and fatty acid metabolism may impact some innate immune functions of PDC or may be involved in these functions after Toll-like receptor (TLR 7/9 triggering. Some differences may be related to the origin of PDC (human versus mouse PDC or blood-sorted versus FLT3 ligand stimulated-bone marrow-sorted PDC. The kinetics of glycolysis may differ between human and murine PDC. In mouse PDC, metabolism changes promoted by TLR7/9 activation may depend on an autocrine/paracrine loop, implicating type I IFN and its receptor IFNAR, explaining a delayed glycolysis. Moreover, PDC functions can be modulated by the metabolism of cholesterol and fatty acids. This may occur via the production of lipid ligands that activate nuclear receptors (e.g., liver X receptor [LXR] in PDC or through limiting intracellular cholesterol pool size (by statins or LXR agonists in these cells. Finally, lipid-activated nuclear receptors (i.e., LXR or peroxisome proliferator activated receptor may also directly interact with pro-inflammatory transcription factors, such as NF-κB. Here, we discuss how glycolysis and lipid metabolism may modulate PDC functions and how

Effect of pH in a Pd-based ethanol membraneless air breathing nanofluidic fuel cell with flow-through electrodes

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López-Rico, C. A.; Galindo-de-la-Rosa, J.; Ledesma-García, J.; Arriaga, L. G.; Guerra-Balcázar, M.; Arjona, N.

2015-12-01

In this work, a nanofluidic fuel cell (NFC) in which streams flow through electrodes was used to investigate the role of pH in the cell performance using ethanol as fuel and two Pd nanoparticles as electrocatalysts: one commercially available (Pd/C from ETEK) and other synthesized using ionic liquids (Pd/C IL). The cell performances for both electrocatalysts in acid/acid (anodic/cathodic) streams were of 18.05 and 9.55 mW cm-2 for Pd/C ETEK and Pd/C IL. In alkaline/alkaline streams, decrease to 15.94 mW cm-2 for Pd/C ETEK and increase to 15.37 mW cm-2 for Pd/C IL. In alkaline/acidic streams both electrocatalysts showed similar cell voltages (up to 1 V); meanwhile power densities were of 87.6 and 99.4 mW cm-2 for Pd/C ETEK and Pd/C IL. The raise in cell performance can be related to a decrease in activation losses, the combined used of alkaline and acidic streams and these high values compared with flow-over fuel cells can be related to the enhancement of the cathodic mass transport by using three dimensional porous electrodes and two sources of oxygen: from air and from a saturated solution.

Effect of pH in a Pd-based ethanol membraneless air breathing nanofluidic fuel cell with flow-through electrodes

International Nuclear Information System (INIS)

López-Rico, C A; Arriaga, L G; Galindo-de-la-Rosa, J; Ledesma-García, J; Guerra-Balcázar, M; Arjona, N

2015-01-01

In this work, a nanofluidic fuel cell (NFC) in which streams flow through electrodes was used to investigate the role of pH in the cell performance using ethanol as fuel and two Pd nanoparticles as electrocatalysts: one commercially available (Pd/C from ETEK) and other synthesized using ionic liquids (Pd/C IL). The cell performances for both electrocatalysts in acid/acid (anodic/cathodic) streams were of 18.05 and 9.55 mW cm -2 for Pd/C ETEK and Pd/C IL. In alkaline/alkaline streams, decrease to 15.94 mW cm -2 for Pd/C ETEK and increase to 15.37 mW cm -2 for Pd/C IL. In alkaline/acidic streams both electrocatalysts showed similar cell voltages (up to 1 V); meanwhile power densities were of 87.6 and 99.4 mW cm -2 for Pd/C ETEK and Pd/C IL. The raise in cell performance can be related to a decrease in activation losses, the combined used of alkaline and acidic streams and these high values compared with flow-over fuel cells can be related to the enhancement of the cathodic mass transport by using three dimensional porous electrodes and two sources of oxygen: from air and from a saturated solution. (paper)

From field data to numerical models: application of the Box-Model to infer the dynamics of PDC generated during the AD 79 eruption of Somma-Vesuvio

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Tadini, Alessandro; Neri, Augusto; Cioni, Raffaello; Bevilacqua, Andrea; Esposti Ongaro, Tomaso; Gurioli, Lucia

2017-04-01

The purpose of this work is to present a validation procedure for a physical and numerical model of Pyroclastic Density Currents (PDC) using feedbacks from well-known deposits emplaced by specific single eruptive units. The study is specifically focused on the PDCs generated during the overall famous AD 79 eruption of the Somma-Vesuvio volcano. To this purpose, values of the maximum runout, volumes and Total Grain Size Distributions have been estimated for two eruptive units (i.e. EU3pf and EU4; Cioni et al. 2000) of the AD 79 eruption. These units have been used to define the input volcanological parameters for testing the Box-Model of Dade and Huppert (1995), when reproducing one specific end-member of the complex spectrum of PDCs, that is the more dilute, turbulent part of the PDCs reconstructed in the Somma-Vesuvio record (stratified flows with concentration of solid particles in volume up to about 5%). The Box-Model is a kinematic approach, which calculates the flow density and velocity along time and the kinetic energy of the flow front. This can be compared with the potential energy needed to overcome topographic obstacles to estimate flow invasion across complex topographies. Validation of the model has been performed with respect to: i) the degree of overlapping between inundation areas given by the model and by field data; ii) the thickness of the deposit versus the thickness of the model output with distance; iii) the mass fractions of the different grain size classes with distance in the real deposit versus the model output. Several simulations have been performed considering i) polydisperse (with 10 grain size classes) and monodisperse (with the Mdφ values) systems; ii) a direct version (where the initial volume is released and the invasion area is computed) and an inverse version (where the initial collapsing volume is a function of an inundation area defined by the user); iii) axisymmetrical and asymmetrical collapses. Results allow to obtain first

Vehicle exhaust gas clearance by low temperature plasma-driven nano-titanium dioxide film prepared by radiofrequency magnetron sputtering.

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Shuang Yu

Full Text Available A novel plasma-driven catalysis (PDC reactor with special structure was proposed to remove vehicle exhaust gas. The PDC reactor which consisted of three quartz tubes and two copper electrodes was a coaxial dielectric barrier discharge (DBD reactor. The inner and outer electrodes firmly surrounded the outer surface of the corresponding dielectric barrier layer in a spiral way, respectively. Nano-titanium dioxide (TiO2 film prepared by radiofrequency (RF magnetron sputtering was coated on the outer wall of the middle quartz tube, separating the catalyst from the high voltage electrode. The spiral electrodes were designed to avoid overheating of microdischarges inside the PDC reactor. Continuous operation tests indicated that stable performance without deterioration of catalytic activity could last for more than 25 h. To verify the effectiveness of the PDC reactor, a non-thermal plasma(NTP reactor was employed, which has the same structure as the PDC reactor but without the catalyst. The real vehicle exhaust gas was introduced into the PDC reactor and NTP reactor, respectively. After the treatment, compared with the result from NTP, the concentration of HC in the vehicle exhaust gas treated by PDC reactor reduced far more obviously while that of NO decreased only a little. Moreover, this result was explained through optical emission spectrum. The O emission lines can be observed between 870 nm and 960 nm for wavelength in PDC reactor. Together with previous studies, it could be hypothesized that O derived from catalytically O3 destruction by catalyst might make a significant contribution to the much higher HC removal efficiency by PDC reactor. A series of complex chemical reactions caused by the multi-components mixture in real vehicle exhaust reduced NO removal efficiency. A controllable system with a real-time feedback module for the PDC reactor was proposed to further improve the ability of removing real vehicle exhaust gas.

An internal deletion in MTH1 enables growth on glucose of pyruvate-decarboxylase negative, non-fermentative Saccharomyces cerevisiae

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Oud Bart

2012-09-01

Full Text Available Abstract Background Pyruvate-decarboxylase negative (Pdc- strains of Saccharomyces cerevisiae combine the robustness and high glycolytic capacity of this yeast with the absence of alcoholic fermentation. This makes Pdc-S. cerevisiae an interesting platform for efficient conversion of glucose towards pyruvate-derived products without formation of ethanol as a by-product. However, Pdc- strains cannot grow on high glucose concentrations and require C2-compounds (ethanol or acetate for growth under conditions with low glucose concentrations, which hitherto has limited application in industry. Results Genetic analysis of a Pdc- strain previously evolved to overcome these deficiencies revealed a 225bp in-frame internal deletion in MTH1, encoding a transcriptional regulator involved in glucose sensing. This internal deletion contains a phosphorylation site required for degradation, thereby hypothetically resulting in increased stability of the protein. Reverse engineering of this alternative MTH1 allele into a non-evolved Pdc- strain enabled growth on 20 g l-1 glucose and 0.3% (v/v ethanol at a maximum specific growth rate (0.24 h-1 similar to that of the evolved Pdc- strain (0.23 h-1. Furthermore, the reverse engineered Pdc- strain grew on glucose as sole carbon source, albeit at a lower specific growth rate (0.10 h-1 than the evolved strain (0.20 h-1. The observation that overexpression of the wild-type MTH1 allele also restored growth of Pdc-S. cerevisiae on glucose is consistent with the hypothesis that the internal deletion results in decreased degradation of Mth1. Reduced degradation of Mth1 has been shown to result in deregulation of hexose transport. In Pdc- strains, reduced glucose uptake may prevent intracellular accumulation of pyruvate and/or redox problems, while release of glucose repression due to the MTH1 internal deletion may contribute to alleviation of the C2-compound auxotrophy. Conclusions In this study we have discovered and

Isolation and characterization of cDNA clones for carrot extensin and a proline-rich 33-kDa protein

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Chen, J.; Varner, J.E.

1985-01-01

Extensins are hydroxyproline-rich glycoproteins associated with most dicotyledonous plant cell walls. To isolate cDNA clones encoding extensin, the authors started by isolating poly(A) + RNA from carrot root tissue, and then translating the RNA in vitro, in the presence of tritiated leucine or proline. A 33-kDa peptide was identified in the translation products as a putative extensin precursor. From a cDNA library constructed with poly(A) + RNA from wounded carrots, one cDNA clone (pDC5) was identified that specifically hybridized to poly(A) + RNA encoding this 33-kDa peptide. They isolated three cDNA clones (pDC11, pDC12, and pDC16) from another cDNA library using pCD5 as a probe. DNA sequence data, RNA hybridization analysis, and hybrid released in vitro translation indicate that the cDNA clones pDC11 encodes extensin and that cDNA clones pDC12 and pDC16 encode the 33-kDa peptide, which as yet has an unknown identity and function. The assumption that the 33-kDa peptide was an extensin precursor was invalid. RNA hybridization analysis showed that RNA encoded by both clone types is accumulated upon wounding

Recent insights into the implications of metabolism in plasmacytoid dendritic cell innate functions: Potential ways to control these functions [version 2; referees: 1 approved, 2 approved with reservations

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Philippe Saas

2017-06-01

Full Text Available There are more and more data concerning the role of cellular metabolism in innate immune cells, such as macrophages or conventional dendritic cells. However, few data are available currently concerning plasmacytoid dendritic cells (PDC, another type of innate immune cells. These cells are the main type I interferon (IFN producing cells, but they also secrete other pro-inflammatory cytokines (e.g., tumor necrosis factor or interleukin [IL]-6 or immunomodulatory factors (e.g., IL-10 or transforming growth factor-β. Through these functions, PDC participate in antimicrobial responses or maintenance of immune tolerance, and have been implicated in the pathophysiology of several autoimmune diseases, as well as in tumor immune escape mechanisms. Recent data support the idea that the glycolytic pathway (or glycolysis, as well as lipid metabolism (including both cholesterol and fatty acid metabolism may impact some innate immune functions of PDC or may be involved in these functions after Toll-like receptor (TLR 7/9 triggering. The kinetics of glycolysis after TLR7/9 triggering may differ between human and murine PDC. In mouse PDC, metabolism changes promoted by TLR7/9 activation may depend on an autocrine/paracrine loop, implicating type I IFN and its receptor IFNAR. This could explain a delayed glycolysis in mouse PDC. Moreover, PDC functions can be modulated by the metabolism of cholesterol and fatty acids. This may occur via the production of lipid ligands that activate nuclear receptors (e.g., liver X receptor [LXR] in PDC or through limiting intracellular cholesterol pool size (by statin or LXR agonist treatment in these cells. Finally, lipid-activated nuclear receptors (i.e., LXR or peroxisome proliferator activated receptor may also directly interact with pro-inflammatory transcription factors, such as NF-κB. Here, we discuss how glycolysis and lipid metabolism may modulate PDC functions and how this may be harnessed in pathological situations

Gene expression changes in the retina following subretinal injection of human neural progenitor cells into a rodent model for retinal degeneration.

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Jones, Melissa K; Lu, Bin; Saghizadeh, Mehrnoosh; Wang, Shaomei

2016-01-01

Retinal degenerative diseases (RDDs) affect millions of people and are the leading cause of vision loss. Although treatment options for RDDs are limited, stem and progenitor cell-based therapies have great potential to halt or slow the progression of vision loss. Our previous studies have shown that a single subretinal injection of human forebrain derived neural progenitor cells (hNPCs) into the Royal College of Surgeons (RCS) retinal degenerate rat offers long-term preservation of photoreceptors and visual function. Furthermore, neural progenitor cells are currently in clinical trials for treating age-related macular degeneration; however, the molecular mechanisms of stem cell-based therapies are largely unknown. This is the first study to analyze gene expression changes in the retina of RCS rats following subretinal injection of hNPCs using high-throughput sequencing. RNA-seq data of retinas from RCS rats injected with hNPCs (RCS(hNPCs)) were compared to sham surgery in RCS (RCS(sham)) and wild-type Long Evans (LE(sham)) rats. Differential gene expression patterns were determined with in silico analysis and confirmed with qRT-PCR. Function, biologic, cellular component, and pathway analyses were performed on differentially expressed genes and investigated with immunofluorescent staining experiments. Analysis of the gene expression data sets identified 1,215 genes that were differentially expressed between RCS(sham) and LE(sham) samples. Additionally, 283 genes were differentially expressed between the RCS(hNPCs) and RCS(sham) samples. Comparison of these two gene sets identified 68 genes with inverse expression (termed rescue genes), including Pdc, Rp1, and Cdc42ep5. Functional, biologic, and cellular component analyses indicate that the immune response is enhanced in RCS(sham). Pathway analysis of the differential expression gene sets identified three affected pathways in RCS(hNPCs), which all play roles in phagocytosis signaling. Immunofluorescent staining

Study on the Effect of Diamond Grain Size on Wear of Polycrystalline Diamond Compact Cutter

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Abdul-Rani, A. M.; Che Sidid, Adib Akmal Bin; Adzis, Azri Hamim Ab

2018-03-01

Drilling operation is one of the most crucial step in oil and gas industry as it proves the availability of oil and gas under the ground. Polycrystalline Diamond Compact (PDC) bit is a type of bit which is gaining popularity due to its high Rate of Penetration (ROP). However, PDC bit can easily wear off especially when drilling hard rock. The purpose of this study is to identify the relationship between the grain sizes of the diamond and wear rate of the PDC cutter using simulation-based study with FEA software (ABAQUS). The wear rates of a PDC cutter with a different diamond grain sizes were calculated from simulated cuttings of cutters against granite. The result of this study shows that the smaller the diamond grain size, the higher the wear resistivity of PDC cutter.

LC-MS/MS Determination and Pharmacokinetic Study of Pedunculoside in Rat Plasma after Oral Administration of Pedunculoside and Ilex rotunda Extract

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Waiou Zhao

2015-05-01

Full Text Available Ilex rotunda is widely used to treat many disorders as a traditional Chinese medicine (TCM containing 4%–5% pedunculoside (PDC. A rapid, selective, and sensitive liquid chromatography-tandem mass spectrometry method (LC-MS/MS was developed and validated to determine PDC in rat plasma by using 3β,19α-dihydroxyurs-12-en-28-oic acid 28-β-D-glucopyranosyl ester (DEOG as an internal standard. The analytes were extracted by protein precipitation and eluted on a C18 chromatography column using a mobile phase of methanol–H2O (70:30, v/v delivered at a flow rate of 0.6 mL/min. Detection was performed using positive ion electrospray ionization in multiple reaction monitoring modes. The assay was linear over the concentration range of 0.60 ng/mL to 200 ng/mL, with a quantification limit of 0.60 ng/mL. Intra-day and inter-day precisions (%RSD ranged from 2.12 to 9.51 for PDC, whereas the accuracy was within −7.83%~9.40%. The validated method was successfully applied to the pharmacokinetic study of PDC in rat plasma after oral administration of pure PDC and Ilex rotunda extract (IRE. Pharmacokinetic parameters of PDC in IRE, such as Cmax, AUC0–t, AUC0–∞, t1/2z, and CLz/F, statistically differed from those of the pure monomer (p < 0.01. However, Tmax and MRT showed no significant differences between the two groups. Results suggested that other coexisting components in IRE may decrease the absorption of PDC. Compound-compound interactions between PDC and other herbal extract components can alter the pharmacokinetic behavior of PDC. The study will be helpful in providing references for understanding the action mechanism and clinical application of Ilex rotunda.

Constitutive expression of TNF-related activation-induced cytokine (TRANCE/receptor activating NF-κB ligand (RANK-L by rat plasmacytoid dendritic cells.

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Thomas Anjubault

Full Text Available Plasmacytoid dendritic cells (pDCs are a subset of DCs whose major function relies on their capacity to produce large amount of type I IFN upon stimulation via TLR 7 and 9. This function is evolutionary conserved and place pDC in critical position in the innate immune response to virus. Here we show that rat pDC constitutively express TNF-related activation-induced cytokine (TRANCE also known as Receptor-activating NF-κB ligand (RANKL. TRANCE/RANKL is a member of the TNF superfamily which plays a central role in osteoclastogenesis through its interaction with its receptor RANK. TRANCE/RANK interaction are also involved in lymphoid organogenesis as well as T cell/DC cross talk. Unlike conventional DC, rat CD4(high pDC were shown to constitutively express TRANCE/RANKL both at the mRNA and the surface protein level. TRANCE/RANKL was also induced on the CD4(low subsets of pDC following activation by CpG. The secreted form of TRANCE/RANKL was also produced by rat pDC. Of note, levels of mRNA, surface and secreted TRANCE/RANKL expression were similar to that observed for activated T cells. TRANCE/RANKL expression was found on pDC in all lymphoid organs as well blood and BM with a maximum expression in mesenteric lymph nodes. Despite this TRANCE/RANKL expression, we were unable to demonstrate in vitro osteoclastogenesis activity for rat pDC. Taken together, these data identifies pDC as novel source of TRANCE/RANKL in the immune system.

Risk of developing palatally displaced canines in patients with early detectable dental anomalies: a retrospective cohort study

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Daniela Gamba GARIB

Full Text Available ABSTRACT The early recognition of risk factors for the occurrence of palatally displaced canines (PDC can increase the possibility of impaction prevention. Objective To estimate the risk of PDC occurrence in children with dental anomalies identified early during mixed dentition. Material and Methods The sample comprised 730 longitudinal orthodontic records from children (448 females and 282 males with an initial mean age of 8.3 years (SD=1.36. The dental anomaly group (DA included 263 records of patients with at least one dental anomaly identified in the initial or middle mixed dentition. The non-dental anomaly group (NDA was composed of 467 records of patients with no dental anomalies. The occurrence of PDC in both groups was diagnosed using panoramic and periapical radiographs taken in the late mixed dentition or early permanent dentition. The prevalence of PDC in patients with and without early diagnosed dental anomalies was compared using the chi-square test (p<0.01, relative risk assessments (RR, and positive and negative predictive values (PPV and NPV. Results PDC frequency was 16.35% and 6.2% in DA and NDA groups, respectively. A statistically significant difference was observed between groups (p<0.01, with greater risk of PDC development in the DA group (RR=2.63. The PPV and NPV was 16% and 93%, respectively. Small maxillary lateral incisors, deciduous molar infraocclusion, and mandibular second premolar distoangulation were associated with PDC. Conclusion Children with dental anomalies diagnosed during early mixed dentition have an approximately two and a half fold increased risk of developing PDC during late mixed dentition compared with children without dental anomalies.

Risk of developing palatally displaced canines in patients with early detectable dental anomalies: a retrospective cohort study

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GARIB, Daniela Gamba; LANCIA, Melissa; KATO, Renata Mayumi; OLIVEIRA, Thais Marchini; NEVES, Lucimara Teixeira das

2016-01-01

ABSTRACT The early recognition of risk factors for the occurrence of palatally displaced canines (PDC) can increase the possibility of impaction prevention. Objective To estimate the risk of PDC occurrence in children with dental anomalies identified early during mixed dentition. Material and Methods The sample comprised 730 longitudinal orthodontic records from children (448 females and 282 males) with an initial mean age of 8.3 years (SD=1.36). The dental anomaly group (DA) included 263 records of patients with at least one dental anomaly identified in the initial or middle mixed dentition. The non-dental anomaly group (NDA) was composed of 467 records of patients with no dental anomalies. The occurrence of PDC in both groups was diagnosed using panoramic and periapical radiographs taken in the late mixed dentition or early permanent dentition. The prevalence of PDC in patients with and without early diagnosed dental anomalies was compared using the chi-square test (p<0.01), relative risk assessments (RR), and positive and negative predictive values (PPV and NPV). Results PDC frequency was 16.35% and 6.2% in DA and NDA groups, respectively. A statistically significant difference was observed between groups (p<0.01), with greater risk of PDC development in the DA group (RR=2.63). The PPV and NPV was 16% and 93%, respectively. Small maxillary lateral incisors, deciduous molar infraocclusion, and mandibular second premolar distoangulation were associated with PDC. Conclusion Children with dental anomalies diagnosed during early mixed dentition have an approximately two and a half fold increased risk of developing PDC during late mixed dentition compared with children without dental anomalies. PMID:28076458

Comparison of the dental anomalies found in maxillary canine-first premolar transposition cases with those in palatally displaced canine cases.

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Scerri, Erica Sultana; McDonald, Fraser; Camilleri, Simon

2016-02-01

To compare the developmental dental anomalies associated with maxillary canine-first premolar (MxCP1) transposition and those of palatally displaced canine (PDC) with each other and with the background prevalence in the Maltese population in order to elucidate whether the two conditions have similar or differing genetic backgrounds. Dental records of 477 subjects with PDC, 57 subjects with MxCP1, and a control group of 500 subjects with no history of a PDC or tooth transposition were compared for canine eruption anomalies and hypodontia. A high frequency of bilateral occurrence was present for both canine malpositions and when unilateral, a trend to right-sided occurrence was evident. The occurrence of transpositions in the PDC group and of PDC in the MxCP1 group was higher than expected. The prevalence of incisor hypodontia was significantly higher in subjects with PDC and MxCP1, as compared to the control group. The size of the MxCP1 group is relatively small. The study population is a small isolated Caucasian population and the results may not be applicable to other populations. There is no significant difference between the MxCP1 and PDC groups in the prevalence or distribution of hypodontia and each of these groups exhibits a higher prevalence of the other canine anomaly. These findings support the theory that PDC and MxCP1 form part of a group of interrelated dental anomalies that share a common genetic basis. © The Author 2015. Published by Oxford University Press on behalf of the European Orthodontic Society. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Doses monitoring in radiology: calibration of air kerma-area product (P{sub KA}) meters; Monitoracao de doses em radiologia: a calibracao de medidores do produto kerma-area (P{sub KA})

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Terini, Ricardo Andrade; Campelo, Maria Carolina de Santana; Almeida Junior, Jose Neres de, E-mail: rterini@pucsp.br [Pontificia Universidade Catolica de Sao Paulo (PUC-SP), SP (Brazil); Herdade, Silvio Bruni; Pereira, Marco Aurelio Guedes [Universidade de Sao Paulo (IEE/USP), SP (Brazil). Instituto de Energia e Ambiente

2013-11-15

Materials and methods: different qualities of both incident and transmitted beams were utilized in conditions similar to a clinical setting, analyzing the influence from the reference dosimeter, from the distance between meters, from the filtration and from the average beam energy. Calibrations were performed directly against a standard 30 cm{sup 3} cylindrical chamber or a parallel-plate monitor chamber, and indirectly against the PDC meter. Results: the lowest energy dependence was observed for transmitted beams. The cross calibration between the Diamentor E2 and the PDC meters, and the PDC presented the greatest propagation of uncertainties. Conclusion: the calibration coefficient of the PDC meter showed to be more stable with voltage, while the Diamentor E2 calibration coefficient was more variable. On the other hand, the PDC meter presented greater uncertainty in readings (5.0%) than with the use of the monitor chamber (3.5%) as a reference. (author)

Comparison of recording of hepatitis B infection in the NSW Perinatal Data Collection with linked hepatitis B notifications

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Lucy Deng

2017-12-01

Full Text Available Objective: Results of routine maternal antenatal hepatitis B (HBV screening have been recorded in the New South Wales (NSW Perinatal Data Collection (PDC since January 2011. We evaluated the accuracy of this reporting in 2012, the first year that comprehensive data were available, by linking the PDC to HBV notifications. Methods: PDC records of mothers giving birth in 2012 were probabilistically linked to HBV notifications recorded in the NSW Notifiable Conditions Information Management System (NCIMS. Sensitivity and specificity of the PDC record of HBV status were determined using a linked HBV notification from the NCIMS database as the gold standard. Results were also examined according to health service (area health service, hospital level, public or private and individual factors (maternal age, country of birth, Aboriginality, parity, timing of first antenatal visit. Results: Among 99 510 records of women giving birth in NSW in 2012, positive HBV status was recorded for 0.69% of the women according to the PDC record and 0.90% from linked NCIMS records. The overall sensitivity of the HBV status variable in the PDC data was 65.5% (95% confidence interval [CI] 62.4, 68.7 and positive predictive value was 85.3% (95% CI 82.6, 87.9. In general, the low prevalence of HBV meant we had limited statistical power to assess differences between health service factors and maternal factors; however, sensitivity was significantly lower in PDC data for HBV in Australian-born non-Aboriginal women (37.0%; 95% CI 27.5, 46.7 than in overseas-born women (69.9%; 95% CI 66.6, 73.1; p < 0.001. Conclusions: PDC records of HBV status for women giving birth in 2012 had high specificity but poor sensitivity. Sensitivity varied across area health services and levels of maternal services, and by various maternal factors. Because the results of maternal HBV screening can be used to monitor HBV prevalence in adults, analysis of the PDC records in subsequent years is

Arginase II expressed in cancer-associated fibroblasts indicates tissue hypoxia and predicts poor outcome in patients with pancreatic cancer.

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Yoshinori Ino

Full Text Available An adequate level of arginine in the tissue microenvironment is essential for T cell activity and survival. Arginine levels are regulated by the arginine-catabolizing enzyme, arginase (ARG. It has been reported that arginase II (ARG2, one of two ARGs, is aberrantly expressed in prostate cancer cells, which convert arginine into ornithine, resulting in a lack of arginine that weakens tumor-infiltrating lymphocytes and renders them dysfunctional. However, immune suppression mediated by ARG2-expressing cancer cells in lung cancer has not been observed. Here we studied the expression of ARG2 in pancreatic ductal carcinoma (PDC tissue clinicopathologically by examining over 200 cases of PDC. In contrast to prostate cancer, ARG2 expression was rarely demonstrated in PDC cells by immunohistochemistry, and instead ARG2 was characteristically expressed in α-smooth muscle actin-positive cancer-associated fibroblasts (CAFs, especially those located within and around necrotic areas in PDC. The presence of ARG2-expressing CAFs was closely correlated with shorter overall survival (OS; P  = 0.003 and disease-free survival (DFS; P  = 0.0006. Multivariate Cox regression analysis showed that the presence of ARG2-expressing CAFs in PDC tissue was an independent predictor of poorer OS (hazard ratio [HR]  = 1.582, P  = 0.007 and DFS (HR  = 1.715, P  = 0.001 in PDC patients. In addition to the characteristic distribution of ARG2-expressing CAFs, such CAFs co-expressed carbonic anhydrase IX, SLC2A1, or HIF-1α, markers of hypoxia, in PDC tissue. Furthermore, in vitro experiments revealed that cultured fibroblasts extracted from PDC tissue expressed the ARG2 transcript after exposure to hypoxia, which had arginase activity. These results indicate that cancer cell-mediated immune suppression through ARG2 expression is not a general event and that the presence of ARG2-expressing CAFs is an indicator of poor prognosis, as well as hypoxia, in PDC

Use of alternating and pulsed direct current electrified fields for zebra mussel control

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Luoma, James A.; Dean, Jan C.; Severson, Todd J.; Wise, Jeremy K.; Barbour, Matthew

2017-01-01

Alternatives to chemicals for controlling dreissenid mussels are desirable for environmental compatibility, but few alternatives exist. Previous studies have evaluated the use of electrified fields for stunning and/or killing planktonic life stages of dreissenid mussels, however, the available literature on the use of electrified fields to control adult dreissenid mussels is limited. We evaluated the effects of sinusoidal alternating current (AC) and 20% duty cycle square-wave pulsed direct current (PDC) exposure on the survival of adult zebra mussels at water temperatures of 10, 15, and 22 °C. Peak voltage gradients of ~ 17 and 30 Vp/cm in the AC and PDC exposures, respectively, were continuously applied for 24, 48, or 72 h. Peak power densities ranged from 77,999 to 107,199 µW/cm3 in the AC exposures and 245,320 to 313,945 µW/cm3 in the PDC exposures. The peak dose ranged from 6,739 to 27,298 Joules/cm3 and 21,306 to 80,941 Joules/cm3 in the AC and PDC exposures, respectively. The applied power ranged from 16.6 to 68.9 kWh in the AC exposures and from 22.2 to 86.4 kWh in the PDC exposures. Mortality ranged from 2.7 to 92.7% in the AC exposed groups and from 24.0 to 98.7% in PDC exposed groups. Mortality increased with corresponding increases in water temperature and exposure duration, and we observed more zebra mussel mortality in the PDC exposures. Exposures conducted with AC required less of a peak dose (Joules/cm3) but more applied power (kWh) to achieve the same level of adult zebra mussel mortality as corresponding PDC exposures. The results demonstrate that 20% duty cycle square-wave PDC requires less energy than sinusoidal AC to inducing the same level of adult zebra mussel mortality.

Primary biliary cirrhosis is characterized by IgG3 antibodies cross-reactive with the major mitochondrial autoepitope and its Lactobacillus mimic.

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Bogdanos, Dimitrios-Petrou; Baum, Harold; Okamoto, Manabu; Montalto, Paolo; Sharma, Umesh C; Rigopoulou, Eirini I; Vlachogiannakos, John; Ma, Yun; Burroughs, Andrew K; Vergani, Diego

2005-08-01

The serological hallmark of primary biliary cirrhosis (PBC) is the presence of pyruvate dehydrogenase complex E2 subunit (PDC-E2) antimitochondrial antibodies (AMAs). Anti-PDC-E2 antibodies cross-react specifically with mycobacterial hsp65, and we have demonstrated that the motif SxGDL[ILV]AE shared by PDC-E2(212-226) and hsp's is a cross-reactive target. Having found that this same motif is present only in beta-galactosidase of Lactobacillus delbrueckii (BGAL LACDE), we hypothesized that this homology would also lead to cross-reactivity. The mimics were tested via ELISA for reactivity and competitive cross-reactivity using sera from 100 AMA-positive and 23 AMA-negative PBC patients and 190 controls. An Escherichia coli (ECOLI) PDC-E2 mimic that has been pathogenetically linked to PBC but lacks this motif has been also tested. Anti-BGAL(266-280) LACDE antibodies were restricted to AMA-positive patients (54 of 95, 57%) and belonged to immunoglobulin (Ig) G3. Of the 190 controls, 22 (12%; P ECOLI PDC-E2 reactivity was virtually absent. BGAL(266-280)/PDC-E2(212-226) reactivity of the IgG3 isotype was found in 52 (52%) AMA-positive PBC patients but in only 1 of the controls (P ECOLI PDC-E2 mimics. In conclusion, IgG3 antibodies to BGAL LACDE cross-react with the major mitochondrial autoepitope and are characteristic of PBC.

CD4- and dynamin-dependent endocytosis of HIV-1 into plasmacytoid dendritic cells

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Pritschet, Kathrin; Donhauser, Norbert; Schuster, Philipp; Ries, Moritz; Haupt, Sabrina; Kittan, Nicolai A.; Korn, Klaus [Institute of Clinical and Molecular Virology, National Reference Centre for Retroviruses, Friedrich-Alexander-Universitaet Erlangen-Nuernberg, 91054 Erlangen (Germany); Poehlmann, Stefan [Institute of Virology, Hannover Medical School, 30625 Hannover (Germany); Holland, Gudrun; Bannert, Norbert [Robert Koch-Institute, Center for Biological Security 4, 13353 Berlin (Germany); Bogner, Elke [Institute of Virology, Charite University Hospital, 10117 Berlin (Germany); Schmidt, Barbara, E-mail: baschmid@viro.med.uni-erlangen.de [Institute of Clinical and Molecular Virology, National Reference Centre for Retroviruses, Friedrich-Alexander-Universitaet Erlangen-Nuernberg, 91054 Erlangen (Germany)

2012-02-20

Chronic immune activation, triggered by plasmacytoid dendritic cell (PDC) interferon (IFN)-alpha production, plays an important role in HIV-1 pathogenesis. As the entry of HIV-1 seems to be important for the activation of PDC, we directly characterized the viral entry into these cells using immuno-electron microscopy, cellular fractionation, confocal imaging, and functional experiments. After attachment to PDC, viruses were taken up in an energy-dependent manner. The virions were located in compartments positive for caveolin; early endosomal antigen 1; Rab GTPases 5, 7 and 9; lysosomal-associated membrane protein 1. PDC harbored more virus in endocytic vesicles than CD4+ T cells (p < 0.05). Blocking CD4 inhibited the uptake of virions into cytosolic and endosomal compartments. Dynasore, an inhibitor of dynamin-dependent endocytosis, not the fusion inhibitor T-20, reduced the HIV-1 induced IFN-alpha production. Altogether, our morphological and functional data support the role of endocytosis for the entry and IFN-alpha induction of HIV-1 in PDC.

Effect of polysaccharide of dendrobium candidum on proliferation and apoptosis of human corneal epithelial cells in high glucose

Science.gov (United States)

Li, Qiangxiang; Chen, Jing; Li, Yajia; Chen, Ting; Zou, Jing; Wang, Hua

2017-01-01

Abstract Background: The aim of the study was to observe the effect of polysaccharide of dendrobium candidum (PDC) and high glucose on proliferation, apoptosis of human corneal epithelial cells (HCEC). Methods: The MTT method was used to screen and take the optimal high-glucose concentration, treatment time, and PDC concentration using HCEC and divide it into 4 groups: control group (C), high glucose group (HG), PDC group, and HG + PDC group. We observed and compared the effect of the 4 groups on HCEC proliferation by MTT, apoptosis by Annexin V-FITC/PI double fluorescent staining and flow cytometry (FCM), and expression of bax mRNA and bcl-2 mRNA by RT-qPCR. Results: Compared with the control group, proliferative activity of HCEC cells was reduced; the cells apoptosis ratio was increased; the expression of bax mRNA was increased, and the expression of bcl-2 mRNA was reduced in the HG group. Proliferative activity of HCEC cells in the PDC group was increased, and the expression of bcl-2 mRNA was increased but that of bax mRNA was decreased. Proliferative activity of HCEC cells in the HG + PDC group was increased, but it could not restore to the normal level; the expression of bax mRNA was significantly decreased but the expression of bcl-2 mRNA was significantly increased. Conclusions: Our results demonstrate that high glucose can inhibit proliferative activity and induce apoptosis of HCEC. PDC can improve the proliferative activity of HCEC cells under the high glucose environment and reduce the apoptosis of cells by regulating the expression of bax and bcl-2. PDC play a very important role on protecting and repairing of corneal epithelial cells damage in high glucose. PMID:28796073

The chemokine receptor CCR2 maintains plasmacytoid dendritic cell homeostasis

DEFF Research Database (Denmark)

Cédile, Oriane; Østerby Jørgensen, Line; Frank, Ida

2017-01-01

Thymic dendritic cells (DC) play a role in central tolerance. Three thymic DC subtypes have been described: plasmacytoid DC (pDC) and two conventional DC (cDC), CD8α+ Sirpα- DC and Sirpα+ CD8α- cDC. Both pDC and Sirpα+ cDC can take up antigen in periphery and migrate into the thymus in response t...... by CCL2 or CCR2 deficiency. Although some thymic progenitors expressed CCR2, this did not include those that give rise to pDC. Based on these results, we propose that CCR2 is involved in pDC homeostasis but its ligand CCL2 does not play a major role....

Phosphorylation status of pyruvate dehydrogenase distinguishes metabolic phenotypes of cultured rat brain astrocytes and neurons.

Science.gov (United States)

Halim, Nader D; Mcfate, Thomas; Mohyeldin, Ahmed; Okagaki, Peter; Korotchkina, Lioubov G; Patel, Mulchand S; Jeoung, Nam Ho; Harris, Robert A; Schell, Michael J; Verma, Ajay

2010-08-01

Glucose metabolism in nervous tissue has been proposed to occur in a compartmentalized manner with astrocytes contributing largely to glycolysis and neurons being the primary site of glucose oxidation. However, mammalian astrocytes and neurons both contain mitochondria, and it remains unclear why in culture neurons oxidize glucose, lactate, and pyruvate to a much larger extent than astrocytes. The objective of this study was to determine whether pyruvate metabolism is differentially regulated in cultured neurons versus astrocytes. Expression of all components of the pyruvate dehydrogenase complex (PDC), the rate-limiting step for pyruvate entry into the Krebs cycle, was determined in cultured astrocytes and neurons. In addition, regulation of PDC enzymatic activity in the two cell types via protein phosphorylation was examined. We show that all components of the PDC are expressed in both cell types in culture, but that PDC activity is kept strongly inhibited in astrocytes through phosphorylation of the pyruvate dehydrogenase alpha subunit (PDH alpha). In contrast, neuronal PDC operates close to maximal levels with much lower levels of phosphorylated PDH alpha. Dephosphorylation of astrocytic PDH alpha restores PDC activity and lowers lactate production. Our findings suggest that the glucose metabolism of astrocytes and neurons may be far more flexible than previously believed. (c) 2010 Wiley-Liss, Inc.

Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: implications for movement of the C-terminal cysteine-rich domain

International Nuclear Information System (INIS)

Suzuki, Nobuhiro; Yamazaki, Yasuo; Brown, R. Lane; Fujimoto, Zui; Morita, Takashi; Mizuno, Hiroshi

2008-01-01

The structures of pseudechetoxin and pseudecin suggest that both proteins bind to cyclic nucleotide-gated ion channels in a manner in which the concave surface occludes the pore entrance. Cyclic nucleotide-gated (CNG) ion channels play pivotal roles in sensory transduction by retinal photoreceptors and olfactory neurons. The elapid snake toxins pseudechetoxin (PsTx) and pseudecin (Pdc) are the only known protein blockers of CNG channels. These toxins belong to a cysteine-rich secretory protein (CRISP) family containing an N-terminal pathogenesis-related proteins of group 1 (PR-1) domain and a C-terminal cysteine-rich domain (CRD). PsTx and Pdc are highly homologous proteins, but their blocking affinities on CNG channels are different: PsTx blocks both the olfactory and retinal channels with ∼15–30-fold higher affinity than Pdc. To gain further insights into their structure and function, the crystal structures of PsTx, Pdc and Zn 2+ -bound Pdc were determined. The structures revealed that most of the amino-acid-residue differences between PsTx and Pdc are located around the concave surface formed between the PR-1 domain and the CRD, suggesting that the concave surface is functionally important for CNG-channel binding and inhibition. A structural comparison in the presence and absence of Zn 2+ ion demonstrated that the concave surface can open and close owing to movement of the CRD upon Zn 2+ binding. The data suggest that PsTx and Pdc occlude the pore entrance and that the dynamic motion of the concave surface facilitates interaction with the CNG channels

Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: implications for movement of the C-terminal cysteine-rich domain

Energy Technology Data Exchange (ETDEWEB)

Suzuki, Nobuhiro [Department of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572 (Japan); Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); Yamazaki, Yasuo [Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan); Brown, R. Lane [Neurological Science Institute, Oregon Health and Science University, Beaverton, Oregon 97006 (United States); Fujimoto, Zui [Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); Morita, Takashi, E-mail: tmorita@my-pharm.ac.jp [Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan); Mizuno, Hiroshi, E-mail: tmorita@my-pharm.ac.jp [Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); VALWAY Technology Center, NEC Soft Ltd, Koto-ku, Tokyo 136-8627 (Japan); Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Central 6, Tsukuba, Ibaraki 305-8566 (Japan); Department of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572 (Japan)

2008-10-01

The structures of pseudechetoxin and pseudecin suggest that both proteins bind to cyclic nucleotide-gated ion channels in a manner in which the concave surface occludes the pore entrance. Cyclic nucleotide-gated (CNG) ion channels play pivotal roles in sensory transduction by retinal photoreceptors and olfactory neurons. The elapid snake toxins pseudechetoxin (PsTx) and pseudecin (Pdc) are the only known protein blockers of CNG channels. These toxins belong to a cysteine-rich secretory protein (CRISP) family containing an N-terminal pathogenesis-related proteins of group 1 (PR-1) domain and a C-terminal cysteine-rich domain (CRD). PsTx and Pdc are highly homologous proteins, but their blocking affinities on CNG channels are different: PsTx blocks both the olfactory and retinal channels with ∼15–30-fold higher affinity than Pdc. To gain further insights into their structure and function, the crystal structures of PsTx, Pdc and Zn{sup 2+}-bound Pdc were determined. The structures revealed that most of the amino-acid-residue differences between PsTx and Pdc are located around the concave surface formed between the PR-1 domain and the CRD, suggesting that the concave surface is functionally important for CNG-channel binding and inhibition. A structural comparison in the presence and absence of Zn{sup 2+} ion demonstrated that the concave surface can open and close owing to movement of the CRD upon Zn{sup 2+} binding. The data suggest that PsTx and Pdc occlude the pore entrance and that the dynamic motion of the concave surface facilitates interaction with the CNG channels.

The Role of Pyruvate Dehydrogenase Kinase in Diabetes and Obesity

Directory of Open Access Journals (Sweden)

In-Kyu Lee

2014-06-01

Full Text Available The pyruvate dehydrogenase complex (PDC is an emerging target for the treatment of metabolic syndrome. To maintain a steady-state concentration of adenosine triphosphate during the feed-fast cycle, cells require efficient utilization of fatty acid and glucose, which is controlled by the PDC. The PDC converts pyruvate, coenzyme A (CoA, and oxidized nicotinamide adenine dinucleotide (NAD+ into acetyl-CoA, reduced form of nicotinamide adenine dinucleotide (NADH, and carbon dioxide. The activity of the PDC is up- and down-regulated by pyruvate dehydrogenase kinase and pyruvate dehydrogenase phosphatase, respectively. In addition, pyruvate is a key intermediate of glucose oxidation and an important precursor for the synthesis of glucose, glycerol, fatty acids, and nonessential amino acids.

Lipid Raft, Regulator of Plasmodesmal Callose Homeostasis

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Arya Bagus Boedi Iswanto

2017-04-01

Full Text Available Abstract: The specialized plasma membrane microdomains known as lipid rafts are enriched by sterols and sphingolipids. Lipid rafts facilitate cellular signal transduction by controlling the assembly of signaling molecules and membrane protein trafficking. Another specialized compartment of plant cells, the plasmodesmata (PD, which regulates the symplasmic intercellular movement of certain molecules between adjacent cells, also contains a phospholipid bilayer membrane. The dynamic permeability of plasmodesmata (PDs is highly controlled by plasmodesmata callose (PDC, which is synthesized by callose synthases (CalS and degraded by β-1,3-glucanases (BGs. In recent studies, remarkable observations regarding the correlation between lipid raft formation and symplasmic intracellular trafficking have been reported, and the PDC has been suggested to be the regulator of the size exclusion limit of PDs. It has been suggested that the alteration of lipid raft substances impairs PDC homeostasis, subsequently affecting PD functions. In this review, we discuss the substantial role of membrane lipid rafts in PDC homeostasis and provide avenues for understanding the fundamental behavior of the lipid raft–processed PDC.

Lipid Raft, Regulator of Plasmodesmal Callose Homeostasis.

Science.gov (United States)

Iswanto, Arya Bagus Boedi; Kim, Jae-Yean

2017-04-03

A bstract: The specialized plasma membrane microdomains known as lipid rafts are enriched by sterols and sphingolipids. Lipid rafts facilitate cellular signal transduction by controlling the assembly of signaling molecules and membrane protein trafficking. Another specialized compartment of plant cells, the plasmodesmata (PD), which regulates the symplasmic intercellular movement of certain molecules between adjacent cells, also contains a phospholipid bilayer membrane. The dynamic permeability of plasmodesmata (PDs) is highly controlled by plasmodesmata callose (PDC), which is synthesized by callose synthases (CalS) and degraded by β-1,3-glucanases (BGs). In recent studies, remarkable observations regarding the correlation between lipid raft formation and symplasmic intracellular trafficking have been reported, and the PDC has been suggested to be the regulator of the size exclusion limit of PDs. It has been suggested that the alteration of lipid raft substances impairs PDC homeostasis, subsequently affecting PD functions. In this review, we discuss the substantial role of membrane lipid rafts in PDC homeostasis and provide avenues for understanding the fundamental behavior of the lipid raft-processed PDC.

A critical review of the postulated role of the non-essential amino acid, β-N-methylamino-L-alanine, in neurodegenerative disease in humans

Science.gov (United States)

Chernoff, Neil; Hill, D. J.; Diggs, D. L.; Faison, B. D.; Francis, B. M.; Lang, J. R.; Larue, M. M.; Le, T.-T.; Loftin, Keith A.; Lugo, J. N.; Schmid, J. E.; Winnik, W. W.

2017-01-01

The compound BMAA (β-N-methylamino-L-alanine) has been postulated to play a significant role in four serious neurological human diseases: Amyotrophic Lateral Sclerosis/Parkinsonism Dementia Complex (ALS/PDC) found on Guam, and ALS, Parkinsonism, and dementia that occur globally. ALS/PDC with symptoms of all three diseases first came to the attention of the scientific community during and after World War II. It was initially associated with cycad flour used for food because BMAA is a product of symbiotic cycad root-dwelling cyanobacteria. Human consumption of flying foxes that fed on cycad seeds was later suggested as a source of BMAA on Guam and a cause of ALS/PDC. Subsequently, the hypothesis was expanded to include a causative role for BMAA in other neurodegenerative diseases including Alzheimer’s disease (AD) through exposures attributed to proximity to freshwaters and/or consumption of seafood due to its purported production by most species of cyanobacteria. The hypothesis that BMAA is the critical factor in the genesis of these neurodegenerative diseases received considerable attention in the medical, scientific, and public arenas. This review examines the history of ALS/PDC and the BMAA-human disease hypotheses; similarities and differences between ALS/PDC and the other diseases with similar symptomologies; the relationship of ALS/PDC to other similar diseases, studies of BMAA-mediated effects in lab animals, inconsistencies and data gaps in the hypothesis; and other compounds and agents that were suggested as the cause of ALS/PDC on Guam. The review concludes that the hypothesis of a causal BMAA neurodegenerative disease relationship is not supported by existing data.

Serum Reactivity Against Bacterial Pyruvate Dehydrogenase: Increasing the Specificity of Anti-Mitochondrial Antibodies for the Diagnosis of Primary Biliary Cirrhosis

Directory of Open Access Journals (Sweden)

Hiroshi Miyakawa

2006-01-01

Full Text Available Antimitochondrial antibodies (AMA are the serum hallmark of primary biliary cirrhosis (PBC. However, AMA-positivity can be found in non-PBC sera when lower dilutions are used, thus raising issues about the specificity and sensitivity of the test. AMA reacts primarily with the lipoylated domains of pyruvate dehydrogenase-E2 (PDC-E2 which is highly conserved across species, including bacteria. We studied 77 serum samples, including 24 from patients with anti-PDC-E2-positive PBC and 53 controls (16 with autoimmune hepatitis (AIH, 10 with primary sclerosing cholangitis (PSC, and 27 healthy individuals for their reactivities at serial dilutions (1:10, 1:20 and 1:40 against Escherichia coli DH5 alpha lysate overexpressing human PDC-E2 using immunoblotting (IB. A murine anti-human PDC-E2 monoclonal antibody (mAB was used as control. We further studied positive sera using adsorption with a synthetic E. coli peptide sharing similarity with human PDC-E2. Finally, we verified whether a unique buffer for E. coli preparation could reduce non-specific serum reactivity. Results demonstrated that 100% of anti-PDC-E2-positive PBC and up to 38% of control sera at 1:10 dilution recognized E. coli PDC-E2 at IB while dilution tests indicated that the overall potency of PBC reactivity was 100-fold higher compared to controls. In fact, a subgroup (20-38% of non-PBC sera were positive at low titers but lost the reactivity when absorbed with the synthetic E. coli peptide. Finally, our unique buffer reduced the reactivity of non-PBC sera as measured by ELISA. In conclusion, we demonstrated that weak cross-reactivity with E. coli PDC-E2 occurs in non-PBC sera at lower dilutions and that such reactivity is not due to AMA-positivity. The use of a specific buffer might avoid the risk of false positive AMA determinations when E. coli-expressed recombinant antigens are used.

cGAS Senses Human Cytomegalovirus and Induces Type I Interferon Responses in Human Monocyte-Derived Cells.

Directory of Open Access Journals (Sweden)

Jennifer Paijo

2016-04-01

Full Text Available Human cytomegalovirus (HCMV infections of healthy individuals are mostly unnoticed and result in viral latency. However, HCMV can also cause devastating disease, e.g., upon reactivation in immunocompromised patients. Yet, little is known about human immune cell sensing of DNA-encoded HCMV. Recent studies indicated that during viral infection the cyclic GMP/AMP synthase (cGAS senses cytosolic DNA and catalyzes formation of the cyclic di-nucleotide cGAMP, which triggers stimulator of interferon genes (STING and thus induces antiviral type I interferon (IFN-I responses. We found that plasmacytoid dendritic cells (pDC as well as monocyte-derived DC and macrophages constitutively expressed cGAS and STING. HCMV infection further induced cGAS, whereas STING expression was only moderately affected. Although pDC expressed particularly high levels of cGAS, and the cGAS/STING axis was functional down-stream of STING, as indicated by IFN-I induction upon synthetic cGAMP treatment, pDC were not susceptible to HCMV infection and mounted IFN-I responses in a TLR9-dependent manner. Conversely, HCMV infected monocyte-derived cells synthesized abundant cGAMP levels that preceded IFN-I production and that correlated with the extent of infection. CRISPR/Cas9- or siRNA-mediated cGAS ablation in monocytic THP-1 cells and primary monocyte-derived cells, respectively, impeded induction of IFN-I responses following HCMV infection. Thus, cGAS is a key sensor of HCMV for IFN-I induction in primary human monocyte-derived DC and macrophages.

Directed evolution of pyruvate decarboxylase-negative Saccharomyces cerevisiae, yielding a C2-independent, glucose-tolerant, and pyruvate-hyperproducing yeast

NARCIS (Netherlands)

A.J. van Maris; J.M. Geertman; A. Vermeulen; M.K. Groothuizen; A.A. Winkler; M.D. Piper; J.P. van Dijken; J.T. Pronk

2004-01-01

textabstractThe absence of alcoholic fermentation makes pyruvate decarboxylase-negative (Pdc(-)) strains of Saccharomyces cerevisiae an interesting platform for further metabolic engineering of central metabolism. However, Pdc(-) S. cerevisiae strains have two growth defects:

Distally displaced premolars: A dental anomaly associated with palatally displaced canines.

Science.gov (United States)

Baccetti, Tiziano; Leonardi, Maria; Giuntini, Veronica

2010-09-01

The aim of this study was to evaluate the significance of association between distally displaced premolars (DDP) and palatally displaced canines (PDC) in the pattern of associated phenotypes of dental developmental disturbance. A sample of 2811 subjects (mean age, 9 years 7 months +/- 1 year 3 months) was divided randomly into 2 groups. The first group of 500 subjects was the control group. The reference prevalence rates for the examined parameters were calculated for this group: DDP (measured with the distal angle theta and the premolar-molar angle gamma); PDC; and other dental anomalies, specifically, aplasia of the third molars, aplasia of the contralateral mandibular second premolar, aplasia of the maxillary lateral incisors, and small maxillary lateral incisors. Of the remaining 2311 subjects, the first 100 with a diagnosis of DDP of at least 1 mandibular second premolar comprised experimental group 1 (DDP group). In addition to sex distribution, the same variables that were examined in the control group were analyzed. In the subgroup with the concurrent DDP and PDC (experimental group 2, or DDP-PDC group), the presence of other dental anomalies was investigated. The prevalence rate for PDC in experimental group 1 was compared with that in the control group. The same was done for the prevalence rates for the 4 other dental anomalies in the PDC-DDP group (experimental group 2) vs the prevalence rates for these anomalies in the control group. All comparisons were performed with chi-square tests with the Yates correction (P <0.05), as were the comparisons between the sexes in experimental groups 1 and 2. The values for theta and gamma angles in experimental group 1 were compared with the values for these angles in experimental group 2, as well as with those in the control group. These statistical comparisons were made with analysis of variance (ANOVA) with the Bonferroni post-hoc test (P <0.05). The prevalence rate for PDC in experimental group 1 (28%) was

Determinants of patient satisfaction with cancer care delivered by the Danish healthcare system

DEFF Research Database (Denmark)

Heerdegen, Anne Christine Stender; Petersen, Gitte Stentebjerg; Jervelund, Signe Smith

2017-01-01

, comorbidity, self-reported health, and region of treatment significantly determined ratings of CDT. Patients who reported negative experiences related to waiting time, information, coordination, and continuity of care during PDC and CDT, respectively, were significantly less likely overall to rate their care......BACKGROUND: Patient-reported quality of care, which is often measured by patients' overall rating of care, is gaining more attention within the field of oncology. The aim of this study was to examine factors that determine adult cancer patients' overall rating of prediagnosis care (PDC) and care......). Multivariable logistic regression models were applied. RESULTS: Overall, 55.1% of patients reported excellent PDC and 61.9% reported excellent CDT. The odds of rating PDC and CDT as excellent differed significantly according to sex, age, and cancer diagnosis. Furthermore, the extent of supportive relatives...

Participatory Design in an Era of Participation, Special Issue

DEFF Research Database (Denmark)

This special issue on participatory design in an era of participation presents emerging topics and discussions from the thirteenth Participatory Design conference (PDC), held at Aarhus University in August 2016. The PDC 2016 marked the twenty-fifth anniversary of the Participatory Design conference...... series, which began in 1990 with the first biannual conference in Seattle. Since then, the PDC conferences have continued to bring together a multidisciplinary, international community of researchers and practitioners around issues of cooperative design. The theme for the 2016 PDC conference...... was ‘Participatory Design in an Era of Participation.’ Critical and constructive discussions were invited on the values, characteristics, politics and future practices of participatory design in an era in which participation has now become pervasive (Bossen, Smith, Kanstrup, McDonnell, et al. 2016, Bossen, Smith...

A COMPARATIVE ANALYSIS OF PERCUTANEOUS AND OPEN SURGICAL TECHNIQUESFOR PERITONEAL CATHETER PLACEMENT.

LENUS (Irish Health Repository)

Medani, Samar

2012-05-01

BACKGROUND: Peritoneal dialysis (PD) is the preferred available option of renal replacement therapy for a significant number of end-stage kidney disease patients. A major limiting factor to the successful continuation of PD is the long-term viability of the PD catheter (PDC). Bedside percutaneous placement of the PDC is not commonly practiced despite published data encouraging use of this technique. Its advantages include faster recovery and avoidance of general anesthesia.♢ METHODS: We carried out a retrospective analysis of the outcomes of 313 PDC insertions at our center, comparing all percutaneous PDC insertions between July 1998 and April 2010 (group P, n = 151) with all surgical PDC insertions between January 2003 and April 2010 (group S, n = 162).♢ RESULTS: Compared with group P patients, significantly more group S patients had undergone previous abdominal surgery or PDC insertion (41.8% vs 9.3% and 33.3% vs 3.3% respectively, p = 0.00). More exit-site leaks occurred in group P than in group S (20.5% vs 6.8%, p = 0.002). The overall incidence of peritonitis was higher in group S than in group P (1 episode in 19 catheter-months vs 1 episode in 26 catheter-months, p = 0.017), but the groups showed no significant difference in the peritonitis rate within 1 month of catheter insertion (5% in group P vs 7.4% in group S, p =0.4) or in poor initial drainage or secondary drainage failure (9.9% vs 11.7%, p = 0.1, and 7.9% vs 12.3%, p = 0.38, for groups P and S respectively). Technical survival at 3 months was significantly better for group P than for group S (86.6% vs 77%, p = 0.037); at 12 months, it was 77.7% and 68.7% respectively (p = 0.126). No life-threatening complications attributable to the insertion of the PDC occurred in either group.♢ CONCLUSIONS: Our analysis demonstrates further encouraging outcomes of percutaneous PDC placement compared with open surgical placement. However, the members of the percutaneous insertion group were primarily a

Detection scheme for bioassays based on 2,6-pyridinedicarboxylic acid derivatives and enzyme-amplified lanthanide luminescence

Energy Technology Data Exchange (ETDEWEB)

Steinkamp, Tanja [Department of Chemical Analysis, MESA Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); Karst, Uwe [Department of Chemical Analysis, MESA Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands)]. E-mail: u.karst@utwente.nl

2004-11-15

2,6-Pyridinedicarboxylic acid (PDC) and its derivatives are introduced as a new sensitizer system for enzyme-amplified lanthanide luminescence (EALL), a detection scheme for bioassays, which combines enzymatic amplification with time-resolved luminescence measurements of lanthanide chelates. Various PDC esters have been synthesized as esterase substrates that are cleaved to PDC in the presence of the enzyme. PDC forms luminescent complexes with Tb(III) or Eu(III), and the evaluation of the reaction is used for the selective and sensitive detection of esterases. For an esterase from hog liver a limit of detection of 10{sup -3} u/mL (equivalent to 10{sup -9} mol/L) and a limit of quantification of 3 x 10{sup -3} u/mL (equivalent to 3 x 10{sup -9} mol/L) could be achieved. As a second model reaction, xanthine oxidase (XOD) catalyzes the oxidation of 2,6-pyridinedicarboxaldehyde to PDC. Here, the limit of detection was 3 x 10{sup -3} u/mL and the limit of quantification 10{sup -2} u/mL for XOD from microorganisms. Major advantage of the tridentate PDC ligand is the possibility to perform all steps of the assay within or close to the physiological pH range, while the established EALL schemes based on bidentate salicylates or bisphenols have to be carried out at strongly alkaline pH to ensure sufficient complexation with the lanthanides.

Esterification of oil adsorbed on palm decanter cake into methyl ester using sulfonated rice husk ash as heterogeneous acid catalyst

Science.gov (United States)

Hindryawati, Noor; Erwin, Maniam, Gaanty Pragas

2017-02-01

Palm Decanter cake (PDC) which is categorized as the waste from palm oil mill has been found to contain residual crude palm oil. The oil adsorbed on the PDC (PDC-oil) can be extracted and potentially used as feedstock for biodiesel production. Feedstock from waste like PDC-oil is burdened with high free fatty acids (FFAs) which make the feedstock difficult to be converted into biodiesel using basic catalyst. Therefore, in this study, a solid acid, RHA-SO3H catalyst was synthesized by sulfonating rice husk ash (RHA) with concentrated sulfuric acid. The RHA-SO3H prepared was characterized with TGA, FTIR, BET, XRD, FE-SEM, and Hammett indicators (methyl red, bromophenol blue, and crystal violet). PDC was found to have about 11.3 wt. % oil recovered after 1 hour extraction using ultrasound method. The presence of sulfonate group was observed in IR spectrum, and the surface area of RHA-SO3H was reduced to 37 m2.g-1 after impregnation of sulfonate group. The RHA-SO3H catalyst showed that it can work for both esterification of free fatty acid which is present in PDC-oil, and transesterification of triglycerides into methyl ester. The results showed highest methyl ester content of 70.2 wt.% at optimal conditions, which was 6 wt.% catalyst amount, methanol to oil molar ratio of 17:1 for 5 hours at 120 °C.

Fat tissue after lipolysis of lipomas: a histopathological and immunohistochemical study.

Science.gov (United States)

Bechara, Falk G; Sand, Michael; Hoffmann, Klaus; Sand, Daniel; Altmeyer, Peter; Stücker, Markus

2007-07-01

Injections with Lipostabil, a phosphatidylcholine (PDC) containing substance, have become a popular technique to treat localized fat accumulation and lipomas for aesthetic reasons. Despite its frequent use, the mechanism of action of PDC and histological changes of treated fat tissue still remain unclear. To investigate the histological changes of lipomas after treatment with PDC. In all, fourteen lipomas (n = 14) in five patients presenting with multiple lipomas were treated with intralesional injections of PDC (Lipostabil, Nettermann, Germany). Histological changes with immunohistochemical analysis of the inflammatory process were evaluated 4, 10, 24, 48 h, 10 days, 30 days and 60 days after lipolysis. Between 4 and 48 h after injection, histology shows a lobular neutrophilic infiltrate with partially destroyed fat cells. At day 10 the inflammatory process is accompanied by an infiltration of T-lymphocytes. After 60 days formation of macrophages with foam cells are visible, accompanied by thickened septa and capsula. Lipolysis with PDC results in a distinct inflammatory reaction of affected fat tissue, similar to factitial panniculitis. Early destruction of fat cells may suggest the involvement of detergent or osmotic mechanisms in the process.

Nuclear power desalinating complex with IRIS reactor plant and Russian distillation desalinating unit

International Nuclear Information System (INIS)

Kostin, V. I.; Panov, Yu.K.; Polunichev, V. I.; Fateev, S. A.; Gureeva, L. V.

2004-01-01

This paper has been prepared as a result of Russian activities on the development of nuclear power desalinating complex (NPDC) with the IRIS reactor plant (RP). The purpose of the activities was to develop the conceptual design of power desalinating complex (PDC) and to evaluate technical and economical indices, commercial attractiveness and economical efficiency of PDC based on an IRIS RP with distillation desalinating plants. The paper presents the main results of studies as applied to dual-purpose PDC based on IRIS RP with different types of desalinating plants, namely: characteristics of nuclear power desalinating complex based on IRIS reactor plant using Russian distillation desalinating technologies; prospective options of interface circuits of the IRIS RP with desalinating plants; evaluations of NPDC with IRIS RP output based on selected desalinating technologies for water and electric power supplied to the grid; cost of water generated by NPDC for selected interface circuits made by the IAEA DEEP code as well as by the Russian TEO-INVEST code; cost evaluation results for desalinated water of PDC operating on fossil fuel and conditions for competitiveness of the nuclear PDC based on IRIS RP compared with analog desalinating complexes operating on fossil fuel.(author)

An internal deletion in MTH1 enables growth on glucose of pyruvate-decarboxylase negative, non-fermentative Saccharomyces cerevisiae

NARCIS (Netherlands)

Oud, B.; Flores, C.L.; Gancedo, C.; Zhang, X.; Trueheart, J.; Daran, J.M.; Pronk, J.T.; Van Maris, A.J.A.

2012-01-01

Background Pyruvate-decarboxylase negative (Pdc-) strains of Saccharomyces cerevisiae combine the robustness and high glycolytic capacity of this yeast with the absence of alcoholic fermentation. This makes Pdc-S. cerevisiae an interesting platform for efficient conversion of glucose towards

Stemcell Information: SKIP000600 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000600 ... Diseased PDC3F-1 PDC3F-1 ... パーキンソン病 G20 Parkinson disease 168600 ... ...titute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived

Pyruvate decarboxylases from the petite-negative yeast Saccharomyces kluyveri

DEFF Research Database (Denmark)

Møller, Kasper; Langkjær, Rikke Breinhold; Nielsen, Jens

2004-01-01

was controlled by variations in the amount of mRNA. The mRNA level and the pyruvate decarboxylase activity responded to anaerobiosis and growth on different carbon sources in essentially the same fashion as in S. cerevisiae. This indicates that the difference in ethanol formation between these two yeasts...... is not due to differences in the regulation of pyruvate decarboxylase(s), but rather to differences in the regulation of the TCA cycle and the respiratory machinery. However, the PDC genes of Saccharomyces/Kluyveromyces yeasts differ in their genetic organization and phylogenetic origin. While S. cerevisiae...

Integrative proteomics and biochemical analyses define Ptc6p as the Saccharomyces cerevisiae pyruvate dehydrogenase phosphatase.

Science.gov (United States)

Guo, Xiao; Niemi, Natalie M; Coon, Joshua J; Pagliarini, David J

2017-07-14

The pyruvate dehydrogenase complex (PDC) is the primary metabolic checkpoint connecting glycolysis and mitochondrial oxidative phosphorylation and is important for maintaining cellular and organismal glucose homeostasis. Phosphorylation of the PDC E1 subunit was identified as a key inhibitory modification in bovine tissue ∼50 years ago, and this regulatory process is now known to be conserved throughout evolution. Although Saccharomyces cerevisiae is a pervasive model organism for investigating cellular metabolism and its regulation by signaling processes, the phosphatase(s) responsible for activating the PDC in S. cerevisiae has not been conclusively defined. Here, using comparative mitochondrial phosphoproteomics, analyses of protein-protein interactions by affinity enrichment-mass spectrometry, and in vitro biochemistry, we define Ptc6p as the primary PDC phosphatase in S. cerevisiae Our analyses further suggest additional substrates for related S. cerevisiae phosphatases and describe the overall phosphoproteomic changes that accompany mitochondrial respiratory dysfunction. In summary, our quantitative proteomics and biochemical analyses have identified Ptc6p as the primary-and likely sole- S. cerevisiae PDC phosphatase, closing a key knowledge gap about the regulation of yeast mitochondrial metabolism. Our findings highlight the power of integrative omics and biochemical analyses for annotating the functions of poorly characterized signaling proteins. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

PdRu/C catalysts for ethanol oxidation in anion-exchange membrane direct ethanol fuel cells

Science.gov (United States)

Ma, Liang; He, Hui; Hsu, Andrew; Chen, Rongrong

2013-11-01

Carbon supported PdRu catalysts with various Pd:Ru atomic ratios were synthesized by impregnation method, and characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), electrochemical half-cell tests, and the anion-exchange membrane direct ethanol fuel cell (AEM-DEFC) tests. XRD results suggest that the PdRu metal exists on carbon support in an alloy form. TEM study shows that the bimetallic PdRu/C catalysts have slightly smaller average particle size than the single metal Pd/C catalyst. Lower onset potential and peak potential and much higher steady state current for ethanol oxidation in alkaline media were observed on the bimetallic catalysts (PdxRuy/C) than on the Pd/C, while the activity for ethanol oxidation on the pure Ru/C was not noticeable. By using Pd/C anode catalysts and MnO2 cathode catalysts, AEM-DEFCs free from the expensive Pt catalyst were assembled. The AEM DEFC using the bimetallic Pd3Ru/C anode catalyst showed a peak power density as high as 176 mW cm-2 at 80 °C, about 1.8 times higher than that using the single metal Pd/C catalyst. The role of Ru for enhancing the EOR activity of Pd/C catalysts is discussed.

Utilizing a Pediatric Disaster Coalition Model to Increase Pediatric Critical Care Surge Capacity in New York City.

Science.gov (United States)

Frogel, Michael; Flamm, Avram; Sagy, Mayer; Uraneck, Katharine; Conway, Edward; Ushay, Michael; Greenwald, Bruce M; Pierre, Louisdon; Shah, Vikas; Gaffoor, Mohamed; Cooper, Arthur; Foltin, George

2017-08-01

A mass casualty event can result in an overwhelming number of critically injured pediatric victims that exceeds the available capacity of pediatric critical care (PCC) units, both locally and regionally. To address these gaps, the New York City (NYC) Pediatric Disaster Coalition (PDC) was established. The PDC includes experts in emergency preparedness, critical care, surgery, and emergency medicine from 18 of 25 major NYC PCC-capable hospitals. A PCC surge committee created recommendations for making additional PCC beds available with an emphasis on space, staff, stuff (equipment), and systems. The PDC assisted 15 hospitals in creating PCC surge plans by utilizing template plans and site visits. These plans created an additional 153 potential PCC surge beds. Seven hospitals tested their plans through drills. The purpose of this article was to demonstrate the need for planning for disasters involving children and to provide a stepwise, replicable model for establishing a PDC, with one of its primary goals focused on facilitating PCC surge planning. The process we describe for developing a PDC can be replicated to communities of any size, setting, or location. We offer our model as an example for other cities. (Disaster Med Public Health Preparedness. 2017;11:473-478).

Novel polymer derived ceramic-high temperature heat flux sensor for gas turbine environment

International Nuclear Information System (INIS)

Nagaiah, N R; Kapat, J S; An, L; Chow, L

2006-01-01

This paper attempts to prove the feasibility of a novel High Temperature Heat Flux (HTHF) sensor for gas turbine environment. Based on the latest improvement in a new type of Polymer-Derived Ceramic (PDC) material, the authors present the design and development of a HTHF sensor based on PDC material, and show that such a sensor is indeed feasible. The PDC-HTHF sensor is fabricated using newly developed polymer derived SiCN, whose conductivity is controlled by proper composition and treatment condition. Direct measurements and characterization of the relevant material properties are presented. Electrical conductivity can be varied from 0 (insulator) to 100 (ohm.cm) -1 ; in addition a value of 4000 ppm/ 0 C (at 600 K) is obtained for temperature coefficient of resistance. This novel sensor is found to perform quite satisfactorily at about 1400 0 C for long term as compared to conventional heat flux sensors available commercially. This type of PDC-HTHF sensor can be used in harsh environments due to its high temperature resistance and resistance to oxidation. This paper also discusses lithography as a microfabrication technique to manufacture the proposed PDC-HTHF sensor. In our current design, the sensor dimensions are 2.5mm in diameter and 250 μm thickness

A proteomics study of barley powdery mildew haustoria.

Science.gov (United States)

Godfrey, Dale; Zhang, Ziguo; Saalbach, Gerhard; Thordal-Christensen, Hans

2009-06-01

A number of fungal and oomycete plant pathogens of major economic importance feed on their hosts by means of haustoria, which they place inside living plant cells. The underlying mechanisms are poorly understood, partly due to difficulty in preparing haustoria. We have therefore developed a procedure for isolating haustoria from the barley powdery mildew fungus (Blumeria graminis f.sp. hordei, Bgh). We subsequently aimed to understand the molecular mechanisms of haustoria through a study of their proteome. Extracted proteins were digested using trypsin, separated by LC, and analysed by MS/MS. Searches of a custom Bgh EST sequence database and the NCBI-NR fungal protein database, using the MS/MS data, identified 204 haustoria proteins. The majority of the proteins appear to have roles in protein metabolic pathways and biological energy production. Surprisingly, pyruvate decarboxylase (PDC), involved in alcoholic fermentation and commonly abundant in fungi and plants, was absent in our Bgh proteome data set. A sequence encoding this enzyme was also absent in our EST sequence database. Significantly, BLAST searches of the recently available Bgh genome sequence data also failed to identify a sequence encoding this enzyme, strongly indicating that Bgh does not have a gene for PDC.

Risk factors for peritoneal dialysis catheter failure in children ...

African Journals Online (AJOL)

Background Peritoneal dialysis catheter (PDC) failure still remains a common clinical problem in pediatric patients despite advancements in catheter placement and dialysis techniques. Our aim was to determine the risk factors that may lead to PDC failure, especially those factors that could be potentially modified to ...

Evaluating the Performance Diagnostic Checklist-Human Services to Assess Incorrect Error-Correction Procedures by Preschool Paraprofessionals

Science.gov (United States)

Bowe, Melissa; Sellers, Tyra P.

2018-01-01

The Performance Diagnostic Checklist-Human Services (PDC-HS) has been used to assess variables contributing to undesirable staff performance. In this study, three preschool teachers completed the PDC-HS to identify the factors contributing to four paraprofessionals' inaccurate implementation of error-correction procedures during discrete trial…

Partners in Dementia Care: A Care Coordination Intervention for Individuals with Dementia and Their Family Caregivers

Science.gov (United States)

Judge, Katherine S.; Bass, David M.; Snow, A. Lynn; Wilson, Nancy L.; Morgan, Robert; Looman, Wendy J.; McCarthy, Catherine; Kunik, Mark E.

2011-01-01

Purpose: This article provides a detailed description of a telephone-based care coordination intervention, Partners in Dementia Care (PDC), for veterans with dementia and their family caregivers. Essential features of PDC included (a) formal partnerships between Veterans Affairs (VA) medical centers and Alzheimer's Association Chapters; (b) a…

Risk of developing palatally displaced canines in patients with early detectable dental anomalies: a retrospective cohort study.

Science.gov (United States)

Garib, Daniela Gamba; Lancia, Melissa; Kato, Renata Mayumi; Oliveira, Thais Marchini; Neves, Lucimara Teixeira das

2016-01-01

To estimate the risk of PDC occurrence in children with dental anomalies identified early during mixed dentition. The sample comprised 730 longitudinal orthodontic records from children (448 females and 282 males) with an initial mean age of 8.3 years (SD=1.36). The dental anomaly group (DA) included 263 records of patients with at least one dental anomaly identified in the initial or middle mixed dentition. The non-dental anomaly group (NDA) was composed of 467 records of patients with no dental anomalies. The occurrence of PDC in both groups was diagnosed using panoramic and periapical radiographs taken in the late mixed dentition or early permanent dentition. The prevalence of PDC in patients with and without early diagnosed dental anomalies was compared using the chi-square test (pdental anomalies diagnosed during early mixed dentition have an approximately two and a half fold increased risk of developing PDC during late mixed dentition compared with children without dental anomalies.

Medication Adherence Improvements in Employees Participating in a Pharmacist-Run Risk Reduction Program

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Mallory C. McKenzie

2012-01-01

Full Text Available Objective: To evaluate the medication adherence of individuals participating in a pharmacist-run employee health Cardiovascular and Diabetes Risk Reduction Program. Design: Retrospective analysis of medication adherence using pharmacy refill data. Setting: A medium sized university located in the Midwest United States and the organization's outpatient pharmacy. Participants: 38 participants ≥ 18 years of age, employed and receiving their health insurance through the organization, and have a diagnosis of hypertension, hyperlipidemia, diabetes mellitus, or a combination thereof. Intervention: Participation in the risk reduction program that emphasizes medication therapy management (MTM, lifestyle medicine and care coordination. Main Outcome Measures: The Proportion of Days Covered (PDC and the Medication Possession Ratio (MPR. Results: PDC and MPR analysis showed a statistically significant improvement in medication adherence for 180 days and 360 days post enrollment versus the 180 days prior to enrollment (P<0.01. The PDC analysis demonstrated a statistically significant improvement in the number of medications that achieved a PDC ≥ 80% (high adherence for the 180 days post enrollment versus the 180 days prior to enrollment (+30%, P<0.01. The MPR analysis showed a non-statistically significant improvement in the number of medications that achieved an MPR ≥ 80% (high adherence pre enrollment versus post enrollment (+10%, P=0.086. The percentage of participants in the program that reached a PDC and MPR adherence rate ≥ 80% at 180 days post enrollment was 78.9% and 94.4%, respectively which exceeds that of a matched cohort that reached a PDC and MPR adherence rate ≥ 80% of 66.4% and 82.8%, respectively. Conclusion: Pharmacists can improve medication adherence as measured by PDC and MPR when working with employees enrolled in a novel pharmacist-run employee health risk reduction program. Medication adherence was shown to be sustainable for

JAK-inhibitor tofacitinib suppresses interferon alfa production by plasmacytoid dendritic cells and inhibits arthrogenic and antiviral effects of interferon alfa.

Science.gov (United States)

Boor, Patrick P C; de Ruiter, Petra E; Asmawidjaja, Patrick S; Lubberts, Erik; van der Laan, Luc J W; Kwekkeboom, Jaap

2017-10-01

Tofacitinib is an oral Janus kinase inhibitor that is effective for the treatment of rheumatoid arthritis and shows encouraging therapeutic effects in several other autoimmune diseases. A prominent adverse effect of tofacitinib therapy is the increased risk of viral infections. Despite its advanced stage of clinical development, the modes of action that mediate the beneficial and adverse effects of tofacitinib in autoimmune diseases remain unclear. Interferon alfa (IFNα) produced by plasmacytoid dendritic cells (PDCs) is critically involved in the pathogenesis of many systemic autoimmune diseases and in immunity to viral infections. Using in vitro culture models with human cells, we studied the effects of tofacitinib on PDC survival and IFNα production, and on arthrogenic and antiviral effects of IFNα. Tofacitinib inhibited the expression of antiapoptotic BCL-A1 and BCL-XL in human PDC and induced PDC apoptosis. TLR7 stimulation upregulated the levels of antiapoptotic Bcl-2 family members and prevented the induction of PDC apoptosis by tofacitinib. However, tofacitinib robustly inhibited the production of IFNα by toll like receptor-stimulated PDC. In addition, tofacitinib profoundly suppressed IFNα-induced upregulation of TLR3 on synovial fibroblasts, thereby inhibiting their cytokine and protease production in response to TLR3 ligation. Finally, tofacitinib counteracted the suppressive effects of IFNα on viral replication. Tofacitinib inhibits PDC survival and IFNα production and suppresses arthrogenic and antiviral effects of IFNα signaling. Inhibition of the IFNα pathway at 2 levels may contribute to the beneficial effects of tofacitinib in autoimmune diseases and explain the increased viral infection rates observed during tofacitinib treatment. Copyright © 2016 Elsevier Inc. All rights reserved.

Pasture v. standard dairy cream in high-fat diet-fed mice: improved metabolic outcomes and stronger intestinal barrier.

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Benoit, Bérengère; Plaisancié, Pascale; Géloën, Alain; Estienne, Monique; Debard, Cyrille; Meugnier, Emmanuelle; Loizon, Emmanuelle; Daira, Patricia; Bodennec, Jacques; Cousin, Olivier; Vidal, Hubert; Laugerette, Fabienne; Michalski, Marie-Caroline

2014-08-28

Dairy products derived from the milk of cows fed in pastures are characterised by higher amounts of conjugated linoleic acid and α-linolenic acid (ALA), and several studies have shown their ability to reduce cardiovascular risk. However, their specific metabolic effects compared with standard dairy in a high-fat diet (HFD) context remain largely unknown; this is what we determined in the present study with a focus on the metabolic and intestinal parameters. The experimental animals were fed for 12 weeks a HFD containing 20 % fat in the form of a pasture dairy cream (PDC) or a standard dairy cream (SDC). Samples of plasma, liver, white adipose tissue, duodenum, jejunum and colon were analysed. The PDC mice, despite a higher food intake, exhibited lower fat mass, plasma and hepatic TAG concentrations, and inflammation in the adipose tissue than the SDC mice. Furthermore, they exhibited a higher expression of hepatic PPARα mRNA and adipose tissue uncoupling protein 2 mRNA, suggesting an enhanced oxidative activity of the tissues. These results might be explained, in part, by the higher amounts of ALA in the PDC diet and in the liver and adipose tissue of the PDC mice. Moreover, the PDC diet was found to increase the proportions of two strategic cell populations involved in the protective function of the intestinal epithelium, namely Paneth and goblet cells in the small intestine and colon, compared with the SDC diet. In conclusion, a PDC HFD leads to improved metabolic outcomes and to a stronger gut barrier compared with a SDC HFD. This may be due, at least in part, to the protective mechanisms induced by specific lipids.

A controlled trial of Partners in Dementia Care: veteran outcomes after six and twelve months.

Science.gov (United States)

Bass, David M; Judge, Katherine S; Snow, A Lynn; Wilson, Nancy L; Morgan, Robert O; Maslow, Katie; Randazzo, Ronda; Moye, Jennifer A; Odenheimer, Germaine L; Archambault, Elizabeth; Elbein, Richard; Pirraglia, Paul; Teasdale, Thomas A; McCarthy, Catherine A; Looman, Wendy J; Kunik, Mark E

2014-01-01

"Partners in Dementia Care" (PDC) tested the effectiveness of a care-coordination program integrating healthcare and community services and supporting veterans with dementia and their caregivers. Delivered via partnerships between Veterans Affairs medical centers and Alzheimer's Association chapters, PDC targeted both patients and caregivers, distinguishing it from many non-pharmacological interventions. Hypotheses posited PDC would improve five veteran self-reported outcomes: 1) unmet need, 2) embarrassment about memory problems, 3) isolation, 4) relationship strain and 5) depression. Greater impact was expected for more impaired veterans. A unique feature was self-reported research data collected from veterans with dementia. Five matched communities were study sites. Two randomly selected sites received PDC for 12 months; comparison sites received usual care. Three structured telephone interviews were completed every 6 months with veterans who could participate. Of 508 consenting veterans, 333 (65.6%) completed baseline interviews. Among those who completed baseline interviews, 263 (79.0%) completed 6-month follow-ups and 194 (58.3%) completed 12-month follow-ups. Regression analyses showed PDC veterans had significantly less adverse outcomes than those receiving usual care, particularly for more impaired veterans after 6 months, including reduced relationship strain (B = -0.09; p = 0.05), depression (B = -0.10; p = 0.03), and unmet need (B = -0.28; p = 0.02; and B = -0.52; p = 0.08). PDC veterans also had less embarrassment about memory problems (B = -0.24; p = 0.08). At 12 months, more impaired veterans had further reductions in unmet need (B = -0.96; p needs and improve the psychosocial functioning of persons with dementia. NCT00291161.

Anatomia radicular de milho em solo compactado Anatomy of maize roots in compacted soil

Directory of Open Access Journals (Sweden)

Anderson Cristian Bergamin

2010-03-01

Full Text Available O objetivo deste trabalho foi avaliar a relação entre a estrutura anatômica das raízes de milho e os atributos físicos de solo submetido a diferentes graus de compactação. O estudo foi realizado em campo, no Município de Dourados, MS, em Latossolo Vermelho distroférrico, textura muito argilosa. O delineamento experimental foi o de blocos ao acaso, com cinco repetições. O solo utilizado apresentava histórico de oito anos com plantio direto. A compactação adicional do solo foi realizada por meio de tráfego com trator, com uma (PDc1, duas (PDc2, quatro (PDc4 e seis passadas (PDc6 sucessivas, sobre toda a área da parcela. Houve aumento na razão entre o córtex e o cilindro vascular da raiz com o aumento na compactação do solo. Essa razão correlacionou-se negativamente com a macroporosidade e positivamente com a densidade do solo e com a resistência do solo à penetração. O grau de compactação afeta a anatomia radicular do milho, e a resistência do solo à penetração é o indicador físico que melhor expressa esse efeito.The objective of this work was to evaluate the relationship between maize root anatomy and physical attributes of soil subjected to levels of compaction. The experiment was carried out in field conditions, in Dourados, Mato Grosso do Sul state, Brazil, in a clayed Latossolo Vermelho (Rhodic Acrustox. A randomized complete block design was used, with five replicates. The soil was cultivated for eight years under no-tillage. The additional compaction of the soil was done by tractor traffic in one (PDc1, two (PDc2, four (PDc4 and six successive passes (PDc6, in the entire area of the experimental plots. Ratio between the cortex and vascular cylinder of the root increased with soil compaction. This ratio was negatively correlated to macroporosity, and positively to soil density and soil penetration resistance. Soil compaction level affects the anatomy of maize roots, and its penetration resistance is the best

An evaluation of the impact of patient cost sharing for antihypertensive medications on adherence, medication and health care utilization, and expenditures

Directory of Open Access Journals (Sweden)

Pesa JA

2012-01-01

Full Text Available Jacqueline A Pesa1, Jill Van Den Bos2, Travis Gray2, Colleen Hartsig2, Robert Brett McQueen3, Joseph J Saseen3, Kavita V Nair31Janssen Scientific Affairs, LLC, Louisville, CO, USA; 2Milliman, Inc, Denver, CO, USA; 3University of Colorado Anschutz Medical Campus, Aurora, CO, USAObjective: To assess the impact of patient cost-sharing for antihypertensive medications on the proportion of days covered (PDC by antihypertensive medications, medical utilization, and health care expenditures among commercially insured individuals assigned to different risk categories.Methods: Participants were identified from the Consolidated Health Cost Guidelines (CHCG database (January 1, 2006–December 31, 2008 based on a diagnosis (index claim for hypertension, continuous enrollment ≥12 months pre- and post-index, and no prior claims for antihypertensive medications. Participants were assigned to: low-risk group (no comorbidities, high-risk group (1+ selected comorbidities, or very high-risk group (prior hospitalization for 1+ selected comorbidities. The relationship between patient cost sharing and PDC by antihypertensive medications was assessed using standard linear regression models, controlling for risk group membership, and various demographic and clinical factors. The relationship between PDC and health care service utilization was subsequently examined using negative binomial regression models.Results: Of the 28,688 study patients, 66% were low risk. The multivariate regression model supported a relationship between patient cost sharing per 30-day fill and PDC in the following year. For every US$1.00 increase in cost sharing, PDC decreased by 1.1 days (P < 0.0001. Significant predictors of PDC included high risk, older age, gender, Charlson Comorbidity Index score, geography, and total post-index insurer- and patient-paid costs. An increase in PDC was associated with a decrease in all-cause and hypertension-related inpatient, outpatient, and emergency

Use of the Performance Diagnostic Checklist to Select an Intervention Designed to Increase the Offering of Promotional Stamps at Two Sites of a Restaurant Franchise

Science.gov (United States)

Rodriguez, Manuel; Wilder, David A.; Therrien, Kelly; Wine, Byron; Miranti, Reylissa; Daratany, Kenneth; Salume, Gloria; Baranovsky, Greg; Rodriquez, Matias

2006-01-01

The performance diagnostic checklist (PDC) was administered to examine the variables influencing the offering of promotional stamps by employees at two sites of a restaurant franchise. PDC results suggested that a lack of appropriate antecedents, equipment and processes, and consequences were responsible for the deficits. Based on these results,…

Interference contrast in multi-source few photon optics

OpenAIRE

Laskowski, Wieslaw; Wiesniak, Marcin; Zukowski, Marek; Bourennane, Mohamed; Weinfurter, Harald

2009-01-01

Many recent experiments employ several parametric down conversion (PDC) sources to get multiphoton interference. Such interference has applications in quantum information. We study here how effects due to photon statistics, misalignment, and partial distinguishability of the PDC pairs originating from different sources may lower the interference contrast in the multiphoton experiments.

Plasmacytoid dendritic cells accumulate and secrete interferon alpha in lymph nodes of HIV-1 patients.

Directory of Open Access Journals (Sweden)

Clara Lehmann

2010-06-01

Full Text Available Circulating plasmacytoid dendritic cells (pDC decline during HIV-1 infection, but at the same time they express markedly higher levels of interferon alpha (IFNalpha, which is associated with HIV-1 disease progression. Here we show an accumulation of pDC in lymph nodes (LN of treatment-naïve HIV-1 patients. This phenomenon was associated with elevated expression of the LN homing marker, CCR7, on pDC in peripheral blood of HIV-1 patients, which conferred increased migratory capacity in response to CCR7 ligands in ex vivo functional assays. LN-homed pDC of HIV-1 patients presented higher CD40 and lower BDCA2 levels, but unchanged CD83 and CD86 expression. In addition, these cells expressed markedly higher amounts of IFNalpha compared to uninfected individuals, and were undergoing faster rates of cell death. These results demonstrate for the first time that in asymptomatic, untreated HIV-1 patients circulating pDC up-regulate CCR7 expression, accumulate in lymph nodes, and express high amounts of IFNalpha before undergoing cell death. Since IFNalpha inhibits cell proliferation and modulates immune responses, chronically high levels of this cytokine in LN of HIV-1 patients may impair differentiation and immune function of bystander CD4(+ T cells, thus playing into the mechanisms of AIDS immunopathogenesis.

12 Weeks of Combined Endurance and Resistance Training Reduces Innate Markers of Inflammation in a Randomized Controlled Clinical Trial in Patients with Multiple Sclerosis

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Nathalie Deckx

2016-01-01

Full Text Available Previously, we reported that patients with multiple sclerosis (MS demonstrate improved muscle strength, exercise tolerance, and lean tissue mass following a combined endurance and resistance exercise program. However, the effect of exercise on the underlying disease pathogenesis remains elusive. Since recent evidence supports a crucial role of dendritic cells (DC in the pathogenesis of MS, we investigated the effect of a 12-week combined exercise program in MS patients on the number and function of DC. We demonstrate an increased number of plasmacytoid DC (pDC following the exercise program. These pDC display an activated phenotype, as evidenced by increased numbers of circulating CD62L+ and CD80+ pDC. Interestingly, the number of CD80+ pDC positively correlates with the presence of IL-10-producing regulatory type 1 cells (Tr1, an important cell type for maintaining peripheral tolerance to self-antigens. In addition, decreased production of the inflammatory mediators, TNF-α and MMP-9, upon Toll-like receptor (TLR stimulation was found at the end of the exercise program. Overall, our findings suggest that the 12-week exercise program reduces the secretion of inflammatory mediators upon TLR stimulation and promotes the immunoregulatory function of circulating pDC, suggestive for a favorable impact of exercise on the underlying immunopathogenesis of MS.

Purine derivatives/creatinine ratio as an index of microbial protein synthesis in lactating Holstein cows

International Nuclear Information System (INIS)

Orellana, R.; Pulido, P.; Briones, M.; Sarabia, A.

2004-01-01

Three experiments were conducted to study creatinine excretion in milking cows, and its relationship to food intake and purine derivatives (PD) excretion as an index of microbial N synthesized in the rumen. In the first experiment, differences in creatinine determination method were studied: creatinine excretion was 26.8 ± 1.2 and 27.4 ± 2.2 mg/kg live weight, or 1,175.39 ± 74.69 and 1,199.9 ± 103.9 mmol/kgW 0.75 respectively for HPLC and colorimetry analysis. In the second experiment, the effect of concentrate supplement on the PDC index was studied. The inclusion of different levels of concentrate (0, 16, 33 and 50%) increased the PDC index significantly. The PDC index (Y) also showed a significant relationship with DOMI (X, kg/d): Y 16.85 X + 6.23; R 2 =0.84. Total PD excretion was calculated assuming constant daily excretion of creatinine (1.199 mmol/kgW 0.75 ). In the third experiment the effect of different roughage on the PDC index was studied. The substitution of a 23% of rye grass (Lolium sp.) silage by alkali treated wheat straw did not modify DOMI and the PDC index although among groups there was a significant decrease in milk production (1.5 L/cow/d) and in growth rate (-380 g/cow/d). (author)

An Evaluation of the Performance Diagnostic Checklist-Human Services to Assess an Employee Performance Problem in a Center-Based Autism Treatment Facility

Science.gov (United States)

Ditzian, Kyle; Wilder, David A.; King, Allison; Tanz, Jeanine

2015-01-01

The Performance Diagnostic Checklist-Human Services (PDC-HS) is an informant-based tool designed to assess the environmental variables that contribute to poor employee performance in human services settings. We administered the PDC-HS to 3 supervisors to assess the variables that contributed to poor performance by 4 staff members when securing…

Oral Health Disparities and Unmet Dental Needs among Preschool Children in Chelsea, MA: Exploring Mechanisms, Defining Solutions.

Science.gov (United States)

Isong, Inyang; Dantas, Laila; Gerard, Macda; Kuhlthau, Karen

Significant disparities exist in children's receipt of preventive dental care (PDC) in the United States. Many of the children at greatest risk of dental disease do not receive timely PDC; when they do receive dental care, it is often more for relief of dental pain. Chelsea is a low-income, diverse Massachusetts community with high rates of untreated childhood caries. There are various dental resources available in Chelsea, yet many children do not access dental care at levels equivalent to their needs. Using Chelsea as a case-study, to explore factors contributing to forgone PDC (including the age 1 dental visit) in an in-depth way. We used a qualitative study design that included semi-structured interviews with parents of preschool children residing in Chelsea, and Chelsea-based providers including pediatricians, dentists, a dental hygienist and early childhood care providers. We examined: a) parents' dental attitudes and oral health cultural beliefs; b) parents' and providers' perspectives on facilitators and barriers to PDC, reasons for unmet needs, and proposed solutions to address the problem. We recorded, transcribed and independently coded all interviews. Using rigorous, iterative qualitative data analyses procedures, we identified emergent themes. Factors perceived to facilitate receipt of PDC included Head-Start oral health policies, strong pediatric primary care/dental linkages, community outreach and advertising, and parents' own oral health experiences. Most parents and providers perceived there to be an adequate number of accessible dental services and resources in Chelsea, including for Medicaid enrollees. However, several barriers impeded children from receiving timely PDC, the most frequently cited being insurance related problems for children and adults. Other barriers included limited dental services for children strategic oral health policies, community outreach and improved care coordination between physicians, dentists and early childhood care

A plasmacytoid dendritic cell (CD123+/CD11c-) based assay system to predict contact allergenicity of chemicals

Science.gov (United States)

Ayehunie, Seyoum; Snell, Maureen; Child, Matthew; Klausner, Mitchell

2009-01-01

A predictive allergenicity test system for assessing the contact allergenicity of chemicals is needed by the cosmetic and pharmaceutical industry to monitor product safety in the marketplace. Development of such non-animal alternative assay systems for skin sensitization and hazard identification has been pursued by policy makers and regulatory agencies. We investigated whether phenotypic and functional changes to a subset of dendritic cells (DC), plasmacytoid DC (pDC), could be used to identify contact allergens. To achieve this goal, normal human DC were generated from CD34+ progenitor cells and cryopreserved. Frozen DC were thawed and the pDC fraction (CD123+/CD11c-) was harvested using FACS sorting. The pDC were cultured, expanded, and exposed to chemical allergens (N=26) or non-allergens (N=22). Concentrations of each chemical that resulted in >50% viability was determined using FACS analysis of propidium iodide stained cells using pDC from 2-5 donors. Expression of the surface marker, CD86, which has been implicated in dendritic cell maturation, was used as a marker of allergenicity. CD86 expression increased (≥ 1.5 fold) for 25 of 26 allergens (sensitivity = 96%) but did not increase for 19 of 22 non-allergens (specificity = 86%). In a direct comparison to historical data for the regulatory approved, mouse local lymph node assay (LLNA) for 23 allergens and 22 non-allergens, the pDC method had sensitivity and specificity of 96% and 86%, respectively, while the sensitivity and specificity of the LLNA assay was 83% and 82%, respectively. In conclusion, CD86 expression in pDC appears to be a sensitive and specific indicator to identify contact allergenicity. Such an assay method utilizing normal human cells will be useful for high throughput screening of chemicals for allergenicity. PMID:19665512

A plasmacytoid dendritic cell (CD123+/CD11c-) based assay system to predict contact allergenicity of chemicals

International Nuclear Information System (INIS)

Ayehunie, Seyoum; Snell, Maureen; Child, Matthew; Klausner, Mitchell

2009-01-01

A predictive allergenicity test system for assessing the contact allergenicity of chemicals is needed by the cosmetic and pharmaceutical industry to monitor product safety in the marketplace. Development of such non-animal alternative assay systems for skin sensitization and hazard identification has been pursued by policy makers and regulatory agencies. We investigated whether phenotypic and functional changes to a subset of dendritic cells (DC), plasmacytoid DC (pDC), could be used to identify contact allergens. To achieve this goal, normal human DC were generated from CD34+ progenitor cells and cryopreserved. Frozen DC were thawed and the pDC fraction (CD123+/CD11c-) was harvested using FACS sorting. The pDC were cultured, expanded, and exposed to chemical allergens (N = 26) or non-allergens (N = 22). Concentrations of each chemical that resulted in >50% viability was determined using FACS analysis of propidium iodide stained cells using pDC from 2 to 5 donors. Expression of the surface marker, CD86, which has been implicated in dendritic cell maturation, was used as a marker of allergenicity. CD86 expression increased (≥1.5-fold) for 25 of 26 allergens (sensitivity = 96%) but did not increase for 19 of 22 non-allergens (specificity = 86%). In a direct comparison to historical data for the regulatory approved, mouse local lymph node assay (LLNA) for 23 allergens and 22 non-allergens, the pDC method had sensitivity and specificity of 96% and 86%, respectively, while the sensitivity and specificity of the LLNA assay was 83% and 82%, respectively. In conclusion, CD86 expression in pDC appears to be a sensitive and specific indicator to identify contact allergenicity. Such an assay method utilizing normal human cells will be useful for high throughput screening of chemicals for allergenicity.

The Effects of Vent Location, Event Scale, and Time Forecasts on Pyroclastic Density Current Hazard Maps at Campi Flegrei Caldera (Italy

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Andrea Bevilacqua

2017-09-01

Full Text Available This study presents a new method for producing long-term hazard maps for pyroclastic density currents (PDC originating at Campi Flegrei caldera. Such method is based on a doubly stochastic approach and is able to combine the uncertainty assessments on the spatial location of the volcanic vent, the size of the flow and the expected time of such an event. The results are obtained by using a Monte Carlo approach and adopting a simplified invasion model based on the box model integral approximation. Temporal assessments are modeled through a Cox-type process including self-excitement effects, based on the eruptive record of the last 15 kyr. Mean and percentile maps of PDC invasion probability are produced, exploring their sensitivity to some sources of uncertainty and to the effects of the dependence between PDC scales and the caldera sector where they originated. Conditional maps representative of PDC originating inside limited zones of the caldera, or of PDC with a limited range of scales are also produced. Finally, the effect of assuming different time windows for the hazard estimates is explored, also including the potential occurrence of a sequence of multiple events. Assuming that the last eruption of Monte Nuovo (A.D. 1538 marked the beginning of a new epoch of activity similar to the previous ones, results of the statistical analysis indicate a mean probability of PDC invasion above 5% in the next 50 years on almost the entire caldera (with a probability peak of ~25% in the central part of the caldera. In contrast, probability values reduce by a factor of about 3 if the entire eruptive record is considered over the last 15 kyr, i.e., including both eruptive epochs and quiescent periods.

Pyrrolo-dC modified duplex DNA as a novel probe for the sensitive assay of base excision repair enzyme activity.

Science.gov (United States)

Lee, Chang Yeol; Park, Ki Soo; Park, Hyun Gyu

2017-12-15

We develop a novel approach to determine formamidopyrimidine DNA glycosylase (Fpg) activity by taking advantage of the unique fluorescence property of pyrrolo-dC (PdC) positioned opposite to 8-oxoguanine (8-oxoG) in duplex DNA. In its initial state, PdC in duplex DNA undergoes the efficient stacking and collisional quenching interactions, showing the low fluorescence signal. In contrast, the presence of Fpg, which specifically removes 8-oxoG and incises resulting apurinic (AP) site, transforms duplex DNA into single-stranded (ss) DNAs. As a result, the intrinsic fluorescence signal of PdC in ssDNA is recovered to exhibit the significantly enhanced fluorescence signal. Based on this Fpg-dependent fluorescence response of PdC, we could reliably determine Fpg activity down to 1.25U/ml with a linear response from 0 to 50U/ml. In addition, the diagnostic capability of this strategy was successfully demonstrated by reliably assaying Fpg activity in human blood serum, showing its great potential in the practical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

A novel design and analysis of a MEMS ceramic hot-wire anemometer for high temperature applications

International Nuclear Information System (INIS)

Nagaiah, N R; Sleiti, A K; Rodriguez, S; Kapat, J S; An, L; Chow, L

2006-01-01

This paper attempts to prove the feasibility of high temperature MEMS hot-wire anemometer for gas turbine environment. No such sensor exists at present. Based on the latest improvement in a new type of Polymer-Derived Ceramic (PDC) material, the authors present a Novel design, structural and thermal analysis of MEMS hot-wire anemometer (HWA) based on PDC material, and show that such a sensor is indeed feasible. This MEMS Sensor is microfabricated by using three types of PDC materials such as SiAlCN, SiCN (lightly doped) and SiCN (heavily doped) for sensing element (hot-wire), support prongs and connecting leads respectively. This novel hot wire anemometer can perform better than a conventional HWA in which the hot wire is made of tungsten or platinum-iridium. This type of PDC-HWA can be used in harsh environment due to its high temperature resistance, tensile strength and resistance to oxidation. This HWA is fabricated using microstereolithography as a novel microfabrication technique to manufacture the proposed MEMS Sensor

Anti-tumor effect of polysaccharides from rhizome of Curculigo ...

African Journals Online (AJOL)

The anti-tumor effect of PDC on cervical cancer was investigated in vivo in mice injected with Hela cells. The parameters measured were tumor volume and weight. In vitro anti-tumor effects of PDC were assessed by measuring expressions of caspase-3, caspase-9 and P53 proteins in Hela cells via ELISA assay. Thymus ...

Genes and Gene Therapy

Science.gov (United States)

... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

Pyruvate Decarboxylase Activity Assay in situ of Different Industrial Yeast Strains

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Dorota Kręgiel

2009-01-01

Full Text Available Cytoplasmic pyruvate decarboxylase (PDC, EC 4.1.1.1 is one of the key enzymes of yeast fermentative metabolism. PDC is the first enzyme which, under anaerobic conditions, leads to decarboxylation of pyruvate with acetaldehyde as the end product. The aim of this study is to develop a suitable method for PDC activity assay in situ for different industrial yeast strains. Saccharomyces sp. and Debaryomyces sp. yeast strains grew in fermentative medium with 12 % of glucose. Enzymatic assay was conducted in cell suspension treated with digitonin as permeabilisation agent, and with sodium pyruvate as a substrate, at temperature of 30 °C. Metabolites of PDC pathway were detected using gas chromatographic (GC technique. Various parameters like type and molar concentration of the substrate, minimal effective mass fraction of digitonin, cell concentration, reaction time and effect of pyrazole (alcohol dehydrogenase inhibitor were monitored to optimize PDC enzymatic assay in situ. In the concentration range of yeast cells from 1⋅10^7 to 1⋅10^8 per mL, linear correlation between the produced acetaldehyde and cell density was noticed. Only pyruvate was the specific substrate for pyruvate decarboxylase. In the presence of 0.05 M sodium pyruvate and 0.05 % digitonin, the enzymatic reaction was linear up to 20 min of the assay. During incubation, there was no formation of ethanol and, therefore, pyrazole was not necessary for the assay.

Expression of the T cell receptor αβ on a CD123+ BDCA2+ HLA-DR+ subpopulation in head and neck squamous cell carcinoma.

Directory of Open Access Journals (Sweden)

Annette Thiel

Full Text Available Human Plasmacytoid Dendritic Cells (PDCs infiltrating solid tumor tissues and draining lymph nodes of Head and Neck Squamous Cell Carcinoma (HNSCC show an impaired immune response. In addition to an attenuated secretion of IFN-α little is known about other HNSCC-induced functional alterations in PDCs. Particular objectives in this project were to gain new insights regarding tumor-induced phenotypical and functional alterations in the PDC population. We showed by FACS analysis and RT-PCR that HNSCC orchestrates an as yet unknown subpopulation exhibiting functional autonomy in-vitro and in-vivo besides bearing phenotypical resemblance to PDCs and T cells. A subset, positive for the PDC markers CD123, BDCA-2, HLA-DR and the T cell receptor αβ (TCR-αβ was significantly induced subsequent to stimulation with HNSCC in-vitro (p = 0.009 and also present in metastatic lymph nodes in-vivo. This subgroup could be functionally distinguished due to an enhanced production of IL-2 (p = 0.02, IL-6 (p = 0.0007 and TGF-β (not significant. Furthermore, after exposure to HNSCC cells, mRNA levels revealed a D-J-beta rearrangement of the TCR-beta chain besides a strong enhancement of the CD3ε chain in the PDC population. Our data indicate an interface between the PDC and T cell lineage. These findings will improve our understanding of phenotypical and functional intricacies concerning the very heterogeneous PDC population in-vivo.

Exxon nuclear power distribution control for pressurized water reactors: Phase II

International Nuclear Information System (INIS)

Holm, J.S.; Burnside, R.J.

1978-01-01

The power distribution control procedure, denoted PDC-II, described in this report enables nuclear plants to manage core power distributions such that Technical Specification Limits on F/sub Q//sup T/ are not violated during normal operation and limits on MDNBR are not violated during steady-state, load-follow, and anticipated transients. The PDC-II data base described provides the means for predicting the maximum F/sub Q//sup T/(z) distribution anticipated during operation under the PDC-II procedure taking into account the incore measured equilibrium power distribution data for the reactor in question. A comparison of this distribution with the Technical Specification limit curve determines whether the Technical Specification limit can be protected by PDC-II procedure. If such protection can be confirmed for a given operating cycle interval, APDMS monitoring is not necessary over this interval and the excore monitored constant axial offset limits will protect the Technical Specification F/sub Q//sup T/ limits. This document describes the maximum possible variation in F/sub Q//sup T/(z) which can occur during operation when following the PDC-II procedures. This bounding variation in F/sub Q//sup T/(z) is referred to as V(z). This V(z) distribution represents the maximun variation in F/sub Q//sup T/(z) when the axial offset is maintained within the range defined in this report [+- 5% at full power condition

Study of the indirect calibration of clinical air kerma-area meters

International Nuclear Information System (INIS)

Almeida Junior, Jose N.; Terini, Ricardo A.; Herdade, Silvio B.

2011-01-01

Kerma-area product (P KA ) is a quantity which is independent of the distance to the X-ray tube focal spot and that can be used to assess the effective dose in patients. Clinical P KA meters are usually calibrated on-site by measuring the air kerma with an ion chamber and evaluating the irradiated area by means of a radiographic image. This work presents a preliminary metrological evaluation of the calibration of a device marketed recently (PDC, Patient Dose Calibrator, Radcal), designed for calibrating clinical P KA meters. Results are also shown of applying the PDC to the cross calibration of a clinical P KA meter from a radiology equipment. Results confirm a lower energy dependence of the PDC relative to the tested clinical meter. (author)

Plasmacytoid dendritic cell interferon-α production to R-848 stimulation is decreased in male infants.

Science.gov (United States)

Wang, Jennifer P; Zhang, Lei; Madera, Rachel F; Woda, Marcia; Libraty, Daniel H

2012-07-06

Sex differences in response to microbial infections, especially viral ones, may be associated with Toll-like receptor (TLR)-mediated responses by plasmacytoid dendritic cells (pDCs). In this study, we identified sex differences in human infant pDC interferon-α production following challenge with the TLR7/8 agonist R-848. Male pDC responses were significantly lower than those of females during early infancy. This difference may be attributed to the androgen surge experienced by males during the early infancy period. Pretreatment of human pDCs with dihydrotestosterone produced a significant reduction in interferon-α production following R-848 challenge. Androgen-mediated regulation of pDC TLR7-driven innate immune responses may contribute to the observed sex differences in response to infections during early infancy.

The Diogene 4π detector at Saturne

International Nuclear Information System (INIS)

Alard, J.P.; Arnold, J.; Augerat, J.; Bastid, N.; Costilhes, J.P.; Crouau, M.; Dupieux, P.; Fraysse, L.; Montarou, G.; Parizet, M.J.; Tamain, J.C.; Valero, J.; Babinet, R.; Marco, N. de; Drouet, M.; Fanet, H.; Fodor, Z.; Girard, J.; Gosset, J.; Laspalles, C.; Lemaire, M.C.; L'Hote, D.; Lucas, B.; Papineau, A.; Poitou, J.; Schimmerling, W.; Terrien, Y.; Valette, O.; Brochard, F.; Gorodetzky, P.; Racca, C.

1987-01-01

Diogene, an electronic 4π detector, has been built and installed at the Saturne synchrotron in Saclay. The forward angular range (0 0 -6 0 ) is covered by 48 time-of-flight scintillator telescopes that provide charge identification. The trajectories of fragments emitted at larger angles are recorded in a cylindrical 0.4 m 3 Pictorial Drift Chamber (PDC) surrounding the target. The PDC is inside a 1-T magnetic field; the axis of the PDC cylinder and the magnetic field are parallel to the beam. Good identification has been obtained for both positive and negative π mesons and for hydrogen and helium isotopes. Multiplicities in relativistic nucleus-nucleus reactions up to 40 have been detected, limited mainly by the present electronics. (orig.)

Ethylene and 1-MCP regulate major volatile biosynthetic pathways in apple fruit.

Science.gov (United States)

Yang, Xiaotang; Song, Jun; Du, Lina; Forney, Charles; Campbell-Palmer, Leslie; Fillmore, Sherry; Wismer, Paul; Zhang, Zhaoqi

2016-03-01

The effects of ethylene and 1-methylcyclopropene (1-MCP) on apple fruit volatile biosynthesis and gene expression were investigated. Statistical analysis identified 17 genes that changed significantly in response to ethylene and 1-MCP treatments. Genes encoding branched-chain amino acid aminotransferase (BCAT), aromatic amino acid aminotransferase (ArAT) and amino acid decarboxylases (AADC) were up-regulated during ripening and further enhanced by ethylene treatment. Genes related to fatty acid synthesis and metabolism, including acyl-carrier-proteins (ACPs), malonyl-CoA:ACP transacylase (MCAT), acyl-ACP-desaturase (ACPD), lipoxygenase (LOX), hydroperoxide lyase (HPL), alcohol dehydrogenase (ADH), pyruvate decarboxylase (PDC2), β-oxidation, acyl-CoA synthetase (ACS), enoyl-CoA hydratase (ECHD), acyl-CoA dehydrogenase (ACAD), and alcohol acyltransferases (AATs) also increased during ripening and in response to ethylene treatment. Allene oxide synthase (AOS), alcohol dehydrogenase 1 (ADH1), 3-ketoacyl-CoA thiolase and branched-chain amino acid aminotransferase 2 (BCAT2) decreased in ethylene-treated fruit. Treatment with 1-MCP and ethylene generally produced opposite effects on related genes, which provides evidence that regulation of these genes is ethylene dependent. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Truncation of a mannanase from Trichoderma harzianum improves its enzymatic properties and expression efficiency in Trichoderma reesei.

Science.gov (United States)

Wang, Juan; Zeng, Desheng; Liu, Gang; Wang, Shaowen; Yu, Shaowen

2014-01-01

To obtain high expression efficiency of a mannanase gene, ThMan5A, cloned from Trichoderma harzianum MGQ2, both the full-length gene and a truncated gene (ThMan5AΔCBM) that contains only the catalytic domain, were expressed in Trichoderma reesei QM9414 using the strong constitutive promoter of the gene encoding pyruvate decarboxylase (pdc), and purified to homogeneity, respectively. We found that truncation of the gene improved its expression efficiency as well as the enzymatic properties of the encoded protein. The recombinant strain expressing ThMan5AΔCBM produced 2,460 ± 45.1 U/ml of mannanase activity in the culture supernatant; 2.3-fold higher than when expressing the full-length ThMan5A gene. In addition, the truncated mannanase had superior thermostability compared with the full-length enzyme and retained 100 % of its activity after incubation at 60 °C for 48 h. Our results clearly show that the truncated ThMan5A enzyme exhibited improved characteristics both in expression efficiency and in its thermal stability. These characteristics suggest that ThMan5AΔCBM has potential applications in the food, feed, paper, and pulp industries.

Calibration of PKA meters against ion chambers of two geometries

International Nuclear Information System (INIS)

Almeida Junior, Jose N.; Terini, Ricardo A.; Pereira, Marco A.G.; Herdade, Silvio B.

2011-01-01

Kerma-area product (KAP or PKA) is a quantity that is independent of the distance to the X-ray tube focal spot and that can be used in radiological exams to assess the effective dose in patients. Clinical KAP meters are generally fixed in tube output and they are usually calibrated on-site by measuring the air kerma with an ion chamber and by evaluating the irradiated area by means of a radiographic image. Recently, a device was marketed (PDC, Patient Dose Calibrator, Radcal Co.), which was designed for calibrating clinical KAP meters with traceability to a standard laboratory. This paper presents a metrological evaluation of two methods that can be used in standard laboratories for the calibration of this device, namely, against a reference 30 cc ionization chamber or a reference parallel plates monitor chamber. Lower energy dependence was also obtained when the PDC calibration was made with the monitor chamber. Results are also shown of applying the PDC in hospital environment to the cross calibration of a clinical KAP meter from a radiology equipment. Results confirm lower energy dependence of the PDC relatively to the tested clinical meter. (author)

Prescription drug coupons: evolution and need for regulation in direct-to-consumer advertising.

Science.gov (United States)

Mackey, Tim K; Yagi, Nozomi; Liang, Bryan A

2014-01-01

Pharmaceutical marketing in the United States had undergone a shift from largely exclusively targeting physicians to considerable efforts in targeting patients through various forms of direct-to-consumer advertising ("DTCA"). This includes the use of DTCA in prescription drug coupons ("PDCs"), a new form of DTCA that offers discounts and rebates directly to consumers to lower costs of drug purchasing. Our examination of PDCs reveals that the use and types of PDC programs is expanding and includes promotion of the vast majority of top grossing pharmaceuticals. However, controversy regarding this emerging form of DTCA has given rise to health policy concerns about their overall impact on prescription drug expenditures for consumers, payers, and the health care system, and whether they lead to optimal long-term utilization of pharmaceuticals. In response to these concerns and the growing popularity of PDCs, what we propose here are clearer regulation and regulatory guidance for PDC DTCA use. This would include review for appropriate disclosure of marketing claims, increased transparency in PDC use for pharmaceutical pricing, and leveraging potential positive benefits of PDC use for vulnerable or underserved patient populations. Copyright © 2014 Elsevier Inc. All rights reserved.

Novel composite membranes based on PBI and dicationic ionic liquids for high temperature polymer electrolyte membrane fuel cells

International Nuclear Information System (INIS)

Hooshyari, Khadijeh; Javanbakht, Mehran; Adibi, Mina

2016-01-01

Two types of innovative composite membranes based on polybenzimidazole (PBI) containing dicationic ionic liquid 1,3-di(3-methylimidazolium) propane bis (trifluoromethylsulfonyl) imide (PDC 3 ) and monocationic ionic liquid 1-hexyl-3-methylimidazolium bis (trifluoromethanesulfonyl) imide (PMC 6 ) are prepared as electrolyte for high temperature fuel cells applications under anhydrous conditions. The analyses of results display promising characteristics such as high proton conductivity and thermal stability. Moreover the fuel cell performance of PA doped PDC 3 composite membranes is enhanced in comparison with PA doped PMC 6 and PA doped PBI membranes at high temperatures. Dicationic ionic liquid with high number of charge carriers provides well-developed ionic channels which form facile pathways and considerably develop the anhydrous proton conductivity. The highest proton conductivity of 81 mS/cm is achieved for PA doped PDC 3 composite membranes with PBI/IL mole ratio: 4 at 180 °C. A power density of 0.44 W/cm 2 is obtained at 0.5 V and 180 °C for PA doped PDC 3 composite membranes, which proves that these developed composite membranes can be considered as most promising candidates for high temperature fuel cell applications with enhanced proton conductivity.

Interplay of foot-and-mouth disease virus, antibodies and plasmacytoid dendritic cells: virus opsonization under non-neutralizing conditions results in enhanced interferon-alpha responses

Directory of Open Access Journals (Sweden)

Lannes Nils

2012-08-01

Full Text Available Abstract Foot-and-mouth disease virus (FMDV is a highly infectious member of the Picornaviridae inducing an acute disease of cloven-hoofed species. Vaccine-induced immune protection correlates with the presence of high levels of neutralizing antibodies but also opsonising antibodies have been proposed as an important mechanism of the immune response contributing to virus clearance by macrophages and leading to the production of type-I interferon (IFN by plasmacytoid dendritic cells (pDC. The present study demonstrates that the opsonising antibody titres mediating enhanced IFN-α responses in pDC were similar to neutralizing titres, when antigenically related viruses from the same serotype were employed. However, sera cross-reacted also with non-neutralized isolates of multiple serotypes, when tested in this assay. Both uncomplexed virus and immune complexed virus stimulated pDC via Toll-like receptor 7. An additional finding of potential importance for strain-specific differences in virulence and/or immunogenicity was that pDC activation by FMDV strongly differed between viral isolates. Altogether, our results indicate that opsonising antibodies can have a broader reactivity than neutralizing antibodies and may contribute to antiviral responses induced against antigenically distant viruses.

Gene expression and gene therapy imaging

International Nuclear Information System (INIS)

Rome, Claire; Couillaud, Franck; Moonen, Chrit T.W.

2007-01-01

The fast growing field of molecular imaging has achieved major advances in imaging gene expression, an important element of gene therapy. Gene expression imaging is based on specific probes or contrast agents that allow either direct or indirect spatio-temporal evaluation of gene expression. Direct evaluation is possible with, for example, contrast agents that bind directly to a specific target (e.g., receptor). Indirect evaluation may be achieved by using specific substrate probes for a target enzyme. The use of marker genes, also called reporter genes, is an essential element of MI approaches for gene expression in gene therapy. The marker gene may not have a therapeutic role itself, but by coupling the marker gene to a therapeutic gene, expression of the marker gene reports on the expression of the therapeutic gene. Nuclear medicine and optical approaches are highly sensitive (detection of probes in the picomolar range), whereas MRI and ultrasound imaging are less sensitive and require amplification techniques and/or accumulation of contrast agents in enlarged contrast particles. Recently developed MI techniques are particularly relevant for gene therapy. Amongst these are the possibility to track gene therapy vectors such as stem cells, and the techniques that allow spatiotemporal control of gene expression by non-invasive heating (with MRI guided focused ultrasound) and the use of temperature sensitive promoters. (orig.)

Pyruvate dehydrogenase complexes from the equine nematode, Parascaris equorum, and the canine cestode, Dipylidium caninum, helminths exhibiting anaerobic mitochondrial metabolism.

Science.gov (United States)

Diaz, F; Komuniecki, R W

1994-10-01

The pyruvate dehydrogenase complex (PDC) has been purified to apparent homogeneity from 2 parasitic helminths exhibiting anaerobic mitochondrial metabolism, the equine nematode, Parascaris equorum, and the canine cestode, Dipylidium caninum. The P. equorum PDC yielded 7 major bands when separated by SDS-PAGE. The bands of 72, 55-53.5, 41 and 36 kDa corresponded to E2, E3, E1 alpha and E1 beta, respectively. The complex also contained additional unidentified proteins of 43 and 45 kDa. Incubation of the complex with [2-14C]pyruvate resulted in the acetylation of only E2. These results suggest that the P. equorum PDC lacks protein X and exhibits an altered subunit composition, as has been described previously for the PDC of the related nematode, Ascaris suum. In contrast, the D. caninum PDC yielded only four major bands after SDS-PAGE of 59, 58, 39 and 34 kDa, which corresponded to E3, E2, E1 alpha and E1 beta, respectively. Incubation of the D. caninum complex with [2-14C]pyruvate resulted in the acetylation of E2 and a second protein which comigrated with E3, suggesting that the D. caninum complex contained protein X and had a subunit composition similar to PDCs from other eukaryotic organisms. Both helminth complexes appeared less sensitive to inhibition by elevated NADH/NAD+ ratios than complexes isolated from aerobic organisms, as would be predicted for PDCs from organisms exploiting microaerobic habitats. These results suggest that although these helminths have similar anaerobic mitochondrial pathways, they contain significantly different PDCs.

Second primary pancreatic ductal carcinoma in the remnant pancreas after pancreatectomy for pancreatic ductal carcinoma: High cumulative incidence rates at 5 years after pancreatectomy.

Science.gov (United States)

Ishida, Jun; Toyama, Hirochika; Matsumoto, Ippei; Asari, Sadaki; Goto, Tadahiro; Terai, Sachio; Nanno, Yoshihide; Yamashita, Azusa; Mizumoto, Takuya; Ueda, Yuki; Kido, Masahiro; Ajiki, Tetsuo; Fukumoto, Takumi; Ku, Yonson

2016-01-01

The aim of this study was to determine the incidence rate and clinical features of second primary pancreatic ductal carcinoma (SPPDC) in the remnant pancreas after pancreatectomy for pancreatic ductal carcinoma (PDC). Data of patients undergoing R0 resection for PDC at a single high-volume center were reviewed. SPPDC was defined as a tumor in the remnant pancreas after R0 resection for PDC, and SPPDC met at least one of the following conditions: 1) the time interval between initial pancreatectomy and development of a new tumor was 3 years or more; 2) the new tumor was not located in contact with the pancreatic stump. We investigated the clinical features and treatment outcomes of patients with SPPDC. This study included 130 patients who underwent surgical resection for PDC between 2005 and 2014. Six (4.6%) patients developed SPPDC. The cumulative 3- and 5-year incidence rates were 3.1% and 17.7%, respectively. Four patients underwent remnant pancreatectomy for SPPDC. They were diagnosed with the disease in stage IIA or higher and developed recurrence within 6 months after remnant pancreatectomy. One patient received carbon ion radiotherapy and survived 45 months. One patient refused treatment and died 19 months after the diagnosis of SPPDC. The incidence rate of SPPDC is not negligible, and the cumulative 5-year incidence rate of SPPDC is markedly high. Post-operative surveillance of the remnant pancreas is critical for the early detection of SPPDC, even in long-term survivors after PDC resection. Copyright © 2016 IAP and EPC. Published by Elsevier B.V. All rights reserved.

Validation of Montgomery-Åsberg Rating Scale and Cornell Scale for Depression in Dementia in Brazilian elderly patients.

Science.gov (United States)

Portugal, Maria da Glória; Coutinho, Evandro Silva Freire; Almeida, Cloyra; Barca, Maria Lage; Knapskog, Anne-Brita; Engedal, Knut; Laks, Jerson

2012-08-01

There are few studies on validation of depression scales in the elderly in Latin America. This study aimed to assess the validity of Montgomery-Åsberg. Depression Rating Scale (MADRS) and Cornell Scale for Depression in Dementia (CSDD) in Brazilian elderly outpatients. A convenience sample of 95 outpatients was diagnosed for dementia and depression according to DSM-IV-TR, ICD-10, and PDC-dAD criteria. Receiver Operating Curves (ROC) were used to calculate the area under the curve (AUC) and to assess MADRS and CSDD cut-offs for each diagnostic criterion. Dementia was diagnosed in 71 of 95 patients. Depression was diagnosed in 35, 30, and 51 patients by ICD-10, DSM-IV, and PDC-dAD, respectively. MADRS cut-off score of 10 correctly diagnosed 67.4% and 66.3% patients as depressed according to DSM-IV and ICD-10. A cut-off of 9 correctly identified 74.7% by PDC-dAD criteria; a CSDD cut-off score of 13 best recognized depression according to DSM-IV and ICD-10. A score of 11 diagnosed depression according to PDC-dAD, while MADRS = 9 recognized depression in dementia. CSDD was more efficient in showing depression in mild than in moderate/severe dementia according to DSM-IV/ICD-10. PDC-dAD behaved nicely for any severity stage. MADRS and CSDD cut-offs of 10 and 13 were the optimal ones to diagnose depression in elderly, respectively. CSDD cut-offs are higher than those found in other countries. Other Latin American studies are needed to compare results with our study.

End points in discharge cleaning on TFTR [Tokamak Fusion Test Reactor

International Nuclear Information System (INIS)

Mueller, D.; Dylla, H.F.; Bell, M.G.

1989-07-01

It has been found necessary to perform a series of first-wall conditioning steps prior to successful high power plasma operation in the Tokamak Fusion Test Reactor (TFTR). This series begins with glow discharge cleaning (GDC) and is followed by pulse discharge cleaning (PDC). During machine conditioning, the production of impurities is monitored by a Residual Gas Analyzer (RGA). PDC is made in two distinct modes: Taylor discharge cleaning (TDC), where the plasma current is kept low (15--50 kA) and of short duration (50 ms) by means of a relatively high prefill pressure and aggressive PDC, where lower prefill pressure and higher toroidal field result in higher current (200--400 kA) limited by disruptions at q(a) approx 3 at approx 250 ms. At a constant repetition rate of 12 discharges/minute, the production rate of H 2 O, CO, or other impurities has been found to be an unreliable measure of progress in cleaning. However, the ability to produce aggressive PDC with substantial limiter heating, but without the production of x-rays from runaway electrons, is an indication that TDC is no longer necessary after approx 10 5 pulses. During aggressive PDC, the uncooled limiters are heated by the plasma from the bakeout temperature of 150 degree C to about 250 degree C over a period of three to eight hours. This limiter heating is important to enhance the rate at which H 2 O is removed from the graphite limiter. 14 refs., 3 figs., 1 tab

End points in discharge cleaning on TFTR (Tokamak Fusion Test Reactor)

Energy Technology Data Exchange (ETDEWEB)

Mueller, D.; Dylla, H.F.; Bell, M.G.; Blanchard, W.R.; Bush, C.E.; Gettelfinger, G.; Hawryluk, R.J.; Hill, K.W.; Janos, A.C.; Jobes, F.C.

1989-07-01

It has been found necessary to perform a series of first-wall conditioning steps prior to successful high power plasma operation in the Tokamak Fusion Test Reactor (TFTR). This series begins with glow discharge cleaning (GDC) and is followed by pulse discharge cleaning (PDC). During machine conditioning, the production of impurities is monitored by a Residual Gas Analyzer (RGA). PDC is made in two distinct modes: Taylor discharge cleaning (TDC), where the plasma current is kept low (15--50 kA) and of short duration (50 ms) by means of a relatively high prefill pressure and aggressive PDC, where lower prefill pressure and higher toroidal field result in higher current (200--400 kA) limited by disruptions at q(a) /approx/ 3 at /approx/ 250 ms. At a constant repetition rate of 12 discharges/minute, the production rate of H/sub 2/O, CO, or other impurities has been found to be an unreliable measure of progress in cleaning. However, the ability to produce aggressive PDC with substantial limiter heating, but without the production of x-rays from runaway electrons, is an indication that TDC is no longer necessary after /approx/ 10/sup 5/ pulses. During aggressive PDC, the uncooled limiters are heated by the plasma from the bakeout temperature of 150/degree/C to about 250/degree/C over a period of three to eight hours. This limiter heating is important to enhance the rate at which H/sub 2/O is removed from the graphite limiter. 14 refs., 3 figs., 1 tab.

ORF Alignment: NC_002755 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available reductase pdb|1P9L|B Chain B, Structure Of M. ... Tuberculosis Dihydrodipicolinate Reductase In Comp...lex ... With Nadh And 2,6 Pdc pdb|1P9L|A Chain A, Structure Of ... M. Tuberculosis Dihydrodipi..., ... Dihydrodipicolinate Reductase From Mycobacterium ... Tuberculosis Complexed With Nadph A...nd Pdc pdb|1C3V|A ... Chain A, Dihydrodipicolinate Reductase From ... Mycobacterium Tuberculosis

ORF Alignment: NC_000962 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available reductase pdb|1P9L|B Chain B, Structure Of M. ... Tuberculosis Dihydrodipicolinate Reductase In Comp...lex ... With Nadh And 2,6 Pdc pdb|1P9L|A Chain A, Structure Of ... M. Tuberculosis Dihydrodipi..., ... Dihydrodipicolinate Reductase From Mycobacterium ... Tuberculosis Complexed With Nadph A...nd Pdc pdb|1C3V|A ... Chain A, Dihydrodipicolinate Reductase From ... Mycobacterium Tuberculosis

Efficient utilization of waste date pits for the synthesis of green diesel and jet fuel fractions

International Nuclear Information System (INIS)

Al-Muhtaseb, Ala’a H.; Jamil, Farrukh; Al-Haj, Lamya; Al-Hinai, Mohab A.; Baawain, Mahad; Myint, Myo Tay Zar; Rooney, David

2016-01-01

Highlights: • Active catalysts Pt/C and Pd/C were developed from waste date pits. • Catalysts showed good activity in hydrodeoxygenation of date pit oil to alkane fuels. • The liquid product fractions lay within the range of the jet fuel and green diesel. • Green diesel fraction obtained by Pd/C was 72.03% and jet fuel was 30.39%. • Date pits can be a promising platform for the production of catalysts and biofuels. - Abstract: Date pits are considered one of the major agricultural wastes in Oman. The present work involves the synthesis of active catalysts from waste date pits carbon produced by carbonization and impregnation with Pt and Pd metals. Synthesized catalysts Pt/C and Pd/C were characterized by XRD, SEM, TEM, EDX, BET and XPS. The activity of the catalysts’ performance was evaluated by the hydrodeoxygenation of date pits oil for the production of second-generation biofuels, which includes jet fuel and green diesel fractions. Results indicate that the synthesized catalysts were highly active for the hydrodeoxygenation of date pits oil. Based on the elemental analysis, the degree of deoxygenation (DOD) of product oil was 97.5% and 89.4% for the Pd/C and Pt/C catalysts respectively. The high DOD was also confirmed by product analyses that mainly consist of paraffinic hydrocarbons. Results also showed that between the two catalysts, Pd/C showed a higher activity towards hydrodeoxygenation, a conclusion that was based on the high DOD of the product oil due to hydrocarbons formation. Based on the type of components in the product oil, the maximum fraction of hydrocarbons formed lay within the range of 72.03% and 72.78% green diesel, and 30.39% and 28.25% jet fuel using Pd/C and Pt/C catalysts respectively. It can be concluded that waste date pits can be a promising platform for the production of catalysts and biofuels.

Spontaneously Bi decorated carbon supported Pd nanoparticles for formic acid electro-oxidation

International Nuclear Information System (INIS)

Bauskar, Akshay S.; Rice, Cynthia A.

2013-01-01

Highlights: • Selective decoration of Bi onto commercial Pd/C is carried out by a simple gas controlled surface potential modulation technique. • Bi decorated Pd/C catalyst exhibits higher and sustained formic acid oxidation activity presumably via the electronic effect. • Shielding of Pd atoms by Bi increases long term stability. • Formic acid electro-oxidation current increased by 121% at 0.2 V vs. RHE. -- Abstract: The activity and stability of carbon supported palladium (Pd/C) nanoparticles decorated with a submonolayer of bismuth (Bi) for formic acid (FA) electro-oxidation was investigated herein. The FA electro-oxidation activity enhancement of Bi decorated Pd/C was evaluated electrochemically using a rotating disk electrode configuration by linear sweep voltammetric and chronoamperometric measurements. Commercial Pd/C was decorated by irreversible adsorption of Bi via a simple gas controlled surface potential modulation technique, and the coverage of Bi adatoms as measured by cyclic voltammetry was controlled in the range of 30–87%. An optimal Bi coverage was observed to be 40%, resulting in a favorable decrease in the FA onset potential by greater than 0.1 V and increase in electro-oxidation current density from 0.25 mA cm −2 SA to 0.55 mA cm −2 SA at 0.2 V vs. RHE, compared to commercial Pd/C. The results indicate that Bi decorated Pd nanoparticles have excellent properties for the electro-oxidation of FA, i.e. high electro-catalytic activity and excellent stability, due to sustained promotion of dehydrogenation pathway attributed to the electronic effect, thereby promoting FA adsorption in the CH-down orientation. Based on no significant shifting in the CO stripping peak position, minimal impact of Bi on the Pd-CO bond strength is observed. Chronoamperometry results show much better long-term electro-catalytic activity for Bi decorated Pd nanoparticles attributed to shielding of surface Pd atoms by Bi and reducing Pd dissolution

A break-even analysis for dementia care collaboration: Partners in Dementia Care.

Science.gov (United States)

Morgan, Robert O; Bass, David M; Judge, Katherine S; Liu, C F; Wilson, Nancy; Snow, A Lynn; Pirraglia, Paul; Garcia-Maldonado, Maurilio; Raia, Paul; Fouladi, N N; Kunik, Mark E

2015-06-01

Dementia is a costly disease. People with dementia, their families, and their friends are affected on personal, emotional, and financial levels. Prior work has shown that the "Partners in Dementia Care" (PDC) intervention addresses unmet needs and improves psychosocial outcomes and satisfaction with care. We examined whether PDC reduced direct Veterans Health Administration (VHA) health care costs compared with usual care. This study was a cost analysis of the PDC intervention in a 30-month trial involving five VHA medical centers. Study subjects were veterans (N = 434) 50 years of age and older with dementia and their caregivers at two intervention (N = 269) and three comparison sites (N = 165). PDC is a telephone-based care coordination and support service for veterans with dementia and their caregivers, delivered through partnerships between VHA medical centers and local Alzheimer's Association chapters. We tested for differences in total VHA health care costs, including hospital, emergency department, nursing home, outpatient, and pharmacy costs, as well as program costs for intervention participants. Covariates included caregiver reports of veterans' cognitive impairment, behavior problems, and personal care dependencies. We used linear mixed model regression to model change in log total cost post-baseline over a 1-year follow-up period. Intervention participants showed higher VHA costs than usual-care participants both before and after the intervention but did not differ significantly regarding change in log costs from pre- to post-baseline periods. Pre-baseline log cost (p ≤ 0.001), baseline cognitive impairment (p ≤ 0.05), number of personal care dependencies (p ≤ 0.01), and VA service priority (p ≤ 0.01) all predicted change in log total cost. These analyses show that PDC meets veterans' needs without significantly increasing VHA health care costs. PDC addresses the priority area of care coordination in the National Plan to Address Alzheimer

Thermal interactions of the AD79 Vesuvius pyroclastic density currents and their deposits at Villa dei Papiri (Herculaneum archaeological site, Italy)

Science.gov (United States)

Giordano, G.; Zanella, E.; Trolese, M.; Baffioni, C.; Vona, A.; Caricchi, C.; De Benedetti, A. A.; Corrado, S.; Romano, C.; Sulpizio, R.; Geshi, N.

2018-05-01

Pyroclastic density currents (PDCs) can have devastating impacts on urban settlements, due to their dynamic pressure and high temperatures. Our degree of understanding of the interplay between these hot currents and the affected infrastructures is thus fundamental not only to implement our strategies for risk reduction, but also to better understand PDC dynamics. We studied the temperature of emplacement of PDC deposits that destroyed and buried the Villa dei Papiri, an aristocratic Roman edifice located just outside the Herculaneum city, during the AD79 plinian eruption of Mt Vesuvius (Italy) by using the thermal remanent magnetization of embedded lithic clasts. The PDC deposits around and inside the Villa show substantial internal thermal disequilibrium. In areas affected by convective mixing with surface water or with collapsed walls, temperatures average at around 270 °C (min 190 °C, max 300 °C). Where the deposits show no evidence of mixing with external material, the temperature is much higher, averaging at 350 °C (min 300 °C; max 440 °C). Numerical simulations and comparison with temperatures retrieved at the very same sites from the reflectance of charcoal fragments indicate that such thermal disequilibrium can be maintained inside the PDC deposit for time-scales well over 24 hours, i.e. the acquisition time of deposit temperatures for common proxies. We reconstructed in detail the history of the progressive destruction and burial of Villa dei Papiri and infer that the rather homogeneous highest deposit temperatures (average 350 °C) were carried by the ash-sized fraction in thermal equilibrium with the fluid phase of the incoming PDCs. These temperatures can be lowered on short time- (less than hours) and length-scales (meters to tens of meters) only where convective mixing with external materials or fluids occurs. By contrast, where the Villa walls remained standing the thermal exchange was only conductive and very slow, i.e. negligible at 50 cm

Aprendizaje activo en el PDC

OpenAIRE

Hernández Mor, Jordi

2015-01-01

Treball Final del Màster Universitari en Professor/a d'Educació Secundària Obligatòria i Batxillerat, Formació Professional i Ensenyaments d'Idiomes. Codi: SAP139. Curs acadèmic 2014-2015 El siguiente Trabajo Final de Máster (TFM), ha sido realizado bajo el modelo de mejora educativa, según la normativa de la Universitat Jaume I, con la metodología de investigaciónacción. Este proyecto se realizó en el I.E.S. Professor Broch i Llop de Vila-real, en el aula de 4º Educación Secundar...

Response of the 'patient dose calibrator' chamber for incident positions and sizes of X-ray fields

International Nuclear Information System (INIS)

Oliveira, Cassio M.; Abrantes, Marcos Eugenio S.; Ferreira, Flavia C. Bastos; Lacerda, Marco A. de Souza; Alonso, Thessa C.; Silva, Teogenes A. da; Oliveira, Paulo Marcio C.

2009-01-01

The evaluation of patient doses is an important tool for optimizing radiodiagnostic medical procedures with conventional X-ray equipment and for improving the quality of the radiographic image. The Patient Dose Calibrator (PDC) chamber is a dosimetric instrument that is used in the evaluation of the air kerma-area product (P KA ) quantity aiming the reduction of patient doses. The objective this work was to study the P KA variation caused by different field incident positions and sizes of the X-ray beam on the PDC chamber. Results showed that the PDC chamber has repeatability lower than 0.6%, beam position dependence of 3% and linearity response within ± 6%; these characteristics are to be taken into account during evaluation of the radiological protection conditions of conventional x-ray equipment. (author)

Plasmacytoid dendritic cell interferon-α production to R-848 stimulation is decreased in male infants

Directory of Open Access Journals (Sweden)

Wang Jennifer P

2012-07-01

Full Text Available Abstract Background Sex differences in response to microbial infections, especially viral ones, may be associated with Toll-like receptor (TLR-mediated responses by plasmacytoid dendritic cells (pDCs. Results In this study, we identified sex differences in human infant pDC interferon-α production following challenge with the TLR7/8 agonist R-848. Male pDC responses were significantly lower than those of females during early infancy. This difference may be attributed to the androgen surge experienced by males during the early infancy period. Pretreatment of human pDCs with dihydrotestosterone produced a significant reduction in interferon-α production following R-848 challenge. Conclusions Androgen-mediated regulation of pDC TLR7-driven innate immune responses may contribute to the observed sex differences in response to infections during early infancy.

Imaging gene expression in gene therapy

International Nuclear Information System (INIS)

Wiebe, Leonard I.

1997-01-01

Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on 'suicide gene therapy' of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k + ) has been use for 'suicide' in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k + gene expression where the H S V-1 t k + gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([ 18 F]F H P G; [ 18 F]-A C V), and pyrimidine- ([ 123 / 131 I]I V R F U; [ 124 / 131I ]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [ 123 / 131I ]I V R F U imaging with the H S V-1 t k + reporter gene will be presented

Imaging gene expression in gene therapy

Energy Technology Data Exchange (ETDEWEB)

Wiebe, Leonard I. [Alberta Univ., Edmonton (Canada). Noujaim Institute for Pharmaceutical Oncology Research

1997-12-31

Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on `suicide gene therapy` of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k{sup +}) has been use for `suicide` in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k{sup +} gene expression where the H S V-1 t k{sup +} gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([{sup 18} F]F H P G; [{sup 18} F]-A C V), and pyrimidine- ([{sup 123}/{sup 131} I]I V R F U; [{sup 124}/{sup 131I}]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [{sup 123}/{sup 131I}]I V R F U imaging with the H S V-1 t k{sup +} reporter gene will be presented

Preparation and characterization of some pyridine-2,6-dicarboxylato thorium(IV) complexes

Energy Technology Data Exchange (ETDEWEB)

Degetto, S; Baracco, L [Consiglio Nazionale delle Ricerche, Padua (Italy). Lab. di Chimica e Tecnologia dei Radioelementi; Graziani, R [Padua Univ. (Italy). Istituto di Chimica Generale ed Inorganica; Celon, E [Padua Univ. (Italy). Istituto di Chimica Organica

1978-12-01

The preparation of complexes of pyridine-2,6-dicarboxylic acid (H/sub 2/PDC) with thorium(IV) is reported and discussed. The reactivity of Th(PDC)/sub 2/(H/sub 2/O)/sub 4/ was tested by preparing adducts with some neutral ligands. The complexes were characterized by i.r. spectroscopy, elemental analysis and thermal behaviour. Preliminary information on the structure obtained by x-ray analysis is also reported.

First-principles study of the Pd–Si system and Pd(0 0 1)/SiC(0 0 1) hetero-structure

Energy Technology Data Exchange (ETDEWEB)

Turchi, P.E.A. [Lawrence Livermore National Laboratory (L-352), 7000 East Avenue, Livermore, CA 94551 (United States); Ivashchenko, V.I. [Institute of Problems of Materials Science, NAS of Ukraine, Krzhyzhanovsky str. 3, 03142 Kyiv (Ukraine)

2014-11-15

Highlights: • A large atomic mixing at the Pd/Si interface occurs at 1500–1800 K. • The Pd/C interface remains sharp even at the highest temperature of 2100 K. • At the Pd/C interface, voids and a graphite-like clustering are detected. • At the Pd/Si interface C22-Pd{sub 2}Si and D0{sub 11}-Pd{sub 3}Si fragments form, in agreement with experiment. - Abstract: First-principles molecular dynamics simulations of the Pd(0 0 1)/3C–SiC(0 0 1) nano-layered structure were carried out at different temperatures ranging from 300 to 2100 K. Various PdSi (Pnma, Fm3{sup ¯}m, P6{sup ¯}m2, Pm3{sup ¯}m), Pd{sub 2}Si (P6{sup ¯}2m, P6{sub 3}/mmc, P3{sup ¯}m1, P3{sup ¯}1m) and Pd{sub 3}Si (Pnma, P6{sub 3}22, Pm3{sup ¯}m, I4/mmm) structures under pressure were studied to identify the structure of the Pd/Si and Pd/C interfaces in the Pd/SiC systems at high temperatures. It was found that a large atomic mixing at the Pd/Si interface occurred at 1500–1800 K, whereas the Pd/C interface remained sharp even at the highest temperature of 2100 K. At the Pd/C interface, voids and a graphite-like clustering were detected. Palladium and silicon atoms interact at the Pd/Si interface to mostly form C22-Pd{sub 2}Si and D0{sub 11}-Pd{sub 3}Si fragments, in agreement with experiment.

Comparison study of positron emission tomography, X-ray CT and MRI in Parkinsonism with dementia

International Nuclear Information System (INIS)

Okada, Junichi; Peppard, R.; Calne, D.B.

1989-01-01

Brain atrophy and local cerebral metabolic rate of glucose (LCMR-glc) in Parkinson's disease with dementia and Parkinsonism-dementia complex (PDC) were studied using positron emission tomography (PET) with F-18-2-deoxy-2-fluoro-D-glucose, X-ray CT and magnetic resonance imaging (MRI). The group of Parkinson's disease with dementia (n=7) had a significantly decreased LCMR-glc in all regions when compared with the age-matched normal group. In the group of Parkinson's disease without dementia (n=6), LCMR-glc was also significantly lower than the control group, although it was higher than the group with associated dementia. Some of the normal aged persons had cortical atrophy. There was no correlation between LCMR-glc and cortical atrophy. Six Guamnian patients had PDC associated with amyotrophic lateral sclerosis (ALS), and four patients had it without ALS. LCMR-glc did not differ in the two groups. It was, however, significantly lower than that in 5 Guamanian and 10 Caucasian normal persons. The group of PDC had a noticeable cortical atrophy and ventricular dilatation, regardless of the presence or absence of ALS. There was correlation between decrease of LCMR-glc and cortical atrophy of the frontal, parietal and temporal lobes. Parkinson's disease and PDC were different from Alzheimer's disease in which a decreased LCMR-glc has been reported to be usually confined to the cerebral cortex. Cortical atrophy and ventricular dilatation were depicted on MRI and CT in the PDC group, but did not in the group of Parkinson's disease. PET was useful in the functional examination and both MRI and CT were useful in the anatomical examination of these diseases. (Namekawa, K)

Adherence With Bisphosphonates and Long-Term Risk of Hip Fractures: A Nested Case-Control Study Using Real-World Data.

Science.gov (United States)

Shalev, Varda; Sharman Moser, Sarah; Goldshtein, Inbal; Yu, Jingbo; Weil, Clara; Ish-Shalom, Sophia; Rouach, Vanessa; Chodick, Gabriel

2017-09-01

Hip fracture is a major complication of osteoporosis. Bisphosphonate medication is the mainstay of treatment for osteoporosis. However, concerns have been raised regarding the effectiveness of bisphosphonates in reducing hip fracture risk after long-term use, particularly among patients with suboptimal adherence. To examine the association between adherence with bisphosphonate therapy and long-term risk of hip fracture. Included in the present nested case-control study were osteoporotic women (n = 14 357) who initiated bisphosphonate therapy in 2000-2010 and were retrospectively followed for incident hip fracture through November 2014. Within this cohort, each case of primary hip fractures was individually matched to 3 controls without a primary hip fracture. Proportion of follow-up days covered (PDC) with bisphosphonates was calculated from bisphosphonate purchases. Adherence was categorized into the following groups: purchase of 1 or 2 months' supply (reference group), at least 3 months' supply to PDC ≤20%, PDC >20% to ≤80%, PDC >80% to ≤100%. Included in the analysis were 426 case-control groups with a mean age (SD) of 73.7 years (7.9). Compared with the reference group, PDC of 80% to 100% with bisphosphonates was associated with a significant reduction in hip fracture risk for patients with 8 to 15 years of follow-up (OR = 0.39; 95% CI = 0.18-0.87). Among patients with a follow-up of up to 3 years, OR was 0.58 (95% CI = 0.31-1.06). Adherence with bisphosphonates among osteoporotic patients is associated with lower risk of hip fracture, with no indication of diminished effectiveness with long-term use.

A contribution to the hazards assessment at Copahue volcano (Argentina-Chile) by facies analysis of a recent pyroclastic density current deposit

Science.gov (United States)

Balbis, C.; Petrinovic, I. A.; Guzmán, S.

2016-11-01

We recognised and interpreted a recent pyroclastic density current (PDC) deposit at the Copahue volcano (Southern Andes), through a field survey and a sedimentological study. The relationships between the behaviour of the PDCs, the morphology of the Río Agrio valley and the eruptive dynamics were interpreted. We identified two lithofacies in the deposit that indicate variations in the eruptive dynamics: i) the opening of the conduit and the formation of a highly explosive eruption that formed a diluted PDC through the immediate collapse of the eruptive column; ii) a continued eruption which followed immediately and records the widening of the conduit, producing a dense PDC. The eruption occurred in 2000 CE, was phreatomagmatic (VEI ≤ 2), with a vesiculation level above 4000 m depth and fragmentation driven by the interaction of magma with an hydrothermal system at ca. 1500 m depth. As deduced from the comparison between the accessory lithics of this deposit and those of the 2012 CE eruption, the depth of onset of vesiculation and fragmentation level in this volcano is constant in depth. In order to reproduce the distribution pattern of this PDC's deposit and to simulate potential PDC's forming-processes, we made several computational modelling from "denser" to "more diluted" conditions. The latter fairly reproduces the distribution of the studied deposit and represents perhaps one of the most dangerous possible scenarios of the Copahue volcanic activity. PDCs occurrence has been considered in the last volcanic hazards map as a low probability process; evidences found in this contribution suggest instead to include them as more probable and thus very important for the hazards assessment of the Copahue volcano.

Calibration methodology application of kerma area product meters in situ: Preliminary results

Science.gov (United States)

Costa, N. A.; Potiens, M. P. A.

2014-11-01

The kerma-area product (KAP) is a useful quantity to establish the reference levels of conventional X-ray examinations. It can be obtained by measurements carried out with a KAP meter on a plane parallel transmission ionization chamber mounted on the X-ray system. A KAP meter can be calibrated in laboratory or in situ, where it is used. It is important to use one reference KAP meter in order to obtain reliable quantity of doses on the patient. The Patient Dose Calibrator (PDC) is a new equipment from Radcal that measures KAP. It was manufactured following the IEC 60580 recommendations, an international standard for KAP meters. This study had the aim to calibrate KAP meters using the PDC in situ. Previous studies and the quality control program of the PDC have shown that it has good function in characterization tests of dosimeters with ionization chamber and it also has low energy dependence. Three types of KAP meters were calibrated in four different diagnostic X-ray equipments. The voltages used in the two first calibrations were 50 kV, 70 kV, 100 kV and 120 kV. The other two used 50 kV, 70 kV and 90 kV. This was related to the equipments limitations. The field sizes used for the calibration were 10 cm, 20 cm and 30 cm. The calibrations were done in three different cities with the purpose to analyze the reproducibility of the PDC. The results gave the calibration coefficient for each KAP meter and showed that the PDC can be used as a reference instrument to calibrate clinical KAP meters.

Comparison study of positron emission tomography, X-ray CT and MRI in Parkinsonism with dementia

Energy Technology Data Exchange (ETDEWEB)

Okada, Junichi; Peppard, R; Calne, D B

1989-05-01

Brain atrophy and local cerebral metabolic rate of glucose (LCMR-glc) in Parkinson's disease with dementia and Parkinsonism-dementia complex (PDC) were studied using positron emission tomography (PET) with F-18-2-deoxy-2-fluoro-D-glucose, X-ray CT and magnetic resonance imaging (MRI). The group of Parkinson's disease with dementia (n=7) had a significantly decreased LCMR-glc in all regions when compared with the age-matched normal group. In the group of Parkinson's disease without dementia (n=6), LCMR-glc was also significantly lower than the control group, although it was higher than the group with associated dementia. Some of the normal aged persons had cortical atrophy. There was no correlation between LCMR-glc and cortical atrophy. Six Guamnian patients had PDC associated with amyotrophic lateral sclerosis (ALS), and four patients had it without ALS. LCMR-glc did not differ in the two groups. It was, however, significantly lower than that in 5 Guamanian and 10 Caucasian normal persons. The group of PDC had a noticeable cortical atrophy and ventricular dilatation, regardless of the presence or absence of ALS. There was correlation between decrease of LCMR-glc and cortical atrophy of the frontal, parietal and temporal lobes. Parkinson's disease and PDC were different from Alzheimer's disease in which a decreased LCMR-glc has been reported to be usually confined to the cerebral cortex. Cortical atrophy and ventricular dilatation were depicted on MRI and CT in the PDC group, but did not in the group of Parkinson's disease. PET was useful in the functional examination and both MRI and CT were useful in the anatomical examination of these diseases. (Namekawa, K).

Overexpression, purification, crystallization and preliminary structural studies of p-coumaric acid decarboxylase from Lactobacillus plantarum

International Nuclear Information System (INIS)

Rodríguez, Héctor; Rivas, Blanca de las; Muñoz, Rosario; Mancheño, José M.

2007-01-01

The enzyme p-coumaric acid decarboxylase (PDC) from L. plantarum has been recombinantly expressed, purified and crystallized. The structure has been solved at 2.04 Å resolution by the molecular-replacement method. The substrate-inducible p-coumaric acid decarboxylase (PDC) from Lactobacillus plantarum has been overexpressed in Escherichia coli, purified and confirmed to possess decarboxylase activity. The recombinant His 6 -tagged enzyme was crystallized using the hanging-drop vapour-diffusion method from a solution containing 20%(w/v) PEG 4000, 12%(w/v) 2-propanol, 0.2 M sodium acetate, 0.1 M Tris–HCl pH 8.0 with 0.1 M barium chloride as an additive. Diffraction data were collected in-house to 2.04 Å resolution. Crystals belonged to the tetragonal space group P4 3 , with unit-cell parameters a = b = 43.15, c = 231.86 Å. The estimated Matthews coefficient was 2.36 Å 3 Da −1 , corresponding to 48% solvent content, which is consistent with the presence of two protein molecules in the asymmetric unit. The structure of PDC has been determined by the molecular-replacement method. Currently, the structure of PDC complexed with substrate analogues is in progress, with the aim of elucidating the structural basis of the catalytic mechanism

Discharge cleaning on TFTR after boronization

International Nuclear Information System (INIS)

Mueller, D.; Dylla, H.F.; LaMarche, P.H.; Bell, M.G.; Blanchard, W.; Bush, C.E.; Gentile, C.; Hawryluk, R.J.; HIll, K.W.; Janos, A.C.; Jobes, F.C; Owens, D.K.; Pearson, G.; Schivell, J.; Ulrickson, M.A.; Vannoy, C.; Wong, K.L.

1991-05-01

At the beginning of the 1990 TFTR experimental run, after replacement of POCO-AXF-5Q graphite tiles on the midplane of the bumper limiter by carbon fiber composite (CFC) tiles and prior to any Pulse Discharge Cleaning (PDC), boronization was performed. Boronization is the deposition of a layer of boron and carbon on the vacuum vessel inner surface by a glow discharge in a diborane, methane and helium mixture. The amount of discharge cleaning required after boronization was substantially reduced compared to that which was needed after previous openings when boronization was not done. Previously, after a major shutdown, about 10 5 low current (∼20 kA) Taylor Discharge Cleaning (TDC) pulses were required before high current (∼400 kA) aggressive Pulse Discharge Cleaning (PDC) pulses could be performed successfully. Aggressive PDC is used to heat the limiters from the vessel bakeout temperature of 150 degrees C to 250 degrees C for a period of several hours. Heating the limiters is important to increase the rate at which water is removed from the carbon limiter tiles. After boronization, the number of required TDC pulses was reduced to <5000. The number of aggressive PDC pulses required was approximately unchanged. 14 refs., 1 tab

Overexpression, purification, crystallization and preliminary structural studies of p-coumaric acid decarboxylase from Lactobacillus plantarum

Energy Technology Data Exchange (ETDEWEB)

Rodríguez, Héctor; Rivas, Blanca de las; Muñoz, Rosario [Instituto de Fermentaciones Industriales, CSIC, Juan de la Cierva 3, 28006 Madrid (Spain); Mancheño, José M., E-mail: xjosemi@iqfr.csic.es [Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain); Instituto de Fermentaciones Industriales, CSIC, Juan de la Cierva 3, 28006 Madrid (Spain)

2007-04-01

The enzyme p-coumaric acid decarboxylase (PDC) from L. plantarum has been recombinantly expressed, purified and crystallized. The structure has been solved at 2.04 Å resolution by the molecular-replacement method. The substrate-inducible p-coumaric acid decarboxylase (PDC) from Lactobacillus plantarum has been overexpressed in Escherichia coli, purified and confirmed to possess decarboxylase activity. The recombinant His{sub 6}-tagged enzyme was crystallized using the hanging-drop vapour-diffusion method from a solution containing 20%(w/v) PEG 4000, 12%(w/v) 2-propanol, 0.2 M sodium acetate, 0.1 M Tris–HCl pH 8.0 with 0.1 M barium chloride as an additive. Diffraction data were collected in-house to 2.04 Å resolution. Crystals belonged to the tetragonal space group P4{sub 3}, with unit-cell parameters a = b = 43.15, c = 231.86 Å. The estimated Matthews coefficient was 2.36 Å{sup 3} Da{sup −1}, corresponding to 48% solvent content, which is consistent with the presence of two protein molecules in the asymmetric unit. The structure of PDC has been determined by the molecular-replacement method. Currently, the structure of PDC complexed with substrate analogues is in progress, with the aim of elucidating the structural basis of the catalytic mechanism.

Catalytic Hydrodeoxygenation of Fatty Acids for Biodiesel Production

Directory of Open Access Journals (Sweden)

Аntonina A. Stepacheva

2016-08-01

Full Text Available This paper is devoted to the production of second generation biodiesel via catalytic hydrodeoxygenation of fatty acids. Pd/C catalysts with different metal loading were used. The palladium catalysts were characterized using low-temperature nitrogen physisorption and X-ray photoelectron spectroscopy. It was revealed that the most active and selective catalyst was 1%-Pd/C which allowed reaching up 97.5% of selectivity (regarding to n-heptadecane at 100% conversion of substrate. Moreover, the chosen catalyst is more preferable according to lower metal content that leads the decrease of the process cost. The analysis of the catalysts showed that 1%-Pd/C had the highest specific surface area compared with 5%-Pd/C. Copyright © 2016 BCREC GROUP. All rights reserved Received: 31st July 2015; Revised: 9th December 2015; Accepted: 30th December 2015 How to Cite: Stepacheva, A.A., Sapunov, V.N., Sulman, E.M., Nikoshvili, L.Z., Sulman, M.G., Sidorov, A.I., Demidenko, G.N., Matveeva, V.G. (2016. Catalytic Hydrodeoxygenation of Fatty Acids for Biodiesel Production. Bulletin of Chemical Reaction Engineering & Catalysis, 11 (2: 125-132 (doi:10.9767/bcrec.11.2.538.125-132 Permalink/DOI: http://dx.doi.org/10.9767/bcrec.11.2.538.125-132

GoGene: gene annotation in the fast lane.

Science.gov (United States)

Plake, Conrad; Royer, Loic; Winnenburg, Rainer; Hakenberg, Jörg; Schroeder, Michael

2009-07-01

High-throughput screens such as microarrays and RNAi screens produce huge amounts of data. They typically result in hundreds of genes, which are often further explored and clustered via enriched GeneOntology terms. The strength of such analyses is that they build on high-quality manual annotations provided with the GeneOntology. However, the weakness is that annotations are restricted to process, function and location and that they do not cover all known genes in model organisms. GoGene addresses this weakness by complementing high-quality manual annotation with high-throughput text mining extracting co-occurrences of genes and ontology terms from literature. GoGene contains over 4,000,000 associations between genes and gene-related terms for 10 model organisms extracted from more than 18,000,000 PubMed entries. It does not cover only process, function and location of genes, but also biomedical categories such as diseases, compounds, techniques and mutations. By bringing it all together, GoGene provides the most recent and most complete facts about genes and can rank them according to novelty and importance. GoGene accepts keywords, gene lists, gene sequences and protein sequences as input and supports search for genes in PubMed, EntrezGene and via BLAST. Since all associations of genes to terms are supported by evidence in the literature, the results are transparent and can be verified by the user. GoGene is available at http://gopubmed.org/gogene.

Radionuclide reporter gene imaging for cardiac gene therapy

International Nuclear Information System (INIS)

Inubushi, Masayuki; Tamaki, Nagara

2007-01-01

In the field of cardiac gene therapy, angiogenic gene therapy has been most extensively investigated. The first clinical trial of cardiac angiogenic gene therapy was reported in 1998, and at the peak, more than 20 clinical trial protocols were under evaluation. However, most trials have ceased owing to the lack of decisive proof of therapeutic effects and the potential risks of viral vectors. In order to further advance cardiac angiogenic gene therapy, remaining open issues need to be resolved: there needs to be improvement of gene transfer methods, regulation of gene expression, development of much safer vectors and optimisation of therapeutic genes. For these purposes, imaging of gene expression in living organisms is of great importance. In radionuclide reporter gene imaging, ''reporter genes'' transferred into cell nuclei encode for a protein that retains a complementary ''reporter probe'' of a positron or single-photon emitter; thus expression of the reporter genes can be imaged with positron emission tomography or single-photon emission computed tomography. Accordingly, in the setting of gene therapy, the location, magnitude and duration of the therapeutic gene co-expression with the reporter genes can be monitored non-invasively. In the near future, gene therapy may evolve into combination therapy with stem/progenitor cell transplantation, so-called cell-based gene therapy or gene-modified cell therapy. Radionuclide reporter gene imaging is now expected to contribute in providing evidence on the usefulness of this novel therapeutic approach, as well as in investigating the molecular mechanisms underlying neovascularisation and safety issues relevant to further progress in conventional gene therapy. (orig.)

Pyroclastic density currents at Etna volcano, Italy: The 11 February 2014 case study

Science.gov (United States)

Andronico, Daniele; Di Roberto, Alessio; De Beni, Emanuela; Behncke, Boris; Bertagnini, Antonella; Del Carlo, Paola; Pompilio, Massimo

2018-05-01

On 11 February 2014, a considerable volume (0.82 to 1.29 × 106 m3) of unstable and hot rocks detached from the lower-eastern flank of the New Southeast Crater (NSEC) at Mt. Etna, producing a pyroclastic density current (PDC). This event was by far the most extensive ever recorded at Mt. Etna since 1999 and has attracted the attention of the scientific community and civil protection to this type of volcanic phenomena, usually occurring without any clear volcanological precursor and especially toward the mechanisms which led to the crater collapse, the PDC flow dynamics and the related volcanic hazard. We present here the results of the investigation carried out on the 11 February 2014 collapse and PDC events; data were obtained through a multidisciplinary approach which includes the analysis of photograph, images from visible and thermal surveillance cameras, and the detailed stratigraphic, textural and petrographic investigations of the PDC deposits. Results suggest that the collapse and consequent PDC was the result of a progressive thermal and mechanical weakening of the cone by repeated surges of magma passing through it during the eruptive activity prior to the 11 February 2014 events, as well as pervasive heating and corrosion by volcanic gas. The collapse of the lower portion of the NSEC was followed by the formation of a relatively hot (up to 750 °C) dense flow which travelled about 2.3 km from the source, stopping shortly after the break of the slope and emplacing the main body of the deposit which ranges between 0.39 and 0.92 × 106 m3. This flow was accompanied a relatively hot cloud of fine ash that dispersed over a wider area. The results presented may contribute to the understanding of this very complex type of volcanic phenomena at Mt. Etna and in similar volcanic settings of the world. In addition, results will lay the basis for the modeling of crater collapse and relative PDC events and consequently for the planning of hazard assessment strategies

Renoprotective Effect of Lactoferrin against Chromium-Induced Acute Kidney Injury in Rats: Involvement of IL-18 and IGF-1 Inhibition.

Directory of Open Access Journals (Sweden)

Rehab Hegazy

Full Text Available Hexavalent chromium (CrVI is a heavy metal widely used in more than 50 industries. Nephrotoxicity is a major adverse effect of chromium poisoning. The present study investigated the potential renoprotective effect of lactoferrin (Lf against potassium dichromate (PDC-induced acute kidney injury (AKI in rats. Beside, because previous studies suggest that interlukin-18 (IL-18 and insulin-like growth factor-1 (IGF-1 play important roles in promoting kidney damage, the present work aimed to evaluate the involvement of these two cytokines in PDC model of AKI and in the potential renoprotective effect of lactoferrin. Adult male albino Wistar rats were pretreated with Lf (200 mg/kg/day, p.o. or (300 mg/kg/day, p.o.; the doses that are usually used in the experiment studies, for 14 days followed by a single dose of PDC (15 mg/kg, s.c.. PDC caused significant increase in serum urea, creatinine, and total protein levels. This was accompanied with decreased renal glutathione content, and increased renal malondialdehyde, IL-18, IL-4, nuclear factor kappa B (NFκB, IGF-1, and the phosphorylated form of forkhead box protein O1 (FoxO1 levels. Moreover, normal expression IFN-γ mRNA and enhanced expression of TNF-α mRNA was demonstrated in renal tissues. Histopathological investigations provoked deleterious changes in the renal tissues. Tubular epithelial hyperplasia and apoptosis were demonstrated immunohistochemically by positive proliferating cell nuclear antigen (PCNA, Bax, and Caspase-3 expression, respectively. Pretreatment of rats with Lf in both doses significantly corrected all previously mentioned PDC-induced changes with no significant difference between both doses. In conclusion, the findings of the present study demonstrated the involvement of oxidative stress, inflammatory reactions, tubular hyperplasia and apoptosis in PDC-induced AKI. It suggested a role of IL-18 through stimulation of IL-4-induced inflammatory pathway, and IGF-1 through

Gene cluster statistics with gene families.

Science.gov (United States)

Raghupathy, Narayanan; Durand, Dannie

2009-05-01

Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In distantly related genomes, clusters of homologous gene pairs are evidence of candidate homologous regions. Demonstrating the statistical significance of such "gene clusters" is an essential component of comparative genomic analyses. However, currently there are no practical statistical tests for gene clusters that model the influence of the number of homologs in each gene family on cluster significance. In this work, we demonstrate empirically that failure to incorporate gene family size in gene cluster statistics results in overestimation of significance, leading to incorrect conclusions. We further present novel analytical methods for estimating gene cluster significance that take gene family size into account. Our methods do not require complete genome data and are suitable for testing individual clusters found in local regions, such as contigs in an unfinished assembly. We consider pairs of regions drawn from the same genome (paralogous clusters), as well as regions drawn from two different genomes (orthologous clusters). Determining cluster significance under general models of gene family size is computationally intractable. By assuming that all gene families are of equal size, we obtain analytical expressions that allow fast approximation of cluster probabilities. We evaluate the accuracy of this approximation by comparing the resulting gene cluster probabilities with cluster probabilities obtained by simulating a realistic, power-law distributed model of gene family size, with parameters inferred from genomic data. Surprisingly, despite the simplicity of the underlying assumption, our method accurately approximates the true cluster probabilities. It slightly overestimates these probabilities, yielding a conservative test. We present additional simulation results indicating the best choice of parameter values for data

Gene therapy prospects--intranasal delivery of therapeutic genes.

Science.gov (United States)

Podolska, Karolina; Stachurska, Anna; Hajdukiewicz, Karolina; Małecki, Maciej

2012-01-01

Gene therapy is recognized to be a novel method for the treatment of various disorders. Gene therapy strategies involve gene manipulation on broad biological processes responsible for the spreading of diseases. Cancer, monogenic diseases, vascular and infectious diseases are the main targets of gene therapy. In order to obtain valuable experimental and clinical results, sufficient gene transfer methods are required. Therapeutic genes can be administered into target tissues via gene carriers commonly defined as vectors. The retroviral, adenoviral and adeno-associated virus based vectors are most frequently used in the clinic. So far, gene preparations may be administered directly into target organs or by intravenous, intramuscular, intratumor or intranasal injections. It is common knowledge that the number of gene therapy clinical trials has rapidly increased. However, some limitations such as transfection efficiency and stable and long-term gene expression are still not resolved. Consequently, great effort is focused on the evaluation of new strategies of gene delivery. There are many expectations associated with intranasal delivery of gene preparations for the treatment of diseases. Intranasal delivery of therapeutic genes is regarded as one of the most promising forms of pulmonary gene therapy research. Gene therapy based on inhalation of gene preparations offers an alternative way for the treatment of patients suffering from such lung diseases as cystic fibrosis, alpha-1-antitrypsin defect, or cancer. Experimental and first clinical trials based on plasmid vectors or recombinant viruses have revealed that gene preparations can effectively deliver therapeutic or marker genes to the cells of the respiratory tract. The noninvasive intranasal delivery of gene preparations or conventional drugs seems to be very encouraging, although basic scientific research still has to continue.

Risk of developing palatally displaced canines in patients with early detectable dental anomalies: a retrospective cohort study

OpenAIRE

GARIB, Daniela Gamba; LANCIA, Melissa; KATO, Renata Mayumi; OLIVEIRA, Thais Marchini; NEVES, Lucimara Teixeira das

2016-01-01

ABSTRACT The early recognition of risk factors for the occurrence of palatally displaced canines (PDC) can increase the possibility of impaction prevention. Objective To estimate the risk of PDC occurrence in children with dental anomalies identified early during mixed dentition. Material and Methods The sample comprised 730 longitudinal orthodontic records from children (448 females and 282 males) with an initial mean age of 8.3 years (SD=1.36). The dental anomaly group (DA) included 263...

Gene-gene interactions and gene polymorphisms of VEGFA and EG-VEGF gene systems in recurrent pregnancy loss.

Science.gov (United States)

Su, Mei-Tsz; Lin, Sheng-Hsiang; Chen, Yi-Chi; Kuo, Pao-Lin

2014-06-01

Both vascular endothelial growth factor A (VEGFA) and endocrine gland-derived vascular endothelial growth factor (EG-VEGF) systems play major roles in angiogenesis. A body of evidence suggests VEGFs regulate critical processes during pregnancy and have been associated with recurrent pregnancy loss (RPL). However, little information is available regarding the interaction of these two major major angiogenesis-related systems in early human pregnancy. This study was conducted to investigate the association of gene polymorphisms and gene-gene interaction among genes in VEGFA and EG-VEGF systems and idiopathic RPL. A total of 98 women with history of idiopathic RPL and 142 controls were included, and 5 functional SNPs selected from VEGFA, KDR, EG-VEGF (PROK1), PROKR1 and PROKR2 were genotyped. We used multifactor dimensionality reduction (MDR) analysis to choose a best model and evaluate gene-gene interactions. Ingenuity pathways analysis (IPA) was introduced to explore possible complex interactions. Two receptor gene polymorphisms [KDR (Q472H) and PROKR2 (V331M)] were significantly associated with idiopathic RPL (P<0.01). The MDR test revealed that the KDR (Q472H) polymorphism was the best loci to be associated with RPL (P=0.02). IPA revealed EG-VEGF and VEGFA systems shared several canonical signaling pathways that may contribute to gene-gene interactions, including the Akt, IL-8, EGFR, MAPK, SRC, VHL, HIF-1A and STAT3 signaling pathways. Two receptor gene polymorphisms [KDR (Q472H) and PROKR2 (V331M)] were significantly associated with idiopathic RPL. EG-VEGF and VEGFA systems shared several canonical signaling pathways that may contribute to gene-gene interactions, including the Akt, IL-8, EGFR, MAPK, SRC, VHL, HIF-1A and STAT3.

Evidence for a role of GABA- and glutamate-gated chloride channels in olfactory memory.

Science.gov (United States)

Boumghar, Katia; Couret-Fauvel, Thomas; Garcia, Mikael; Armengaud, Catherine

2012-11-01

In the honeybee, we investigated the role of transmissions mediated by GABA-gated chloride channels and glutamate-gated chloride channels (GluCls) of the mushroom bodies (MBs) on olfactory learning using a single-trial olfactory conditioning paradigm. The GABAergic antagonist picrotoxin (PTX) or the GluCl antagonist L-trans-pyrrolidine-2,4-dicarboxylic acid (L-trans-PDC) was injected alone or in combination into the α-lobes of MBs. PTX impaired early long-term olfactory memory when injected before conditioning or before testing. L-trans-PDC alone induced no significant effect on learning and memory but induced a less specific response to the conditioned odor. When injected before PTX, L-trans-PDC was able to modulate PTX effects. These results emphasize the role of MB GABA-gated chloride channels in consolidation processes and strongly support that GluCls are involved in the perception of the conditioned stimulus.

Low-profile wireless passive resonators for sensing

Energy Technology Data Exchange (ETDEWEB)

Gong, Xun; An, Linan

2017-04-04

A resonator for sensing a physical or an environmental parameter includes a support having a top surface that provides a ground plane, and a polymer-derived ceramic (PDC) element positioned on the top surface including a PDC layer, and a metal patch on the PDC layer. The metal patch is electrically isolated from all surrounding structure, and the resonator has a resonant frequency that changes as a function of the physical or environmental parameter. A system for wirelessly sensing a physical or environmental parameter includes at least one resonator and a wireless RF reader located remotely from the resonator for transmitting a wide-band RF interrogation signal that excites the resonator. The wireless RF reader detects a sensing signal retransmitted by the resonator and includes a processor for determining the physical or environmental parameter at the location of the resonator from the sensing signal.

Ceramic Nanocomposites from Tailor-Made Preceramic Polymers

Directory of Open Access Journals (Sweden)

Gabriela Mera

2015-04-01

Full Text Available The present Review addresses current developments related to polymer-derived ceramic nanocomposites (PDC-NCs. Different classes of preceramic polymers are briefly introduced and their conversion into ceramic materials with adjustable phase compositions and microstructures is presented. Emphasis is set on discussing the intimate relationship between the chemistry and structural architecture of the precursor and the structural features and properties of the resulting ceramic nanocomposites. Various structural and functional properties of silicon-containing ceramic nanocomposites as well as different preparative strategies to achieve nano-scaled PDC-NC-based ordered structures are highlighted, based on selected ceramic nanocomposite systems. Furthermore, prospective applications of the PDC-NCs such as high-temperature stable materials for thermal protection systems, membranes for hot gas separation purposes, materials for heterogeneous catalysis, nano-confinement materials for hydrogen storage applications as well as anode materials for secondary ion batteries are introduced and discussed in detail.

Ceramic Nanocomposites from Tailor-Made Preceramic Polymers.

Science.gov (United States)

Mera, Gabriela; Gallei, Markus; Bernard, Samuel; Ionescu, Emanuel

2015-04-01

The present Review addresses current developments related to polymer-derived ceramic nanocomposites (PDC-NCs). Different classes of preceramic polymers are briefly introduced and their conversion into ceramic materials with adjustable phase compositions and microstructures is presented. Emphasis is set on discussing the intimate relationship between the chemistry and structural architecture of the precursor and the structural features and properties of the resulting ceramic nanocomposites. Various structural and functional properties of silicon-containing ceramic nanocomposites as well as different preparative strategies to achieve nano-scaled PDC-NC-based ordered structures are highlighted, based on selected ceramic nanocomposite systems. Furthermore, prospective applications of the PDC-NCs such as high-temperature stable materials for thermal protection systems, membranes for hot gas separation purposes, materials for heterogeneous catalysis, nano-confinement materials for hydrogen storage applications as well as anode materials for secondary ion batteries are introduced and discussed in detail.

Ceramic Nanocomposites from Tailor-Made Preceramic Polymers

Science.gov (United States)

Mera, Gabriela; Gallei, Markus; Bernard, Samuel; Ionescu, Emanuel

2015-01-01

The present Review addresses current developments related to polymer-derived ceramic nanocomposites (PDC-NCs). Different classes of preceramic polymers are briefly introduced and their conversion into ceramic materials with adjustable phase compositions and microstructures is presented. Emphasis is set on discussing the intimate relationship between the chemistry and structural architecture of the precursor and the structural features and properties of the resulting ceramic nanocomposites. Various structural and functional properties of silicon-containing ceramic nanocomposites as well as different preparative strategies to achieve nano-scaled PDC-NC-based ordered structures are highlighted, based on selected ceramic nanocomposite systems. Furthermore, prospective applications of the PDC-NCs such as high-temperature stable materials for thermal protection systems, membranes for hot gas separation purposes, materials for heterogeneous catalysis, nano-confinement materials for hydrogen storage applications as well as anode materials for secondary ion batteries are introduced and discussed in detail. PMID:28347023

Gene doping: gene delivery for olympic victory

OpenAIRE

Gould, David

2012-01-01

With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called ‘gene doping’. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted...

Liquid-phase pulsed laser ablation synthesis of graphitized carbon-encapsulated palladium core–shell nanospheres for catalytic reduction of nitrobenzene to aniline

Energy Technology Data Exchange (ETDEWEB)

Kim, Yu-jin; Ma, Rory; Reddy, D. Amaranatha; Kim, Tae Kyu, E-mail: tkkim@pusan.ac.kr

2015-12-01

Graphical abstract: - Highlights: • Graphitized carbon-encapsulated palladium core–shell nanospheres fabricated by laser ablation. • Physical characterizations of synthesized Pd@C nanospheres. • Assessments of catalytic performance of Pd@C nanospheres for the reduction of nitrobenzene to aniline. • Significant improvement of the catalytic activity due to the graphitized carbon-layered structure and the high specific surface area. - Abstract: Graphitized carbon-encapsulated palladium (Pd) core–shell nanospheres were produced via pulsed laser ablation of a solid Pd foil target submerged in acetonitrile. The microstructural features and optical properties of these nanospheres were characterized via high resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and UV-visible spectroscopy. Microstructural analysis indicated that the core–shell nanostructures consisted of single-crystalline cubic metallic Pd spheres that serve as the core material, over which graphitized carbon was anchored as a heterogeneous shell. The absorbance spectrum of the synthesized nanostructures exhibited a broad (absorption) band at ∼264 nm; this band corresponded to the typical inter-band transition of a metallic system and resulted possibly from the absorbance of the ionic Pd{sup 2+}. The catalytic properties of the Pd and Pd@C core–shell nanostructures were investigated using the reduction of nitrobenzene to aniline by an excess amount of NaBH{sub 4} in an aqueous solution at room temperature, as a model reaction. Owing to the graphitized carbon-layered structure and the high specific surface area, the resulting Pd@C nanostructures exhibited higher conversion efficiencies than their bare Pd counterparts. In fact, the layered structure provided access to the surface of the Pd nanostructures for the hydrogenation reaction, owing to the synergistic effect between graphitized carbon and the nanostructures. Their

Liquid-phase pulsed laser ablation synthesis of graphitized carbon-encapsulated palladium core–shell nanospheres for catalytic reduction of nitrobenzene to aniline

International Nuclear Information System (INIS)

Kim, Yu-jin; Ma, Rory; Reddy, D. Amaranatha; Kim, Tae Kyu

2015-01-01

Graphical abstract: - Highlights: • Graphitized carbon-encapsulated palladium core–shell nanospheres fabricated by laser ablation. • Physical characterizations of synthesized Pd@C nanospheres. • Assessments of catalytic performance of Pd@C nanospheres for the reduction of nitrobenzene to aniline. • Significant improvement of the catalytic activity due to the graphitized carbon-layered structure and the high specific surface area. - Abstract: Graphitized carbon-encapsulated palladium (Pd) core–shell nanospheres were produced via pulsed laser ablation of a solid Pd foil target submerged in acetonitrile. The microstructural features and optical properties of these nanospheres were characterized via high resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and UV-visible spectroscopy. Microstructural analysis indicated that the core–shell nanostructures consisted of single-crystalline cubic metallic Pd spheres that serve as the core material, over which graphitized carbon was anchored as a heterogeneous shell. The absorbance spectrum of the synthesized nanostructures exhibited a broad (absorption) band at ∼264 nm; this band corresponded to the typical inter-band transition of a metallic system and resulted possibly from the absorbance of the ionic Pd 2+ . The catalytic properties of the Pd and Pd@C core–shell nanostructures were investigated using the reduction of nitrobenzene to aniline by an excess amount of NaBH 4 in an aqueous solution at room temperature, as a model reaction. Owing to the graphitized carbon-layered structure and the high specific surface area, the resulting Pd@C nanostructures exhibited higher conversion efficiencies than their bare Pd counterparts. In fact, the layered structure provided access to the surface of the Pd nanostructures for the hydrogenation reaction, owing to the synergistic effect between graphitized carbon and the nanostructures. Their unique

Comparison study of positron emission tomography, X-ray CT and MRI in Parkinsonism with dementia

Energy Technology Data Exchange (ETDEWEB)

Okada, Junichi; Peppard, R.; Calne, D.B.

1989-05-01

Brain atrophy and local cerebral metabolic rate of glucose (LCMR-glc) in Parkinson's disease with dementia and Parkinsonism-dementia complex (PDC) were studied using positron emission tomography (PET) with F-18-2-deoxy-2-fluoro-D-glucose, X-ray CT and magnetic resonance imaging (MRI). The group of Parkinson's disease with dementia (n=7) had a significantly decreased LCMR-glc in all regions when compared with the age-matched normal group. In the group of Parkinson's disease without dementia (n=6), LCMR-glc was also significantly lower than the control group, although it was higher than the group with associated dementia. Some of the normal aged persons had cortical atrophy. There was no correlation between LCMR-glc and cortical atrophy. Six Guamnian patients had PDC associated with amyotrophic lateral sclerosis (ALS), and four patients had it without ALS. LCMR-glc did not differ in the two groups. It was, however, significantly lower than that in 5 Guamanian and 10 Caucasian normal persons. The group of PDC had a noticeable cortical atrophy and ventricular dilatation, regardless of the presence or absence of ALS. There was correlation between decrease of LCMR-glc and cortical atrophy of the frontal, parietal and temporal lobes. Parkinson's disease and PDC were different from Alzheimer's disease in which a decreased LCMR-glc has been reported to be usually confined to the cerebral cortex. Cortical atrophy and ventricular dilatation were depicted on MRI and CT in the PDC group, but did not in the group of Parkinson's disease. PET was useful in the functional examination and both MRI and CT were useful in the anatomical examination of these diseases. (Namekawa, K).

FunGene: the functional gene pipeline and repository.

Science.gov (United States)

Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

2013-01-01

Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

FunGene: the Functional Gene Pipeline and Repository

Directory of Open Access Journals (Sweden)

Jordan A. Fish

2013-10-01

Full Text Available Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer.While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/ offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

Mining disease genes using integrated protein-protein interaction and gene-gene co-regulation information.

Science.gov (United States)

Li, Jin; Wang, Limei; Guo, Maozu; Zhang, Ruijie; Dai, Qiguo; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Xuan, Ping; Zhang, Mingming

2015-01-01

In humans, despite the rapid increase in disease-associated gene discovery, a large proportion of disease-associated genes are still unknown. Many network-based approaches have been used to prioritize disease genes. Many networks, such as the protein-protein interaction (PPI), KEGG, and gene co-expression networks, have been used. Expression quantitative trait loci (eQTLs) have been successfully applied for the determination of genes associated with several diseases. In this study, we constructed an eQTL-based gene-gene co-regulation network (GGCRN) and used it to mine for disease genes. We adopted the random walk with restart (RWR) algorithm to mine for genes associated with Alzheimer disease. Compared to the Human Protein Reference Database (HPRD) PPI network alone, the integrated HPRD PPI and GGCRN networks provided faster convergence and revealed new disease-related genes. Therefore, using the RWR algorithm for integrated PPI and GGCRN is an effective method for disease-associated gene mining.

Gene-gene, gene-environment, gene-nutrient interactions and single nucleotide polymorphisms of inflammatory cytokines.

Science.gov (United States)

Nadeem, Amina; Mumtaz, Sadaf; Naveed, Abdul Khaliq; Aslam, Muhammad; Siddiqui, Arif; Lodhi, Ghulam Mustafa; Ahmad, Tausif

2015-05-15

Inflammation plays a significant role in the etiology of type 2 diabetes mellitus (T2DM). The rise in the pro-inflammatory cytokines is the essential step in glucotoxicity and lipotoxicity induced mitochondrial injury, oxidative stress and beta cell apoptosis in T2DM. Among the recognized markers are interleukin (IL)-6, IL-1, IL-10, IL-18, tissue necrosis factor-alpha (TNF-α), C-reactive protein, resistin, adiponectin, tissue plasminogen activator, fibrinogen and heptoglobins. Diabetes mellitus has firm genetic and very strong environmental influence; exhibiting a polygenic mode of inheritance. Many single nucleotide polymorphisms (SNPs) in various genes including those of pro and anti-inflammatory cytokines have been reported as a risk for T2DM. Not all the SNPs have been confirmed by unifying results in different studies and wide variations have been reported in various ethnic groups. The inter-ethnic variations can be explained by the fact that gene expression may be regulated by gene-gene, gene-environment and gene-nutrient interactions. This review highlights the impact of these interactions on determining the role of single nucleotide polymorphism of IL-6, TNF-α, resistin and adiponectin in pathogenesis of T2DM.

Diamonds are forever: drill bit advances may offer cheaper and stronger alternatives

Energy Technology Data Exchange (ETDEWEB)

Mahoney, J.

2001-02-01

The rise to prominence of polycrystalline diamond compact (PDC) and diamond-impregnated drill bits, slowly providing stiff competition to the roller-cone type bits that for many years was the standard in the drilling industry, is discussed. A roller-cone drill bit, although much improved by heat treatment of the metal and the addition of tungsten carbide, is still mostly steel. It works by crushing the rock by overcoming its compressive strength, whereas PDC drill bits shear the rock away in a manner similar to scraping ice from a car windshield. PDC bits typically have three to six cutting surfaces, each one edged with a row of polycrystalline diamond cutters, bonded to a tungsten carbide base by a process called microwave sintering. Compared to roller cones, PDCs drill at least twice as fast, especially in the soft rock and clay where they have been used principally. In addition to saving rig time, PDC bits can handle longer runs; in the right application it is possible to drill the total depth of a well with only one bit. The microwave-sintered tungsten carbide also has higher corrosion resistance than the same material bonded under high pressure; PDCs are also less subject to mechanical failure than roller cones which use moveable bearings, seals and rotating cones. 1 photo.

A critical assessment of vector control for dengue prevention.

Directory of Open Access Journals (Sweden)

Nicole L Achee

2015-05-01

Full Text Available Recently, the Vaccines to Vaccinate (v2V initiative was reconfigured into the Partnership for Dengue Control (PDC, a multi-sponsored and independent initiative. This redirection is consistent with the growing consensus among the dengue-prevention community that no single intervention will be sufficient to control dengue disease. The PDC's expectation is that when an effective dengue virus (DENV vaccine is commercially available, the public health community will continue to rely on vector control because the two strategies complement and enhance one another. Although the concept of integrated intervention for dengue prevention is gaining increasingly broader acceptance, to date, no consensus has been reached regarding the details of how and what combination of approaches can be most effectively implemented to manage disease. To fill that gap, the PDC proposed a three step process: (1 a critical assessment of current vector control tools and those under development, (2 outlining a research agenda for determining, in a definitive way, what existing tools work best, and (3 determining how to combine the best vector control options, which have systematically been defined in this process, with DENV vaccines. To address the first step, the PDC convened a meeting of international experts during November 2013 in Washington, DC, to critically assess existing vector control interventions and tools under development. This report summarizes those deliberations.

Suicide genes or p53 gene and p53 target genes as targets for cancer gene therapy by ionizing radiation

International Nuclear Information System (INIS)

Liu Bing; Chinese Academy of Sciences, Beijing; Zhang Hong

2005-01-01

Radiotherapy has some disadvantages due to the severe side-effect on the normal tissues at a curative dose of ionizing radiation (IR). Similarly, as a new developing approach, gene therapy also has some disadvantages, such as lack of specificity for tumors, limited expression of therapeutic gene, potential biological risk. To certain extent, above problems would be solved by the suicide genes or p53 gene and its target genes therapies targeted by ionizing radiation. This strategy not only makes up the disadvantage from radiotherapy or gene therapy alone, but also promotes success rate on the base of lower dose. By present, there have been several vectors measuring up to be reaching clinical trials. This review focused on the development of the cancer gene therapy through suicide genes or p53 and its target genes mediated by IR. (authors)

Neighboring Genes Show Correlated Evolution in Gene Expression

Science.gov (United States)

Ghanbarian, Avazeh T.; Hurst, Laurence D.

2015-01-01

When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. PMID:25743543

Product development capability and marketing strategy for new durable products

OpenAIRE

Banerjee, Sumitro; Soberman, David A.

2013-01-01

Our objective is to understand how a firm’s product development capability (PDC) affects the launch strategy for a durable product that is sequentially improved over time in a market where consumers have heterogeneous valuations for quality. We show that the launch strategy of firms is affected by the degree to which consumers think ahead. However, only the strategy of firms with high PDC is affected by the observability of quality. When consumers are myopic and quality is observable, both hi...

Gene Therapy

Science.gov (United States)

Gene therapy Overview Gene therapy involves altering the genes inside your body's cells in an effort to treat or stop disease. Genes contain your ... that don't work properly can cause disease. Gene therapy replaces a faulty gene or adds a new ...

Evaluating the phylogenetic signal limit from mitogenomes, slow evolving nuclear genes, and the concatenation approach. New insights into the Lacertini radiation using fast evolving nuclear genes and species trees.

Science.gov (United States)

Mendes, Joana; Harris, D James; Carranza, Salvador; Salvi, Daniele

2016-07-01

Estimating the phylogeny of lacertid lizards, and particularly the tribe Lacertini has been challenging, possibly due to the fast radiation of this group resulting in a hard polytomy. However this is still an open question, as concatenated data primarily from mitochondrial markers have been used so far whereas in a recent phylogeny based on a compilation of these data within a squamate supermatrix the basal polytomy seems to be resolved. In this study, we estimate phylogenetic relationships between all Lacertini genera using for the first time DNA sequences from five fast evolving nuclear genes (acm4, mc1r, pdc, βfib and reln) and two mitochondrial genes (nd4 and 12S). We generated a total of 529 sequences from 88 species and used Maximum Likelihood and Bayesian Inference methods based on concatenated multilocus dataset as well as a coalescent-based species tree approach with the aim of (i) shedding light on the basal relationships of Lacertini (ii) assessing the monophyly of genera which were previously questioned, and (iii) discussing differences between estimates from this and previous studies based on different markers, and phylogenetic methods. Results uncovered (i) a new phylogenetic clade formed by the monotypic genera Archaeolacerta, Zootoca, Teira and Scelarcis; and (ii) support for the monophyly of the Algyroides clade, with two sister species pairs represented by western (A. marchi and A. fitzingeri) and eastern (A. nigropunctatus and A. moreoticus) lineages. In both cases the members of these groups show peculiar morphology and very different geographical distributions, suggesting that they are relictual groups that were once diverse and widespread. They probably originated about 11-13 million years ago during early events of speciation in the tribe, and the split between their members is estimated to be only slightly older. This scenario may explain why mitochondrial markers (possibly saturated at higher divergence levels) or slower nuclear markers

Imaging reporter gene for monitoring gene therapy

International Nuclear Information System (INIS)

Beco, V. de; Baillet, G.; Tamgac, F.; Tofighi, M.; Weinmann, P.; Vergote, J.; Moretti, J.L.; Tamgac, G.

2002-01-01

Scintigraphic images can be obtained to document gene function at cellular level. This approach is presented here and the use of a reporter gene to monitor gene therapy is described. Two main ways are presented: either the use of a reporter gene coding for an enzyme the action of which will be monitored by radiolabeled pro-drug, or a cellular receptor gene, the action of which is documented by a radio labeled cognate receptor ligand. (author)

Gene-Gene and Gene-Environment Interactions in the Etiology of Breast Cancer

National Research Council Canada - National Science Library

Adegoke, Olufemi

2003-01-01

The objective of this CDA is to evaluate the gene-gene and gene-environment interactions in the etiology of breast cancer in two ongoing case-control studies, the Shanghai Breast Cancer Study (SBCS...

Gene doping: gene delivery for olympic victory.

Science.gov (United States)

Gould, David

2013-08-01

With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called 'gene doping'. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted from the engineered cells or is retained locally to, or inside engineered cells will, to some extent, determine the likelihood of detection. It is clear that effective gene delivery technologies now exist and it is important that detection and prevention plans are in place. © 2012 The Author. British Journal of Clinical Pharmacology © 2012 The British Pharmacological Society.

Directly assessing interpersonal RSA influences in the frequency domain: An illustration with generalized partial directed coherence.

Science.gov (United States)

Liu, Siwei; Gates, Kathleen M; Blandon, Alysia Y

2018-06-01

Despite recent research indicating that interpersonal linkage in physiology is a common phenomenon during social interactions, and the well-established role of respiratory sinus arrhythmia (RSA) in socially facilitative physiological regulation, little research has directly examined interpersonal influences in RSA, perhaps due to methodological challenges in analyzing multivariate RSA data. In this article, we aim to bridge this methodological gap by introducing a new method for quantifying interpersonal RSA influences. Specifically, we show that a frequency-domain statistic, generalized partial directed coherence (gPDC), can be used to capture lagged relations in RSA between social partners without first estimating RSA for each person. We illustrate its utility by examining the relation between gPDC and marital conflict in a sample of married couples. Finally, we discuss how gPDC complements existing methods in the time domain and provide guidelines for choosing among these different statistical techniques. © 2018 Society for Psychophysiological Research.

Detection and Correction of Step Discontinuities in Kepler Flux Time Series

Science.gov (United States)

Kolodziejczak, J. J.; Morris, R. L.

2011-01-01

PDC 8.0 includes an implementation of a new algorithm to detect and correct step discontinuities appearing in roughly one of every 20 stellar light curves during a given quarter. The majority of such discontinuities are believed to result from high-energy particles (either cosmic or solar in origin) striking the photometer and causing permanent local changes (typically -0.5%) in quantum efficiency, though a partial exponential recovery is often observed [1]. Since these features, dubbed sudden pixel sensitivity dropouts (SPSDs), are uncorrelated across targets they cannot be properly accounted for by the current detrending algorithm. PDC detrending is based on the assumption that features in flux time series are due either to intrinsic stellar phenomena or to systematic errors and that systematics will exhibit measurable correlations across targets. SPSD events violate these assumptions and their successful removal not only rectifies the flux values of affected targets, but demonstrably improves the overall performance of PDC detrending [1].

Synthesis and characterization of heterometallic uranyl pyridinedicarboxylate compounds

Science.gov (United States)

Jayasinghe, Ashini S.; Payne, Maurice K.; Forbes, Tori Z.

2017-10-01

The incorporation of transition metals into hybrid uranyl materials can result in more diverse structural topologies and variations in physical and chemical properties. To explore the impact of transition metals on the uranyl cation, five uranium containing bimetallic chain compounds, [(UO2)M(PDC)2(H2O)4]·4(H2O) (PDC = 2,6 pyridinedicarboxylate; M = Ni2+, Co2+, Fe2+, Zn2+, and Cu2+) were synthesized by evaporation of aqueous solutions at room temperature. The uranyl cation is complex by two PDC ligands and the transition metal cations bond to the complex to form a one-dimensional chain topology. The presence of the transition metal leads to the presence of a stronger uranyl oxo bonds as shown by the single-crystal X-ray diffraction data and the Raman spectra. Solid state diffuse reflectance UV/Visible spectra confirmed the presence of the transition metals in the structure by the broad bands that appeared at relevant wavelengths.

Genes2FANs: connecting genes through functional association networks

Science.gov (United States)

2012-01-01

Background Protein-protein, cell signaling, metabolic, and transcriptional interaction networks are useful for identifying connections between lists of experimentally identified genes/proteins. However, besides physical or co-expression interactions there are many ways in which pairs of genes, or their protein products, can be associated. By systematically incorporating knowledge on shared properties of genes from diverse sources to build functional association networks (FANs), researchers may be able to identify additional functional interactions between groups of genes that are not readily apparent. Results Genes2FANs is a web based tool and a database that utilizes 14 carefully constructed FANs and a large-scale protein-protein interaction (PPI) network to build subnetworks that connect lists of human and mouse genes. The FANs are created from mammalian gene set libraries where mouse genes are converted to their human orthologs. The tool takes as input a list of human or mouse Entrez gene symbols to produce a subnetwork and a ranked list of intermediate genes that are used to connect the query input list. In addition, users can enter any PubMed search term and then the system automatically converts the returned results to gene lists using GeneRIF. This gene list is then used as input to generate a subnetwork from the user’s PubMed query. As a case study, we applied Genes2FANs to connect disease genes from 90 well-studied disorders. We find an inverse correlation between the counts of links connecting disease genes through PPI and links connecting diseases genes through FANs, separating diseases into two categories. Conclusions Genes2FANs is a useful tool for interpreting the relationships between gene/protein lists in the context of their various functions and networks. Combining functional association interactions with physical PPIs can be useful for revealing new biology and help form hypotheses for further experimentation. Our finding that disease genes in

Evaluation of the use of purine derivatives:creatinine ratio in spot urine samples as an index of microbial protein supply in Yerli Kara crossbred cattle

International Nuclear Information System (INIS)

Cetinkaya, N.; Ozdemir, H.; Gucus, A.I.; Ozcan, H.; Sogut, A.; Yaman, S.

2004-01-01

In Experiment I, response of daily purine derivatives (PD) excretion to feed intake in Yerli Kara crossbred (YK-C) cattle on state farms was measured. Animals were fed a mixed diet containing 30% wheat straw and 70% compounded feed. Crude protein and organic matter contents of the diet were 12.4% and 95%, respectively. In Experiment II, spot urine sampling technique was applied at state farm. Four Yerli Kara crossbred bulls with a mean live weight of 211.0 ± 41.3 kg were used. The experimental design, feeding and diet were the same as in Experiment I. The treatments were allocated according to a 4 x 4 Latin Square design. In Experiment III, spot urine sampling technique was applied at smallholder farms. Two to three kg of compound feed (crude protein 12%) containing 65% barley, 25% bran, 6% sunflower seed meal, 3% marmer dust and 1% mineral and vitamin mixture was offered in two parts, one in the morning (0730 h) and the other in the afternoon (1700 h). The ingredients in the compound feed were similar for all animals, but animals in Groups I, II and III received 1 to 2 kg/d of straw (crude protein 3%), grass hay (crude protein 7%), or both straw and grass hay respectively. In Experiment I, a significant correlation (R 2 =0.99) between PD excretion (Y, mmol/d) and digestible organic matter intake, DOMI (X, kg/d) for YK-C cattle was observed (Y = 12.5 + 19.7 X). Moreover, daily PD excretion (mmol/d) was correlated with the PDC index, which was defined as [PD molar concentration] / [Creatinine molar concentration] x kgW 0.75 . In Experiment II, the PDC index increased with level of intake. The coefficient of variation due to time of sampling for uric acid, allantoin, PD, creatinine, total-N, the PDC Index in spot urine samples were less than 5%. In Experiment III, the PDC index were 49.95 ± 13.5, 45.6 ± 13.0, 48.95 ± 15.3 for the three groups respectively. These values were similar to those for 60% intake level in Experiment I. Using the equation DOMI = 344 + 48

Catalytic hydroconversion of tricaprylin and caprylic acid as model reaction for biofuel production from triglycerides

Energy Technology Data Exchange (ETDEWEB)

Boda, L.; Thernesz, A. [MOL Hungarian Oil and Gas Co. Plc., Szazhalombatta (Hungary); Onyestyak, G.; Solt, H.; Lonyi, F.; Valyon, J. [Hungarian Academy of Sciences, Budapest (Hungary). Inst. of Nanochemistry and Catalysis

2010-07-01

Palladium/activated carbon (Pd/C) and non-sulfided Ni,Mo/{gamma}-Al{sub 2}O{sub 3} catalysts were used. The hydroconversion was found to proceed in consecutive steps of tricaprylin (TC) hydrogenolysis (HYS) to caprylic acid (CA) and propane, and hydrodeoxygenation (HDO) of the acid intermediate to get hydrocarbon. Two HDO routes were distinguished: (i) over Pd/C the prevailing reaction route was the decarbonylation, whereas (ii) over molybdena-alumina catalysts the main reaction was the reduction of oxygen to get water. (orig.)

Classifying genes to the correct Gene Ontology Slim term in Saccharomyces cerevisiae using neighbouring genes with classification learning

Directory of Open Access Journals (Sweden)

Tsatsoulis Costas

2010-05-01

Full Text Available Abstract Background There is increasing evidence that gene location and surrounding genes influence the functionality of genes in the eukaryotic genome. Knowing the Gene Ontology Slim terms associated with a gene gives us insight into a gene's functionality by informing us how its gene product behaves in a cellular context using three different ontologies: molecular function, biological process, and cellular component. In this study, we analyzed if we could classify a gene in Saccharomyces cerevisiae to its correct Gene Ontology Slim term using information about its location in the genome and information from its nearest-neighbouring genes using classification learning. Results We performed experiments to establish that the MultiBoostAB algorithm using the J48 classifier could correctly classify Gene Ontology Slim terms of a gene given information regarding the gene's location and information from its nearest-neighbouring genes for training. Different neighbourhood sizes were examined to determine how many nearest neighbours should be included around each gene to provide better classification rules. Our results show that by just incorporating neighbour information from each gene's two-nearest neighbours, the percentage of correctly classified genes to their correct Gene Ontology Slim term for each ontology reaches over 80% with high accuracy (reflected in F-measures over 0.80 of the classification rules produced. Conclusions We confirmed that in classifying genes to their correct Gene Ontology Slim term, the inclusion of neighbour information from those genes is beneficial. Knowing the location of a gene and the Gene Ontology Slim information from neighbouring genes gives us insight into that gene's functionality. This benefit is seen by just including information from a gene's two-nearest neighbouring genes.

Synthesis and Structural Characterization of Magnesium Based Coordination Networks in Different Solvents

Energy Technology Data Exchange (ETDEWEB)

D Banerjee; J Finkelstein; A Smirnov; P Forster; L Borkowski; S Teat; J Parise

2011-12-31

Three magnesium based metal-organic frameworks, Mg{sub 3}(3,5-PDC){sub 3}(DMF){sub 3} {center_dot} DMF [1], Mg(3,5-PDC)(H{sub 2}O) {center_dot} (H{sub 2}O) [3], and Mg{sub 4}(3,5-PDC){sub 4}(DMF){sub 2}(H{sub 2}O){sub 2} {center_dot} 2DMF {center_dot} 4.5H{sub 2}O [4], and a 2-D coordination polymer, [Mg(3,5-PDC)(H{sub 2}O){sub 2}] [2] [PDC = pyridinedicarboxylate], were synthesized using a combination of DMF, methanol, ethanol, and water. Compound 1 [space group P2{sub 1}/n, a = 12.3475(5) {angstrom}, b = 11.1929(5) {angstrom}, c = 28.6734(12) {angstrom}, {beta} = 98.8160(10){sup o}, V = 3916.0(3) {angstrom}{sup 3}] consists of a combination of isolated and corner-sharing magnesium octahedra connected by the organic linkers to form a 3-D network with a 12.2 {angstrom} x 4.6 {angstrom} 1-D channel. The channel contains coordinated and free DMF molecules. In compound 2 [space group C2/c, a = 9.964(5) {angstrom}, b = 12.0694(6) {angstrom}, c = 7.2763(4) {angstrom}, {beta} = 106.4970(6){sup o}, V = 836.70(6) {angstrom}{sup 3}], PDC connects isolated seven coordinated magnesium polyhedra into a layered structure. Compound 3 [space group P6{sub 1}22, a = 11.479(1) {angstrom}, c = 14.735(3) {angstrom}, V = 1681.7(4) {angstrom}{sup 3}] (previously reported) contains isolated magnesium octahedra connected by the organic linker with each other forming a 3D network. Compound 4 [space group P2{sub 1}/c, a = 13.7442(14) {angstrom}, b = 14.2887(15) {angstrom}, c = 14.1178(14) {angstrom}, {beta} = 104.912(2){sup o}, V = 2679.2(5) {angstrom}{sup 3}] also exhibits a 3D network based on isolated magnesium octahedra with square cavities containing both disordered DMF and water molecules. The structural topologies originate due to the variable coordination ability of solvent molecules with the metal center. Water molecules coordinate with the magnesium metal centers preferably over other polar solvents (DMF, methanol, ethanol) used to synthesize the coordination networks. Despite

Electrocatalytic Performance of Carbon Supported WO3-Containing Pd–W Nanoalloys for Oxygen Reduction Reaction in Alkaline Media

Directory of Open Access Journals (Sweden)

Nan Cui

2018-05-01

Full Text Available In this paper, we report that WOx containing nanoalloys exhibit stable electrocatalytic performance in alkaline media, though bulk WO3 is easy to dissolve in NaOH solution. Carbon supported oxide-rich Pd–W alloy nanoparticles (PdW/C with different Pd:W atom ratios were prepared by the reduction–oxidation method. Among the catalysts, the oxide-rich Pd0.8W0.2/C (Pd/W = 8:2, atom ratio exhibits the highest catalytic activity for the oxygen reduction reaction. The X-ray photoelectron spectroscopy data shows that ~40% of Pd atoms and ~60% of the W atoms are in their oxide form. The Pd 3d5/2 binding energy of the oxide-rich Pd–W nanoalloys is higher than that of Pd/C, indicating the electronic structure of Pd is affected by the strong interaction between Pd and W/WO3. Compare to Pd/C, the onset potential of the oxygen reduction reaction at the oxide-rich Pd0.8W0.2/C shifts to a higher potential. The current density (mA·mg Pd−1 at the oxide-rich Pd0.8W0.2/C is ~1.6 times of that at Pd/C. The oxide-rich Pd0.8W0.2/C also exhibits higher catalytic stability than Pd/C, which demonstrates that it is a prospective candidate for the cathode of fuel cells operating with alkaline electrolyte.

Antitumor Effect of AZD4547 in a Fibroblast Growth Factor Receptor 2–Amplified Gastric Cancer Patient–Derived Cell Model

Directory of Open Access Journals (Sweden)

Jiryeon Jang

2017-08-01

Full Text Available BACKGROUND: FGFR2 amplification is associated with aggressive gastric cancer (GC, and targeted drugs have been developed for treatment of GC. We evaluated the antitumor activity of an FGFR inhibitor in FGFR2-amplified GC patients with peritoneal carcinomatosis. METHODS: Two GC patients with FGFR2 amplification confirmed by fluorescence in situ hybridization showed peritoneal seeding and malignant ascites. We used the patient-derived xenograft model; patient-derived cells (PDCs from malignant ascites were used to assess FGFR2 expression and its downstream pathway using immunofluorescence analysis and immunoblot assay in vitro. Apoptosis and cell cycle arrest after treatment of FGFR inhibitor were analyzed by Annexin V-FITC assay and cell cycle analysis. RESULTS: FGFR2 amplification was verified in both PDC lines. AZD4547 as an FGFR inhibitor decreased proliferation of PDCs, and the IC50 value was estimated to be 250 nM in PDC#1 and 210 nM in PDC#2. FGFR inhibitor also significantly decreased levels of phosphorylated FGFR2 and downstream signaling molecules in FGFR2-amplified PDC lines. In cell cycle analysis, apoptosis was significantly increased in AZD4547-treated cells compared with nontreated cells. The proportion of cells in the sub-G1 stage was significantly higher in AZD4547-treated PDCs than in control cells. CONCLUSION: Our findings suggest that FGFR2 amplification is a relevant therapeutic target in GC with peritoneal carcinomatosis.

The structure of nano-palladium deposited on carbon-based supports

International Nuclear Information System (INIS)

Pikna, Ľubomír; Milkovič, Ondrej; Saksl, Karel; Heželová, Mária; Smrčová, Miroslava; Puliš, Pavel; Michalik, Štefan; Gamcová, Jana

2014-01-01

Nano-palladium catalysts, prepared using the same procedure with the same metal content (3 wt%) and two different supports, activated carbon (Pd/C) and activated carbon—multiwalled carbon nanotubes (Pd/C/CNT), are discussed. The simple technique of deposition reduction was applied in the preparation of these two types of Pd catalysts. TEM, XRD analysis, EXAFS signal analysis, and XANES were used for sample characterization. In both samples, transmission electron microscopy identified nanosized Pd particles with nearly spherical morphology but different sizes. The mean diameters of the particles on Pd/C and Pd/C/CNT were estimated to be 5.4 nm and 7.8 nm, respectively. The EXAFS signal analysis showed that Pd atoms on the particle surfaces were coordinated by 4 oxygens to form a PdO monolayer covering a metallic core. The XANES signal analysis indicated a smaller particle size for Pd/C (∅ 5 nm) than for Pd/C/CNT (∅ 10 nm), in good agreement with the TEM observations. - Graphical abstract: Visualization of metallic core (left), oxide monolayer (middle) and nanoparticle of diameter 5 nm (right). - Highlights: • Pd catalysts were prepared on two types of supports: carbon and carbon nanotubes. • BET, TEM, XRD characterization of prepared catalysts. • XAFS: Concentration of Pd in samples Pd/C and Pd/C/CNT. • EXAFS and XANES signal analysis of catalysts. • Visualisation of atoms arrangement at the Pd nanoparticle surface

A novel cancer vaccine strategy based on HLA-A*0201 matched allogeneic plasmacytoid dendritic cells.

Directory of Open Access Journals (Sweden)

Caroline Aspord

Full Text Available BACKGROUND: The development of effective cancer vaccines still remains a challenge. Despite the crucial role of plasmacytoid dendritic cells (pDCs in anti-tumor responses, their therapeutic potential has not yet been worked out. We explored the relevance of HLA-A*0201 matched allogeneic pDCs as vectors for immunotherapy. METHODS AND FINDINGS: Stimulation of PBMC from HLA-A*0201(+ donors by HLA-A*0201 matched allogeneic pDCs pulsed with tumor-derived peptides triggered high levels of antigen-specific and functional cytotoxic T cell responses (up to 98% tetramer(+ CD8 T cells. The pDC vaccine demonstrated strong anti-tumor therapeutic in vivo efficacy as shown by the inhibition of tumor growth in a humanized mouse model. It also elicited highly functional tumor-specific T cells ex-vivo from PBMC and TIL of stage I-IV melanoma patients. Responses against MelA, GP100, tyrosinase and MAGE-3 antigens reached tetramer levels up to 62%, 24%, 85% and 4.3% respectively. pDC vaccine-primed T cells specifically killed patients' own autologous melanoma tumor cells. This semi-allogeneic pDC vaccine was more effective than conventional myeloid DC-based vaccines. Furthermore, the pDC vaccine design endows it with a strong potential for clinical application in cancer treatment. CONCLUSIONS: These findings highlight HLA-A*0201 matched allogeneic pDCs as potent inducers of tumor immunity and provide a promising immunotherapeutic strategy to fight cancer.

Packaging design criteria, transfer and disposal of 102-AP mixer pump

International Nuclear Information System (INIS)

Carlstrom, R.F.

1994-01-01

A mixer pump installed in storage tank 241-AP-102 (102-AP) has failed. This pump is referred to as the 102-AP mixer pump (APMP). The APMP will be removed from 102-AP 1 and a new pump will be installed. The main purpose of the Packaging Design Criteria (PDC) is to establish criteria necessary to design and fabricate a shipping container for the transfer and storage of the APMP from 102-AP. The PDC will be used as a guide to develop a Safety Evaluation for Packaging (SEP)

HMGB1 Is Involved in IFN-α Production and TRAIL Expression by HIV-1-Exposed Plasmacytoid Dendritic Cells: Impact of the Crosstalk with NK Cells.

OpenAIRE

Héla Saïdi; Marlène Bras; Pauline Formaglio; Marie-Thérèse Melki; Bruno Charbit; Jean-Philippe Herbeuval; Marie-Lise Gougeon

2016-01-01

Plasmacytoid dendritic cells (pDCs) are innate sensors of viral infections and important mediators of antiviral innate immunity through their ability to produce large amounts of IFN-?. Moreover, Toll-like receptor 7 (TLR7) and 9 (TLR9) ligands, such as HIV and CpG respectively, turn pDCs into TRAIL-expressing killer pDCs able to lyse HIV-infected CD4+ T cells. NK cells can regulate antiviral immunity by modulating pDC functions, and pDC production of IFN-? as well as cell?cell contact is requ...

Performance of diamond and point attack coal cutter picks

Energy Technology Data Exchange (ETDEWEB)

Liu, Y. [CSIRO, Brisbane, Qld. (Australia). Division of Exploration and Mining

1996-12-31

This paper presents results of laboratory experiments and field trials of PDC (Polycrystalline Diamond Compact) and PA (Point Attack) coal cutter picks. Laboratory cutting tests included linear rock and coal cutting and turning rock cutting. The following parameters were measured to assess performance of PDC and PA cutter picks: cutting force, normal force, specific energy consumption, yield, dust generation and ignitional characteristics (temperature rise). Field trials were conducted on a longwall shearer. Performance of both types of pick interims of pick life and dust generation were assessed. 3 refs., 18 figs., 3 tabs.

Sexy gene conversions: locating gene conversions on the X-chromosome.

Science.gov (United States)

Lawson, Mark J; Zhang, Liqing

2009-08-01

Gene conversion can have a profound impact on both the short- and long-term evolution of genes and genomes. Here, we examined the gene families that are located on the X-chromosomes of human (Homo sapiens), chimpanzee (Pan troglodytes), mouse (Mus musculus) and rat (Rattus norvegicus) for evidence of gene conversion. We identified seven gene families (WD repeat protein family, Ferritin Heavy Chain family, RAS-related Protein RAB-40 family, Diphosphoinositol polyphosphate phosphohydrolase family, Transcription Elongation Factor A family, LDOC1-related family, Zinc Finger Protein ZIC, and GLI family) that show evidence of gene conversion. Through phylogenetic analyses and synteny evidence, we show that gene conversion has played an important role in the evolution of these gene families and that gene conversion has occurred independently in both primates and rodents. Comparing the results with those of two gene conversion prediction programs (GENECONV and Partimatrix), we found that both GENECONV and Partimatrix have very high false negative rates (i.e. failed to predict gene conversions), which leads to many undetected gene conversions. The combination of phylogenetic analyses with physical synteny evidence exhibits high resolution in the detection of gene conversions.

Optimal Reference Genes for Gene Expression Normalization in Trichomonas vaginalis

Science.gov (United States)

dos Santos, Odelta; de Vargas Rigo, Graziela; Frasson, Amanda Piccoli; Macedo, Alexandre José; Tasca, Tiana

2015-01-01

Trichomonas vaginalis is the etiologic agent of trichomonosis, the most common non-viral sexually transmitted disease worldwide. This infection is associated with several health consequences, including cervical and prostate cancers and HIV acquisition. Gene expression analysis has been facilitated because of available genome sequences and large-scale transcriptomes in T. vaginalis, particularly using quantitative real-time polymerase chain reaction (qRT-PCR), one of the most used methods for molecular studies. Reference genes for normalization are crucial to ensure the accuracy of this method. However, to the best of our knowledge, a systematic validation of reference genes has not been performed for T. vaginalis. In this study, the transcripts of nine candidate reference genes were quantified using qRT-PCR under different cultivation conditions, and the stability of these genes was compared using the geNorm and NormFinder algorithms. The most stable reference genes were α-tubulin, actin and DNATopII, and, conversely, the widely used T. vaginalis reference genes GAPDH and β-tubulin were less stable. The PFOR gene was used to validate the reliability of the use of these candidate reference genes. As expected, the PFOR gene was upregulated when the trophozoites were cultivated with ferrous ammonium sulfate when the DNATopII, α-tubulin and actin genes were used as normalizing gene. By contrast, the PFOR gene was downregulated when the GAPDH gene was used as an internal control, leading to misinterpretation of the data. These results provide an important starting point for reference gene selection and gene expression analysis with qRT-PCR studies of T. vaginalis. PMID:26393928

Patenting human genes: Chinese academic articles' portrayal of gene patents.

Science.gov (United States)

Du, Li

2018-04-24

The patenting of human genes has been the subject of debate for decades. While China has gradually come to play an important role in the global genomics-based testing and treatment market, little is known about Chinese scholars' perspectives on patent protection for human genes. A content analysis of academic literature was conducted to identify Chinese scholars' concerns regarding gene patents, including benefits and risks of patenting human genes, attitudes that researchers hold towards gene patenting, and any legal and policy recommendations offered for the gene patent regime in China. 57.2% of articles were written by law professors, but scholars from health sciences, liberal arts, and ethics also participated in discussions on gene patent issues. While discussions of benefits and risks were relatively balanced in the articles, 63.5% of the articles favored gene patenting in general and, of the articles (n = 41) that explored gene patents in the Chinese context, 90.2% supported patent protections for human genes in China. The patentability of human genes was discussed in 33 articles, and 75.8% of these articles reached the conclusion that human genes are patentable. Chinese scholars view the patent regime as an important legal tool to protect the interests of inventors and inventions as well as the genetic resources of China. As such, many scholars support a gene patent system in China. These attitudes towards gene patents remain unchanged following the court ruling in the Myriad case in 2013, but arguments have been raised about the scope of gene patents, in particular that the increasing numbers of gene patents may negatively impact public health in China.

Research progress in machine learning methods for gene-gene interaction detection.

Science.gov (United States)

Peng, Zhe-Ye; Tang, Zi-Jun; Xie, Min-Zhu

2018-03-20

Complex diseases are results of gene-gene and gene-environment interactions. However, the detection of high-dimensional gene-gene interactions is computationally challenging. In the last two decades, machine-learning approaches have been developed to detect gene-gene interactions with some successes. In this review, we summarize the progress in research on machine learning methods, as applied to gene-gene interaction detection. It systematically examines the principles and limitations of the current machine learning methods used in genome wide association studies (GWAS) to detect gene-gene interactions, such as neural networks (NN), random forest (RF), support vector machines (SVM) and multifactor dimensionality reduction (MDR), and provides some insights on the future research directions in the field.

Time-variant partial directed coherence in analysis of the cardiovascular system. A methodological study

International Nuclear Information System (INIS)

Milde, T; Schwab, K; Walther, M; Eiselt, M; Witte, H; Schelenz, C; Voss, A

2011-01-01

Time-variant partial directed coherence (tvPDC) is used for the first time in a multivariate analysis of heart rate variability (HRV), respiratory movements (RMs) and (systolic) arterial blood pressure. It is shown that respiration-related HRV components which also occur at other frequencies besides the RM frequency (= respiratory sinus arrhythmia, RSA) can be identified. These additional components are known to be an effect of the 'half-the-mean-heart-rate-dilemma' ('cardiac aliasing' CA). These CA components may contaminate the entire frequency range of HRV and can lead to misinterpretation of the RSA analysis. TvPDC analysis of simulated and clinical data (full-term neonates and sedated patients) reveals these contamination effects and, in addition, the respiration-related CA components can be separated from the RSA component and the Traube–Hering–Mayer wave. It can be concluded that tvPDC can be beneficially applied to avoid misinterpretations in HRV analyses as well as to quantify partial correlative interaction properties between RM and RSA

Pyruvate decarboxylase provides growing pollen tubes with a competitive advantage in petunia.

Science.gov (United States)

Gass, Nathalie; Glagotskaia, Tatiana; Mellema, Stefan; Stuurman, Jeroen; Barone, Mario; Mandel, Therese; Roessner-Tunali, Ute; Kuhlemeier, Cris

2005-08-01

Rapid pollen tube growth places unique demands on energy production and biosynthetic capacity. The aim of this work is to understand how primary metabolism meets the demands of such rapid growth. Aerobically grown pollen produce ethanol in large quantities. The ethanolic fermentation pathway consists of two committed enzymes: pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH). Because adh mutations do not affect male gametophyte function, the obvious question is why pollen synthesize an abundant enzyme if they could do just as well without. Using transposon tagging in Petunia hybrida, we isolated a null mutant in pollen-specific Pdc2. Growth of the mutant pollen tubes through the style is reduced, and the mutant allele shows reduced transmission through the male, when in competition with wild-type pollen. We propose that not ADH but rather PDC is the critical enzyme in a novel, pollen-specific pathway. This pathway serves to bypass pyruvate dehydrogenase enzymes and thereby maintain biosynthetic capacity and energy production under the unique conditions prevailing during pollen-pistil interaction.

Hybrid NiCoOx adjacent to Pd nanoparticles as a synergistic electrocatalyst for ethanol oxidation

Science.gov (United States)

Wang, Wei; Yang, Yan; Liu, Yanqin; Zhang, Zhe; Dong, Wenkui; Lei, Ziqiang

2015-01-01

To improve the electrocatalytic activity of Pd for ethanol oxidation, hybrid NiCoOx adjacent to Pd catalyst (Pd-NiCoOx/C) is successfully synthesized. Physical characterization shows NiCoOx is closely adjacent to Pd nanoparticles in Pd-NiCoOx/C catalyst, which leads to Strong Metal-Support Interactions (SMSI) between the NiCoOx and Pd nanoparticles, in favor of the electrocatalytic properties. The Pd-NiCoOx/C catalyst is estimated to own larger electrochemically active surface area than Pd/C and Pd-NiO/C catalysts. Moreover, compared to Pd/C catalyst, the onset potential of Pd-NiCoOx/C catalyst is negative 40 mV for ethanol oxidation. Noticeably, the current density of Pd-NiCoOx/C catalyst is 2.05 and 1.43 times higher contrasted to Pd/C and Pd-NiO/C catalysts accordingly. Importantly, the Pd-NiCoOx/C catalyst exhibits better stability during ethanol oxidation, which is a promising electrocatalyst for application in direct alkaline alcohol fuel cells.

Gene Circuit Analysis of the Terminal Gap Gene huckebein

Science.gov (United States)

Ashyraliyev, Maksat; Siggens, Ken; Janssens, Hilde; Blom, Joke; Akam, Michael; Jaeger, Johannes

2009-01-01

The early embryo of Drosophila melanogaster provides a powerful model system to study the role of genes in pattern formation. The gap gene network constitutes the first zygotic regulatory tier in the hierarchy of the segmentation genes involved in specifying the position of body segments. Here, we use an integrative, systems-level approach to investigate the regulatory effect of the terminal gap gene huckebein (hkb) on gap gene expression. We present quantitative expression data for the Hkb protein, which enable us to include hkb in gap gene circuit models. Gap gene circuits are mathematical models of gene networks used as computational tools to extract regulatory information from spatial expression data. This is achieved by fitting the model to gap gene expression patterns, in order to obtain estimates for regulatory parameters which predict a specific network topology. We show how considering variability in the data combined with analysis of parameter determinability significantly improves the biological relevance and consistency of the approach. Our models are in agreement with earlier results, which they extend in two important respects: First, we show that Hkb is involved in the regulation of the posterior hunchback (hb) domain, but does not have any other essential function. Specifically, Hkb is required for the anterior shift in the posterior border of this domain, which is now reproduced correctly in our models. Second, gap gene circuits presented here are able to reproduce mutants of terminal gap genes, while previously published models were unable to reproduce any null mutants correctly. As a consequence, our models now capture the expression dynamics of all posterior gap genes and some variational properties of the system correctly. This is an important step towards a better, quantitative understanding of the developmental and evolutionary dynamics of the gap gene network. PMID:19876378

Gene expression

International Nuclear Information System (INIS)

Hildebrand, C.E.; Crawford, B.D.; Walters, R.A.; Enger, M.D.

1983-01-01

We prepared probes for isolating functional pieces of the metallothionein locus. The probes enabled a variety of experiments, eventually revealing two mechanisms for metallothionein gene expression, the order of the DNA coding units at the locus, and the location of the gene site in its chromosome. Once the switch regulating metallothionein synthesis was located, it could be joined by recombinant DNA methods to other, unrelated genes, then reintroduced into cells by gene-transfer techniques. The expression of these recombinant genes could then be induced by exposing the cells to Zn 2+ or Cd 2+ . We would thus take advantage of the clearly defined switching properties of the metallothionein gene to manipulate the expression of other, perhaps normally constitutive, genes. Already, despite an incomplete understanding of how the regulatory switch of the metallothionein locus operates, such experiments have been performed successfully

Genes from scratch--the evolutionary fate of de novo genes.

Science.gov (United States)

Schlötterer, Christian

2015-04-01

Although considered an extremely unlikely event, many genes emerge from previously noncoding genomic regions. This review covers the entire life cycle of such de novo genes. Two competing hypotheses about the process of de novo gene birth are discussed as well as the high death rate of de novo genes. Despite the high death rate, some de novo genes are retained and remain functional, even in distantly related species, through their integration into gene networks. Further studies combining gene expression with ribosome profiling in multiple populations across different species will be instrumental for an improved understanding of the evolutionary processes operating on de novo genes. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

Monascus ruber as cell factory for lactic acid production at low pH.

Science.gov (United States)

Weusthuis, Ruud A; Mars, Astrid E; Springer, Jan; Wolbert, Emil Jh; van der Wal, Hetty; de Vrije, Truus G; Levisson, Mark; Leprince, Audrey; Houweling-Tan, G Bwee; Pha Moers, Antoine; Hendriks, Sjon Na; Mendes, Odette; Griekspoor, Yvonne; Werten, Marc Wt; Schaap, Peter J; van der Oost, John; Eggink, Gerrit

2017-07-01

A Monascus ruber strain was isolated that was able to grow on mineral medium at high sugar concentrations and 175g/l lactic acid at pH 2.8. Its genome and transcriptomes were sequenced and annotated. Genes encoding lactate dehydrogenase (LDH) were introduced to accomplish lactic acid production and two genes encoding pyruvate decarboxylase (PDC) were knocked out to subdue ethanol formation. The strain preferred lactic acid to glucose as carbon source, which hampered glucose consumption and therefore also lactic acid production. Lactic acid consumption was stopped by knocking out 4 cytochrome-dependent LDH (CLDH) genes, and evolutionary engineering was used to increase the glucose consumption rate. Application of this strain in a fed-batch fermentation resulted in a maximum lactic acid titer of 190g/l at pH 3.8 and 129g/l at pH 2.8, respectively 1.7 and 2.2 times higher than reported in literature before. Yield and productivity were on par with the best strains described in literature for lactic acid production at low pH. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms.

Science.gov (United States)

Li, Zhen; Defoort, Jonas; Tasdighian, Setareh; Maere, Steven; Van de Peer, Yves; De Smet, Riet

2016-02-01

Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of "gene duplicability" is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes. © 2016 American Society of Plant Biologists. All rights reserved.

Advances in study of reporter gene imaging for monitoring gene therapy

International Nuclear Information System (INIS)

Mu Chuanjie; Zhou Jiwen

2003-01-01

To evaluate the efficiency of gene therapy, it is requisite to monitor localization and expression of the therapeutic gene in vivo. Monitoring expression of reporter gene using radionuclide reporter gene technique is the best method. Adenoviral vectors expressing reporter gene are constructed using gene fusion, bicistronic, double promoter or bidirectional transcriptional recombination techniques, and transferred into target cells and tissues, then injected radiolabeled reporter probes which couple to the reporter genes. The reporter genes can be imaged invasively, repeatedly, quantitatively with γ-camera, PET and SPECT. Recently, several reporter gene and reporter probe systems have been used in studies of gene therapy. The part of them has been used for clinic trials

In Vitro Fertilization Using Luteinizing Hormone-Releasing Hormone Injections Resulted in Healthy Triplets without Increased Attack Rates in a Hereditary Angioedema Case

Directory of Open Access Journals (Sweden)

Ceyda Tunakan Dalgıç

2018-01-01

Full Text Available Hereditary angioedema due to C1-inhibitor deficiency (C1-INH-HAE is a rare, autosomal dominant disorder. The management of pregnant patients with C1-INH-HAE is a challenge for the physician. Intravenous plasma-derived nanofiltered C1-INH (pdC1INH is the only recommended option throughout pregnancy, postpartum, and breastfeeding period. In order to increase pregnancy rates, physicians use fertilization therapies increasing endogen levels of estrogens. Therefore, these techniques can provoke an increase in the number and severity of edema attacks in C1-INH-HAE. Our patient is a 32-year-old female, diagnosed with C1-INH-HAE type 1 since 2004. She had been taking danazol 50–200 mg/day for 9 years. Due to her pregnancy plans in 2013, danazol was discontinued. PdC1INH was prescribed regularly for prophylactic purpose. Triplet pregnancy occurred by in vitro fertilization using luteinizing hormone-releasing hormone (LHRH injections. In our patient, LHRH injections were done four times without causing any severe attack during in vitro fertilization. Angioedema did not worsen during pregnancy and delivery due to the prophylactic use of intravenous pdC1INH in our patient. According to the attack frequency and severity, there was no difference between the three pregnancy trimesters. To our knowledge, this is the first published case of C1-INH-HAE receiving in vitro fertilization therapies without any angioedema attacks during pregnancy and delivery and eventually having healthy triplets with the prophylactic use of intravenous pdC1INH.

A Risk Prediction Model Based on Lymph-Node Metastasis in Poorly Differentiated-Type Intramucosal Gastric Cancer.

Directory of Open Access Journals (Sweden)

Jeung Hui Pyo

Full Text Available Endoscopic submucosal dissection (ESD for undifferentiated type early gastric cancer is regarded as an investigational treatment. Few studies have tried to identify the risk factors that predict lymph-node metastasis (LNM in intramucosal poorly differentiated adenocarcinomas (PDC. This study was designed to develop a risk scoring system (RSS for predicting LNM in intramucosal PDC.From January 2002 to July 2015, patients diagnosed with mucosa-confined PDC, among those who underwent curative gastrectomy with lymph node dissection were reviewed. A risk model based on independent predicting factors of LNM was developed, and its performance was internally validated using a split sample approach.Overall, LNM was observed in 5.2% (61 of 1169 patients. Four risk factors [Female sex, tumor size ≥ 3.2 cm, muscularis mucosa (M3 invasion, and lymphatic-vascular involvement] were significantly associated with LNM, which were incorporated into the RSS. The area under the receiver operating characteristic curve for predicting LNM after internal validation was 0.69 [95% confidence interval (CI, 0.59-0.79]. A total score of 2 points corresponded to the optimal RSS threshold with a discrimination of 0.75 (95% CI 0.69-0.81. The LNM rates were 1.6% for low risk (<2 points and 8.9% for high-risk (≥2 points patients, with a negative predictive value of 98.6% (95% CI 0.98-1.00.A RSS could be useful in clinical practice to determine which patients with intramucosal PDC have low risk of LNM.

Use of palm oil decanter cake as a new substrate for the production of bio-oil by vacuum pyrolysis

International Nuclear Information System (INIS)

Dewayanto, Nugroho; Isha, Ruzinah; Nordin, Mohd Ridzuan

2014-01-01

Highlights: • Vacuum pyrolysis has been employed to produce bio-oil from palm oil waste. • Effect of the pyrolysis temperature was investigated in this study. • Bio-oil properties of cellulosic and oily based material were determined. • Bio-oil from decanter cake has potential to be used as fuel. - Abstract: The present study was carried out to investigate the potential of palm oil decanter cake (PDC) for bio-oil production at various temperatures by vacuum pyrolysis. PDC was first dried in oven at 105 °C for 24 h to remove moisture and ground to particle size of 0.85–2 mm. Pyrolysis experiments were carried out at 400, 450, 500, 550 and 600 °C, with heating rate of 15 °C/min. The highest yield of bio-oil (22.12 wt%) was obtained at pyrolysis temperature of 500 °C. The chemical characterization of bio-oil was studied using 1 H NMR, FTIR, CHNS analyzer and GC–MS. The other properties like pH, calorific value and thermal volatilization were also determined. The pH value recorded to be 6.38, which is found to be higher as compared to other bio-oils. The calorific value of PDC bio-oil found to be 36.79 MJ/kg, which is slightly lower than that of conventional liquid fuel such as gasoline and diesel fuel. However, the bio-oil obtained from PDC has better fuel characteristics than that of bio-oil derived from palm kernel shell (PKS)

Down-Regulation of Gene Expression by RNA-Induced Gene Silencing

Science.gov (United States)

Travella, Silvia; Keller, Beat

Down-regulation of endogenous genes via post-transcriptional gene silencing (PTGS) is a key to the characterization of gene function in plants. Many RNA-based silencing mechanisms such as post-transcriptional gene silencing, co-suppression, quelling, and RNA interference (RNAi) have been discovered among species of different kingdoms (plants, fungi, and animals). One of the most interesting discoveries was RNAi, a sequence-specific gene-silencing mechanism initiated by the introduction of double-stranded RNA (dsRNA), homologous in sequence to the silenced gene, which triggers degradation of mRNA. Infection of plants with modified viruses can also induce RNA silencing and is referred to as virus-induced gene silencing (VIGS). In contrast to insertional mutagenesis, these emerging new reverse genetic approaches represent a powerful tool for exploring gene function and for manipulating gene expression experimentally in cereal species such as barley and wheat. We examined how RNAi and VIGS have been used to assess gene function in barley and wheat, including molecular mechanisms involved in the process and available methodological elements, such as vectors, inoculation procedures, and analysis of silenced phenotypes.

Therapeutic genes for anti-HIV/AIDS gene therapy.

Science.gov (United States)

Bovolenta, Chiara; Porcellini, Simona; Alberici, Luca

2013-01-01

The multiple therapeutic approaches developed so far to cope HIV-1 infection, such as anti-retroviral drugs, germicides and several attempts of therapeutic vaccination have provided significant amelioration in terms of life-quality and survival rate of AIDS patients. Nevertheless, no approach has demonstrated efficacy in eradicating this lethal, if untreated, infection. The curative power of gene therapy has been proven for the treatment of monogenic immunodeficiensies, where permanent gene modification of host cells is sufficient to correct the defect for life-time. No doubt, a similar concept is not applicable for gene therapy of infectious immunodeficiensies as AIDS, where there is not a single gene to be corrected; rather engineered cells must gain immunotherapeutic or antiviral features to grant either short- or long-term efficacy mostly by acquisition of antiviral genes or payloads. Anti-HIV/AIDS gene therapy is one of the most promising strategy, although challenging, to eradicate HIV-1 infection. In fact, genetic modification of hematopoietic stem cells with one or multiple therapeutic genes is expected to originate blood cell progenies resistant to viral infection and thereby able to prevail on infected unprotected cells. Ultimately, protected cells will re-establish a functional immune system able to control HIV-1 replication. More than hundred gene therapy clinical trials against AIDS employing different viral vectors and transgenes have been approved or are currently ongoing worldwide. This review will overview anti-HIV-1 infection gene therapy field evaluating strength and weakness of the transgenes and payloads used in the past and of those potentially exploitable in the future.

Discovering implicit entity relation with the gene-citation-gene network.

Directory of Open Access Journals (Sweden)

Min Song

Full Text Available In this paper, we apply the entitymetrics model to our constructed Gene-Citation-Gene (GCG network. Based on the premise there is a hidden, but plausible, relationship between an entity in one article and an entity in its citing article, we constructed a GCG network of gene pairs implicitly connected through citation. We compare the performance of this GCG network to a gene-gene (GG network constructed over the same corpus but which uses gene pairs explicitly connected through traditional co-occurrence. Using 331,411 MEDLINE abstracts collected from 18,323 seed articles and their references, we identify 25 gene pairs. A comparison of these pairs with interactions found in BioGRID reveal that 96% of the gene pairs in the GCG network have known interactions. We measure network performance using degree, weighted degree, closeness, betweenness centrality and PageRank. Combining all measures, we find the GCG network has more gene pairs, but a lower matching rate than the GG network. However, combining top ranked genes in both networks produces a matching rate of 35.53%. By visualizing both the GG and GCG networks, we find that cancer is the most dominant disease associated with the genes in both networks. Overall, the study indicates that the GCG network can be useful for detecting gene interaction in an implicit manner.

Reduced rates of gene loss, gene silencing, and gene mutation in Dnmt1-deficient embryonic stem cells

NARCIS (Netherlands)

Chan, M.F.; van Amerongen, R.; Nijjar, T.; Cuppen, E.; Jones, P.A.; Laird, P.W.

2001-01-01

Tumor suppressor gene inactivation is a crucial event in oncogenesis. Gene inactivation mechanisms include events resulting in loss of heterozygosity (LOH), gene mutation, and transcriptional silencing. The contribution of each of these different pathways varies among tumor suppressor genes and by

A hybrid approach of gene sets and single genes for the prediction of survival risks with gene expression data.

Science.gov (United States)

Seok, Junhee; Davis, Ronald W; Xiao, Wenzhong

2015-01-01

Accumulated biological knowledge is often encoded as gene sets, collections of genes associated with similar biological functions or pathways. The use of gene sets in the analyses of high-throughput gene expression data has been intensively studied and applied in clinical research. However, the main interest remains in finding modules of biological knowledge, or corresponding gene sets, significantly associated with disease conditions. Risk prediction from censored survival times using gene sets hasn't been well studied. In this work, we propose a hybrid method that uses both single gene and gene set information together to predict patient survival risks from gene expression profiles. In the proposed method, gene sets provide context-level information that is poorly reflected by single genes. Complementarily, single genes help to supplement incomplete information of gene sets due to our imperfect biomedical knowledge. Through the tests over multiple data sets of cancer and trauma injury, the proposed method showed robust and improved performance compared with the conventional approaches with only single genes or gene sets solely. Additionally, we examined the prediction result in the trauma injury data, and showed that the modules of biological knowledge used in the prediction by the proposed method were highly interpretable in biology. A wide range of survival prediction problems in clinical genomics is expected to benefit from the use of biological knowledge.

Field-trip guide for exploring pyroclastic density current deposits from the May 18, 1980, eruption of Mount St. Helens, Washington

Science.gov (United States)

Brand, Brittany D.; Pollock, Nicholas; Sarocchi, Damiano; Dufek, Josef; Clynne, Michael A.

2017-07-05

Pyroclastic density currents (PDCs) are one of the most dangerous phenomena associated with explosive volcanism. To help constrain damage potential, a combination of field studies, laboratory experiments, and numerical modeling are used to establish conditions that influence PDC dynamics and depositional processes, including runout distance. The objective of this field trip is to explore field relations that may constrain PDCs at the time of emplacement.The PDC deposits from the May 18, 1980, eruption of Mount St. Helens are well exposed along the steep flanks (10–30° slopes) and across the pumice plain (5–12° slopes) as far as 8 km north of the volcano. The pumice plain deposits represent deposition from a series of concentrated PDCs and are primarily thick (3–12 m), massive, and poorly sorted. In contrast, the steep east-flank deposits are stratified to cross-stratified, suggesting deposition from PDCs where turbulence strongly influenced transport and depositional processes.The PDCs that descended the west flank were largely nondepositional; they maintained a higher flow energy and carrying capacity than PDCs funneled through the main breach, as evidenced by the higher concentration of large blocks in their deposits. The PDC from the west flank collided with PDCs funneled through the breach at various points along the pumice plain. Evidence for flow collision will be explored and debated throughout the field trip.Evidence for substrate erosion and entrainment is found (1) along the steep eastern flank of the volcano, which has a higher degree of rough, irregular topography relative to the west flanks where PDCs were likely nonerosive, (2) where PDCs encountered debris-avalanche hummocks across the pumice plain, and (3) where PDCs eroded and entrained material deposited by PDCs produced during earlier phases of the eruption. Two features interpreted as large-scale (tens of meters wide) levees and a large (~200 m wide) channel scour-and-fill feature

Time-Course Gene Set Analysis for Longitudinal Gene Expression Data.

Directory of Open Access Journals (Sweden)

Boris P Hejblum

2015-06-01

Full Text Available Gene set analysis methods, which consider predefined groups of genes in the analysis of genomic data, have been successfully applied for analyzing gene expression data in cross-sectional studies. The time-course gene set analysis (TcGSA introduced here is an extension of gene set analysis to longitudinal data. The proposed method relies on random effects modeling with maximum likelihood estimates. It allows to use all available repeated measurements while dealing with unbalanced data due to missing at random (MAR measurements. TcGSA is a hypothesis driven method that identifies a priori defined gene sets with significant expression variations over time, taking into account the potential heterogeneity of expression within gene sets. When biological conditions are compared, the method indicates if the time patterns of gene sets significantly differ according to these conditions. The interest of the method is illustrated by its application to two real life datasets: an HIV therapeutic vaccine trial (DALIA-1 trial, and data from a recent study on influenza and pneumococcal vaccines. In the DALIA-1 trial TcGSA revealed a significant change in gene expression over time within 69 gene sets during vaccination, while a standard univariate individual gene analysis corrected for multiple testing as well as a standard a Gene Set Enrichment Analysis (GSEA for time series both failed to detect any significant pattern change over time. When applied to the second illustrative data set, TcGSA allowed the identification of 4 gene sets finally found to be linked with the influenza vaccine too although they were found to be associated to the pneumococcal vaccine only in previous analyses. In our simulation study TcGSA exhibits good statistical properties, and an increased power compared to other approaches for analyzing time-course expression patterns of gene sets. The method is made available for the community through an R package.

Norrie disease gene is distinct from the monoamine oxidase genes

OpenAIRE

Sims, Katherine B.; Ozelius, Laurie; Corey, Timothy; Rinehart, William B.; Liberfarb, Ruth; Haines, Jonathan; Chen, Wei Jane; Norio, Reijo; Sankila, Eeva; de la Chapelle, Albert; Murphy, Dennis L.; Gusella, James; Breakefield, Xandra O.

1989-01-01

The genes for MAO-A and MAO-B appear to be very close to the Norrie disease gene, on the basis of loss and /or disruption of the MAO genes and activities in atypical Norrie disease patients deleted for the DXS7 locus; linkage among the MAO genes, the Norrie disease gene, and the DXS7 locus; and mapping of all these loci to the chromosomal region Xp11. The present study provides evidence that the MAO genes are not disrupted in “classic” Norrie disease patients. Genomic DNA from these “nondelet...

A genetic ensemble approach for gene-gene interaction identification

Directory of Open Access Journals (Sweden)

Ho Joshua WK

2010-10-01

Full Text Available Abstract Background It has now become clear that gene-gene interactions and gene-environment interactions are ubiquitous and fundamental mechanisms for the development of complex diseases. Though a considerable effort has been put into developing statistical models and algorithmic strategies for identifying such interactions, the accurate identification of those genetic interactions has been proven to be very challenging. Methods In this paper, we propose a new approach for identifying such gene-gene and gene-environment interactions underlying complex diseases. This is a hybrid algorithm and it combines genetic algorithm (GA and an ensemble of classifiers (called genetic ensemble. Using this approach, the original problem of SNP interaction identification is converted into a data mining problem of combinatorial feature selection. By collecting various single nucleotide polymorphisms (SNP subsets as well as environmental factors generated in multiple GA runs, patterns of gene-gene and gene-environment interactions can be extracted using a simple combinatorial ranking method. Also considered in this study is the idea of combining identification results obtained from multiple algorithms. A novel formula based on pairwise double fault is designed to quantify the degree of complementarity. Conclusions Our simulation study demonstrates that the proposed genetic ensemble algorithm has comparable identification power to Multifactor Dimensionality Reduction (MDR and is slightly better than Polymorphism Interaction Analysis (PIA, which are the two most popular methods for gene-gene interaction identification. More importantly, the identification results generated by using our genetic ensemble algorithm are highly complementary to those obtained by PIA and MDR. Experimental results from our simulation studies and real world data application also confirm the effectiveness of the proposed genetic ensemble algorithm, as well as the potential benefits of

The Mycoplasma hominis vaa gene displays a mosaic gene structure

DEFF Research Database (Denmark)

Boesen, Thomas; Emmersen, Jeppe M. G.; Jensen, Lise T.

1998-01-01

Mycoplasma hominis contains a variable adherence-associated (vaa) gene. To classify variants of the vaa genes, we examined 42 M. hominis isolated by PCR, DNA sequencing and immunoblotting. This uncovered the existence of five gene categories. Comparison of the gene types revealed a modular...

Identification of Hematopoietic Stem Cell Engraftment Genes in Gene Therapy Studies.

Science.gov (United States)

Powers, John M; Trobridge, Grant D

2013-09-01

Hematopoietic stem cell (HSC) therapy using replication-incompetent retroviral vectors is a promising approach to provide life-long correction for genetic defects. HSC gene therapy clinical studies have resulted in functional cures for several diseases, but in some studies clonal expansion or leukemia has occurred. This is due to the dyregulation of endogenous host gene expression from vector provirus insertional mutagenesis. Insertional mutagenesis screens using replicating retroviruses have been used extensively to identify genes that influence oncogenesis. However, retroviral mutagenesis screens can also be used to determine the role of genes in biological processes such as stem cell engraftment. The aim of this review is to describe the potential for vector insertion site data from gene therapy studies to provide novel insights into mechanisms of HSC engraftment. In HSC gene therapy studies dysregulation of host genes by replication-incompetent vector proviruses may lead to enrichment of repopulating clones with vector integrants near genes that influence engraftment. Thus, data from HSC gene therapy studies can be used to identify novel candidate engraftment genes. As HSC gene therapy use continues to expand, the vector insertion site data collected will be of great interest to help identify novel engraftment genes and may ultimately lead to new therapies to improve engraftment.

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms[OPEN

Science.gov (United States)

Li, Zhen; Van de Peer, Yves; De Smet, Riet

2016-01-01

Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of “gene duplicability” is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes. PMID:26744215

Effect of the absolute statistic on gene-sampling gene-set analysis methods.

Science.gov (United States)

Nam, Dougu

2017-06-01

Gene-set enrichment analysis and its modified versions have commonly been used for identifying altered functions or pathways in disease from microarray data. In particular, the simple gene-sampling gene-set analysis methods have been heavily used for datasets with only a few sample replicates. The biggest problem with this approach is the highly inflated false-positive rate. In this paper, the effect of absolute gene statistic on gene-sampling gene-set analysis methods is systematically investigated. Thus far, the absolute gene statistic has merely been regarded as a supplementary method for capturing the bidirectional changes in each gene set. Here, it is shown that incorporating the absolute gene statistic in gene-sampling gene-set analysis substantially reduces the false-positive rate and improves the overall discriminatory ability. Its effect was investigated by power, false-positive rate, and receiver operating curve for a number of simulated and real datasets. The performances of gene-set analysis methods in one-tailed (genome-wide association study) and two-tailed (gene expression data) tests were also compared and discussed.

Human Gene Therapy: Genes without Frontiers?

Science.gov (United States)

Simon, Eric J.

2002-01-01

Describes the latest advancements and setbacks in human gene therapy to provide reference material for biology teachers to use in their science classes. Focuses on basic concepts such as recombinant DNA technology, and provides examples of human gene therapy such as severe combined immunodeficiency syndrome, familial hypercholesterolemia, and…

Gene function prediction based on Gene Ontology Hierarchy Preserving Hashing.

Science.gov (United States)

Zhao, Yingwen; Fu, Guangyuan; Wang, Jun; Guo, Maozu; Yu, Guoxian

2018-02-23

Gene Ontology (GO) uses structured vocabularies (or terms) to describe the molecular functions, biological roles, and cellular locations of gene products in a hierarchical ontology. GO annotations associate genes with GO terms and indicate the given gene products carrying out the biological functions described by the relevant terms. However, predicting correct GO annotations for genes from a massive set of GO terms as defined by GO is a difficult challenge. To combat with this challenge, we introduce a Gene Ontology Hierarchy Preserving Hashing (HPHash) based semantic method for gene function prediction. HPHash firstly measures the taxonomic similarity between GO terms. It then uses a hierarchy preserving hashing technique to keep the hierarchical order between GO terms, and to optimize a series of hashing functions to encode massive GO terms via compact binary codes. After that, HPHash utilizes these hashing functions to project the gene-term association matrix into a low-dimensional one and performs semantic similarity based gene function prediction in the low-dimensional space. Experimental results on three model species (Homo sapiens, Mus musculus and Rattus norvegicus) for interspecies gene function prediction show that HPHash performs better than other related approaches and it is robust to the number of hash functions. In addition, we also take HPHash as a plugin for BLAST based gene function prediction. From the experimental results, HPHash again significantly improves the prediction performance. The codes of HPHash are available at: http://mlda.swu.edu.cn/codes.php?name=HPHash. Copyright © 2018 Elsevier Inc. All rights reserved.

A Nonlinear Model for Gene-Based Gene-Environment Interaction

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Jian Sa

2016-06-01

Full Text Available A vast amount of literature has confirmed the role of gene-environment (G×E interaction in the etiology of complex human diseases. Traditional methods are predominantly focused on the analysis of interaction between a single nucleotide polymorphism (SNP and an environmental variable. Given that genes are the functional units, it is crucial to understand how gene effects (rather than single SNP effects are influenced by an environmental variable to affect disease risk. Motivated by the increasing awareness of the power of gene-based association analysis over single variant based approach, in this work, we proposed a sparse principle component regression (sPCR model to understand the gene-based G×E interaction effect on complex disease. We first extracted the sparse principal components for SNPs in a gene, then the effect of each principal component was modeled by a varying-coefficient (VC model. The model can jointly model variants in a gene in which their effects are nonlinearly influenced by an environmental variable. In addition, the varying-coefficient sPCR (VC-sPCR model has nice interpretation property since the sparsity on the principal component loadings can tell the relative importance of the corresponding SNPs in each component. We applied our method to a human birth weight dataset in Thai population. We analyzed 12,005 genes across 22 chromosomes and found one significant interaction effect using the Bonferroni correction method and one suggestive interaction. The model performance was further evaluated through simulation studies. Our model provides a system approach to evaluate gene-based G×E interaction.

Vertebrate gene predictions and the problem of large genes

DEFF Research Database (Denmark)

Wang, Jun; Li, ShengTing; Zhang, Yong

2003-01-01

To find unknown protein-coding genes, annotation pipelines use a combination of ab initio gene prediction and similarity to experimentally confirmed genes or proteins. Here, we show that although the ab initio predictions have an intrinsically high false-positive rate, they also have a consistent...

Oil extracted from spent coffee grounds for bio-hydrotreated diesel production

International Nuclear Information System (INIS)

Phimsen, Songphon; Kiatkittipong, Worapon; Yamada, Hiroshi; Tagawa, Tomohiko; Kiatkittipong, Kunlanan; Laosiripojana, Navadol; Assabumrungrat, Suttichai

2016-01-01

Highlights: • The spent coffee oil with high FFAs was hydrotreated to liquid biofuel. • Pd/C gave higher olefins while NiMo/γ-Al_2O_3 gave higher isoparaffins liquid products. • The diesel fuel fraction can have a cetane number as high as 80. • The physiochemical properties of diesel fraction comply with commercial standard. - Abstract: Oil extracted from spent coffee grounds is utilized as a renewable source for bio-hydrotreated fuel production. In the present work, oil yield up to 13% can be obtained by Soxhlet extraction with hexane as a solvent. As the extracted oil contained high content of free fatty acids (6.14%), therefore one step alkali-catalyzed for ester based biodiesel production is impractical. Hydrotreating of extracted oil was performed over two catalysts i.e. NiMo/γ-Al_2O_3 and Pd/C with different operating parameters i.e. reaction time, operating temperature, and H_2/oil. It was found that the reaction time of 2 h and the reaction temperature of 400 °C are favorable operating conditions. The liquid products mostly consisted of n-pentadecane and n-heptadecane, which contain one carbon atom shorter than the corresponding fatty acid (C_n_−_1) i.e. palmitic and stearic acid, respectively. Unfavorable cracking of diesel product is pronounced at high temperature and prolonged reaction time. In addition, although increased H_2/oil promoted overall reaction and hydrodeoxygenation activity (C_n_−_1/C_n decreased) for both catalysts, hydrocracking is enhanced over Pd/C, leading to significant increase in gasoline yield. Moreover, Pd/C gave higher olefin content in liquid product (22.3 wt%) than NiMo/γ-Al_2O_3 (4.8 wt%). However, NiMo/γ-Al_2O_3 shows higher isomerization activity. The amount of isoparaffins catalyzed by NiMo/γ-Al_2O_3 and Pd/C were 10.8 and 1.7 wt%, respectively. Physiochemical analysis of the diesel fraction exhibit satisfactory properties. The density and kinematic viscosity were consistent with the specification of

The Person Centered approach in Gerontology: New validity evidence of the Staff Assessment Person-directed Care Questionnaire

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Teresa Martínez

2016-01-01

Full Text Available Antecedentes/Objetivos La atención centrada en la persona es un enfoque innovador que busca mejorar la calidad asistencial de los servicios para personas mayores que precisan cuidados. Ante el creciente interés hacia este enfoque es necesario contar con instrumentos de medida que permitan evaluar en qué grado los servicios gerontológicos llevan a cabo una atención centrada en la persona. El objetivo de este trabajo es la adaptación y validación del Staff Assessment Person-directed Care (PDC en población espanola. ˜ Método Se llevó a cabo la traducción y adaptación del PDC al espanol ˜ y se aplicó a una muestra de 1.339 profesionales de atención directa, pertenecientes a 56 residencias para personas mayores. El estudio de las propiedades psicométricas se realizó desde el marco de la Teoría Clásica de los Tests y los modelos de Teoría de Respuesta a los Ítems. Resultados El coeficiente alfa de Cronbach fue de 0,97 y el coeficiente de fiabilidad test-retest de 0,89. La Función de Información indica que la prueba mide de forma precisa para un amplio rango de puntuaciones (valores entre -2 y + 2. La estructura factorial del PDC es esencialmente unidimensional, confirmándose la existencia de dos grandes dimensiones que se articulan a su vez en ocho factores muy correlacionados. En cuanto a la validez predictiva destacan las correlaciones del PDC con el The Person-centered Care Assessment Tool (r= 0,68, con el clima organizacional (r = 0,67 y con los factores del burnout, agotamiento emocional (r= -0,41 y realización personal (r = 0,46. Conclusiones La versión espanola ˜ del PDC confirma los resultados encontrados en otras poblaciones, presentando unas excelentes propiedades psicométricas para su uso en la evaluación de residencias de personas mayores, tanto con fines profesionales como de investigación.

Synthesis and electrochemical characterization of highly tolerant Pd electrocatalysts as cathodes in direct ethylene glycol fuel cells (DEGFC)

Energy Technology Data Exchange (ETDEWEB)

Rodriguez Varela, F.J.; Fraire Luna, S. [Cinvestav, Unidad Saltillo, Ramos Arizpe, Coahuila (Mexico)] e-mail: javier.varela@cinvestav.edu.mx; Savadogo, O. [Laboratoire d' Electrochimie et de Materiaux Energetiques, Ecole Polytechnique de Montreal, Montreal, QC (Canada)

2009-09-15

Highly selective Pd electrocatalysts were synthesized by the formic acid method and evaluated as cathodes for DEGFC applications. In rotating disc measurements in acid medium, the Pd/C cathode showed important catalytic activity for the Oxygen Reduction Reaction (ORR). In the presence of ethylene glycol (EG, C{sub 2}H{sub 6}O{sub 2}), Pd/C exhibited an excellent electrochemical behavior and full tolerance to the organic molecule. No current density peaks associated to the EG oxidation reaction emerged and the shift in onset potential for the ORR (Eonset) toward more negative potentials was negligible on this cathode. Moreover, the evaluation of Pd/C in a DEGFC operating at 80 degrees Celsius demonstrated its high performance as cathode. As a comparison, commercial Pt/C was tested under the same conditions showing a limited selectivity for the ORR. The detrimental effect of EG on the Pt electrocatalysts resulted in high intensity current density peaks due to the oxidation of EG and a significant shift in Eonset. Given these results, it is expected that highly efficient Pd-based cathodes can find application in DEGFCs. [Spanish] Se sintetizaron electrocatalizadores altamente selectivos mediante el metodo de acido formico y se evaluaron como catodos en aplicaciones de CCGED. En mediciones de disco rotatorio en medio acido, el catodo Pd/C mostro importante actividad catalitica en la reaccion de reduccion de oxigeno (RRO). En la presencia de glicol de etileno (GE, C{sub 2}H{sub 6}O{sub 2}), Pd/C exhibio un excelente comportamiento electromecanico y tolerancia total a la molecula organica. No surgieron picos de densidad de corriente asociados con la reaccion de oxidacion de GE y el corrimiento en el potencial de inicio para la RRO (Einicio) hacia potenciales mas negativos fue despreciable en este catodo. Como comparacion, se probo un Pt/C bajo las mismas condiciones y se observo una selectividad limitada para el RRO. El efecto perjudicial de GE en el electrocatalizador

In vitro culture and characterization of human umbilical cord blood-derived plasmacytoid dendritic cell subsets

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PENG Jianping

2015-11-01

Full Text Available ObjectiveTo establish a method for in vitro culture of plasmacytoid dendritic cell (pDC. MethodsUmbilical cord blood (40 ml was collected from healthy parturients in the First Affiliated Hospital of Hunan University of Chinese Medicine, and cord blood mononuclear cell (CBMC were isolated. The CBMC were cultured for 7 days with RPMI 1640 complete medium containing rh Flt3-ligand (Flt3-L (100 ng/ml and rh interleukin (IL-3 (10 ng/ml, and the medium was half changed every 2 days. On the eighth day, CpG ODN (2 μg/ml was added to the cells, and the attached cells and supernatant were collected 24 h later for flow cytometry and interferon (IFNα measurement, respectively. On days 1, 3, 5, 7, and 8 of cell culture, the morphological changes of pDC were observed. Results After 2 h of culture, the CBMC showed circular, flat morphology. Twenty-four hours later, the cells began to adhere to the wall, with extended cytoplasm and increased volumes, and they became round and translucent, with scattered small colonies. On days 3-4 of culture, the cell volume continued increasing; most cells were round, and some had small protrusions; few cells were spindle-, tadpole-, star- or irregularly shaped; the number and volumes of colonies increased substantially. On days 5-8 of culture, the number of colonies and the number of cells in colonies gradually decreased, and suspended cells that were round or had small protrusions gradually increased in the medium. The cells expressing CD123, BDCA-2, and BDCA-4, which were considered pDC, were detected by flow cytometry. Flow cytometry revealed that the proportion of pDC in CBMC increased during the culture: increasing from 1.08% at the beginning of culture to 5.32% on day 4, and finally reaching a peak of 19.8% on day 8. On day 8, the level of IFNα in pDC culture supernatant was(11 302.61±1745.31 pg/ml. ConclusionpDC can be successfully induced in vitro by rh Flt3-L combined with IL-3 from human umbilical CBMC.

Functional changes of dendritic cells in hypersensivity reactions to amoxicillin

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C.M.F. Lima

2010-10-01

Full Text Available A better understanding of dendritic cell (DC involvement in responses to haptenic drugs is needed, because it represents a possible approach to the development of an in vitro test, which could identify patients prone to drug allergies. There are two main DC subsets: plasmacytoid DC (pDC and myeloid DC (mDC. β-lactams form hapten-carrier conjugates and may provide a suitable model to study DC behavior in drug allergy reactions. It has been demonstrated that drugs interact differently with DC in drug allergic and non-allergic patients, but there are no studies regarding these subsets. Our aim was to assess the functional changes of mDC and pDC harvested from an amoxicillin-hypersensitive 32-year-old woman who experienced a severe maculopapular exanthema as reflected in interleukin-6 (IL-6 production after stimulation with this drug and penicillin. We also aim to demonstrate, for the first time, the feasibility of this method for dendritic cell isolation followed by in vitro stimulation for studies of drug allergy physiopathology. DC were harvested using a double Percoll density gradient, which generates a basophil-depleted cell (BDC suspension. Further, pDC were isolated by blood DC antigen 4-positive magnetic selection and gravity filtration through magnetized columns. After stimulation with amoxicillin, penicillin and positive and negative controls, IL-6 production was measured by ELISA. A positive dose-response curve for IL-6 after stimulation with amoxicillin and penicillin was observed for pDC, but not for mDC or BDC suspension. These preliminary results demonstrate the feasibility of this methodology to expand the knowledge of the effect of dendritic cell activation by drug allergens.

O acesso a informacao sobre higiene bucal e as perdas dentarias por carie entre adultos

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Desiree Sant'Ana Haikal

2014-01-01

Full Text Available Objetivou-se testar a associação entre perdas dentárias por cárie (PDC e variáveis relativas ao acesso a informações em saúde bucal. Foram analisados dados de 780 adultos (35-44 anos participantes de um estudo epidemiológico. A variável dependente foi o total de PDC e as independentes foram reunidas em blocos de variáveis: demográficas e socioeconômicas; utilização dos serviços odontológicos; acesso a informações em saúde bucal (informações sobre como evitar problemas bucais, sobre higiene bucal e sobre dieta e; comportamentais. Conduziu-se regressão linear múltipla hierarquizada. O número médio de PDC foi de 7,03 (EP= 0,31 e 83% dos adultos haviam perdido algum dente por cárie. As PDC foram maiores entre os mais velhos, os com menor escolaridade, as mulheres, os que raramente ou nunca receberam informações sobre higiene bucal, os que escovavam os dentes uma vez ou menos ao dia e entre os que não usavam fio dental. Adultos que raramente/nunca receberam informações dos serviços odontológicos sobre higiene bucal perderam 2,15 dentes a mais por cárie que aqueles que sempre/frequentemente receberam tais informações (p = 0,000. Assim, sugere-se que a garantia do acesso à informação deva ser incentivada a fim de contribuir com maior equidade em saúde bucal.

Dendritic cells in uninfected infants born to hepatitis B virus-positive mothers.

Science.gov (United States)

Koumbi, Lemonica J; Papadopoulos, Nikolaos G; Anastassiadou, Vassiliki; Machaira, Maria; Kafetzis, Dimitris A; Papaevangelou, Vassiliki

2010-07-01

Plasmacytoid dendritic cells (pDCs) play a central role in antiviral immunity, detecting viruses via Toll-like receptors (TLR) and producing in response vast amounts of type I interferons (IFNs). Hepatitis B virus (HBV) causes chronic infection after vertical transmission. This study investigated whether an HBV-infected maternal environment might influence DC numbers and pDC function in uninfected infants. Blood was collected from inactive HBsAg carrier and control mothers and their infants at birth and 1 and 6 months of age. HBV DNA was measured in maternal and neonatal perinatal sera using real-time PCR. The circulating frequencies of myeloid DCs (mDCs) and pDCs were determined in the babies by flow cytometry. Peripheral blood mononuclear cells (PBMCs) and cord blood pDCs were stimulated with resiquimod, and alpha interferon (IFN-alpha) production and the pDC phenotype were assessed. The effect of the common-cold virus, rhinovirus (RV), on resiquimod stimulation was also determined. HBV DNA was detected in 62.3% of the mothers and 41% of their infants. DC numbers and pDC functions were similar between subjects and controls and were not correlated with maternal or neonatal viremia. RV infection did not induce pDC maturation until the age of 6 months, and it reduced TLR7-dependent resiquimod-induced IFN-alpha production similarly in both groups. Although the DC system is immature at birth, DCs of uninfected neonates of HBV-positive mothers are competent to initiate and maintain T-cell responses. RV is a weak inducer of IFN-alpha production until the age of 6 months and inhibits IFN-alpha responses triggered by the TLR7 pathway.

A Novel Methodology to Validate the Accuracy of Extraoral Dental Scanners and Digital Articulation Systems.

Science.gov (United States)

Ellakwa, A; Elnajar, S; Littlefair, D; Sara, G

2018-05-03

The aim of the current study is to develop a novel method to investigate the accuracy of 3D scanners and digital articulation systems. An upper and a lower poured stone model were created by taking impression of fully dentate male (fifty years old) participant. Titanium spheres were added to the models to allow for an easily recognisable geometric shape for measurement after scanning and digital articulation. Measurements were obtained using a Coordinate Measuring Machine to record volumetric error, articulation error and clinical effect error. Three scanners were compared, including the Imetric 3D iScan d104i, Shining 3D AutoScan-DS100 and 3Shape D800, as well as their respective digital articulation software packages. Stoneglass Industries PDC digital articulation system was also applied to the Imetric scans for comparison with the CMM measurements. All the scans displayed low volumetric error (p⟩0.05), indicating that the scanners themselves had a minor contribution to the articulation and clinical effect errors. The PDC digital articulation system was found to deliver the lowest average errors, with good repeatability of results. The new measuring technique in the current study was able to assess the scanning and articulation accuracy of the four systems investigated. The PDC digital articulation system using Imetric scans was recommended as it displayed the lowest articulation error and clinical effect error with good repeatability. The low errors from the PDC system may have been due to its use of a 3D axis for alignment rather than the use of a best fit. Copyright© 2018 Dennis Barber Ltd.

Reranking candidate gene models with cross-species comparison for improved gene prediction

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Pereira Fernando CN

2008-10-01

Full Text Available Abstract Background Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc. Competing models with similar state-based scores may be distinguishable with additional information. In particular, functional and comparative genomics datasets may help to select among competing models of comparable probability by exploiting features likely to be associated with the correct gene models, such as conserved exon/intron structure or protein sequence features. Results We have investigated the utility of a simple post-processing step for selecting among a set of alternative gene models, using global scoring rules to rerank competing models for more accurate prediction. For each gene locus, we first generate the K best candidate gene models using the gene finder Evigan, and then rerank these models using comparisons with putative orthologous genes from closely-related species. Candidate gene models with lower scores in the original gene finder may be selected if they exhibit strong similarity to probable orthologs in coding sequence, splice site location, or signal peptide occurrence. Experiments on Drosophila melanogaster demonstrate that reranking based on cross-species comparison outperforms the best gene models identified by Evigan alone, and also outperforms the comparative gene finders GeneWise and Augustus+. Conclusion Reranking gene models with cross-species comparison improves gene prediction accuracy. This straightforward method can be readily adapted to incorporate additional lines of evidence, as it requires only a ranked source of candidate gene models.

Evolution of homeobox genes.

Science.gov (United States)

Holland, Peter W H

2013-01-01

Many homeobox genes encode transcription factors with regulatory roles in animal and plant development. Homeobox genes are found in almost all eukaryotes, and have diversified into 11 gene classes and over 100 gene families in animal evolution, and 10 to 14 gene classes in plants. The largest group in animals is the ANTP class which includes the well-known Hox genes, plus other genes implicated in development including ParaHox (Cdx, Xlox, Gsx), Evx, Dlx, En, NK4, NK3, Msx, and Nanog. Genomic data suggest that the ANTP class diversified by extensive tandem duplication to generate a large array of genes, including an NK gene cluster and a hypothetical ProtoHox gene cluster that duplicated to generate Hox and ParaHox genes. Expression and functional data suggest that NK, Hox, and ParaHox gene clusters acquired distinct roles in patterning the mesoderm, nervous system, and gut. The PRD class is also diverse and includes Pax2/5/8, Pax3/7, Pax4/6, Gsc, Hesx, Otx, Otp, and Pitx genes. PRD genes are not generally arranged in ancient genomic clusters, although the Dux, Obox, and Rhox gene clusters arose in mammalian evolution as did several non-clustered PRD genes. Tandem duplication and genome duplication expanded the number of homeobox genes, possibly contributing to the evolution of developmental complexity, but homeobox gene loss must not be ignored. Evolutionary changes to homeobox gene expression have also been documented, including Hox gene expression patterns shifting in concert with segmental diversification in vertebrates and crustaceans, and deletion of a Pitx1 gene enhancer in pelvic-reduced sticklebacks. WIREs Dev Biol 2013, 2:31-45. doi: 10.1002/wdev.78 For further resources related to this article, please visit the WIREs website. The author declares that he has no conflicts of interest. Copyright © 2012 Wiley Periodicals, Inc.

Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes

Science.gov (United States)

2010-01-01

Background Horizontal gene transfer (HGT) is relatively common in plant mitochondrial genomes but the mechanisms, extent and consequences of transfer remain largely unknown. Previous results indicate that parasitic plants are often involved as either transfer donors or recipients, suggesting that direct contact between parasite and host facilitates genetic transfer among plants. Results In order to uncover the mechanistic details of plant-to-plant HGT, the extent and evolutionary fate of transfer was investigated between two groups: the parasitic genus Cuscuta and a small clade of Plantago species. A broad polymerase chain reaction (PCR) survey of mitochondrial genes revealed that at least three genes (atp1, atp6 and matR) were recently transferred from Cuscuta to Plantago. Quantitative PCR assays show that these three genes have a mitochondrial location in the one species line of Plantago examined. Patterns of sequence evolution suggest that these foreign genes degraded into pseudogenes shortly after transfer and reverse transcription (RT)-PCR analyses demonstrate that none are detectably transcribed. Three cases of gene conversion were detected between native and foreign copies of the atp1 gene. The identical phylogenetic distribution of the three foreign genes within Plantago and the retention of cytidines at ancestral positions of RNA editing indicate that these genes were probably acquired via a single, DNA-mediated transfer event. However, samplings of multiple individuals from two of the three species in the recipient Plantago clade revealed complex and perplexing phylogenetic discrepancies and patterns of sequence divergence for all three of the foreign genes. Conclusions This study reports the best evidence to date that multiple mitochondrial genes can be transferred via a single HGT event and that transfer occurred via a strictly DNA-level intermediate. The discovery of gene conversion between co-resident foreign and native mitochondrial copies suggests

Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes

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Hao Weilong

2010-12-01

Full Text Available Abstract Background Horizontal gene transfer (HGT is relatively common in plant mitochondrial genomes but the mechanisms, extent and consequences of transfer remain largely unknown. Previous results indicate that parasitic plants are often involved as either transfer donors or recipients, suggesting that direct contact between parasite and host facilitates genetic transfer among plants. Results In order to uncover the mechanistic details of plant-to-plant HGT, the extent and evolutionary fate of transfer was investigated between two groups: the parasitic genus Cuscuta and a small clade of Plantago species. A broad polymerase chain reaction (PCR survey of mitochondrial genes revealed that at least three genes (atp1, atp6 and matR were recently transferred from Cuscuta to Plantago. Quantitative PCR assays show that these three genes have a mitochondrial location in the one species line of Plantago examined. Patterns of sequence evolution suggest that these foreign genes degraded into pseudogenes shortly after transfer and reverse transcription (RT-PCR analyses demonstrate that none are detectably transcribed. Three cases of gene conversion were detected between native and foreign copies of the atp1 gene. The identical phylogenetic distribution of the three foreign genes within Plantago and the retention of cytidines at ancestral positions of RNA editing indicate that these genes were probably acquired via a single, DNA-mediated transfer event. However, samplings of multiple individuals from two of the three species in the recipient Plantago clade revealed complex and perplexing phylogenetic discrepancies and patterns of sequence divergence for all three of the foreign genes. Conclusions This study reports the best evidence to date that multiple mitochondrial genes can be transferred via a single HGT event and that transfer occurred via a strictly DNA-level intermediate. The discovery of gene conversion between co-resident foreign and native

First-principles study of the Pd–Si system and Pd(001)/SiC(001) hetero-structure

Energy Technology Data Exchange (ETDEWEB)

Turchi, P.E.A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ivashchenko, V.I. [National Academy of Sciences of Ukraine (NASU), Kiev (Ukraine)

2014-11-01

First-principles molecular dynamics simulations of the Pd(001)/3C–SiC(001) nano-layered structure were carried out at different temperatures ranging from 300 to 2100 K. Various PdSi (Pnma, Fm3m, P6m2, Pm3m), Pd₂Si (P6⁻2m, P6₃/mmc, P3m1, P3⁻1m) and Pd₃Si (Pnma, P6₃22, Pm3m, I4/mmm) structures under pressure were studied to identify the structure of the Pd/Si and Pd/C interfaces in the Pd/SiC systems at high temperatures. It was found that a large atomic mixing at the Pd/Si interface occurred at 1500–1800 K, whereas the Pd/C interface remained sharp even at the highest temperature of 2100 K. At the Pd/C interface, voids and a graphite-like clustering were detected. Palladium and silicon atoms interact at the Pd/Si interface to mostly form C22-Pd₂Si and D0₁₁-Pd₃Si fragments, in agreement with experiment.

Hypoglycemia-Induced Decrease of EEG Coherence in Patients with Type 1 Diabetes

DEFF Research Database (Denmark)

Rubega, Maria; Sparacino, Giovanni; Sejling, A. S.

2016-01-01

investigated. The aim of the present work is to use a coherence approach to quantitatively assess how hypoglycemia affects mutual connectivity of different brain areas. MATERIALS AND METHODS: EEG multichannel data were obtained from 19 patients with T1D (58% males; mean age, 55 ± 2.4 years; diabetes duration......: In passing from eu- to hypoglycemia, absolute values of the iPDC function tend to decrease in both bands in all combinations of the considered channels. In particular, the scalar indicator [Formula: see text], which summarizes iPDC information, significantly decreased (P ...-A1A2 to C3-A1A2 from O1-A1A2 to C4-A1A2 and from O2-A1A2 to Cz-A1A2 in the theta band and from O1-A1A2 to T4-A1A2 and from O1-A1A2 to C4-A1A2 in the alpha band. CONCLUSIONS: The coherence decrease measured by iPDC in passing from eu- to hypoglycemia is likely related to the progressive loss...

Photodecarboxylative Cyclizations of ω-Phthalimido-para-phenoxy Carboxylates

Energy Technology Data Exchange (ETDEWEB)

Kim, Ae Rhan; Lee, Younsik; Yoo, Dong Jin [Chonbuk National Univ., Jeonju (Korea, Republic of); Cho, Hyunseung [Seonam Univ., Namwon (Korea, Republic of)

2012-10-15

The chemistry of electronically-excited phthalimides is dictated by electron and/or hydrogen transfer reactions. The photochemistry of phthalimides has been intensively studied, and numerous synthetically useful transformations with high chemical and quantum yields have been developed. 3 Among the synthetic applications, intra- and intermolecular photodecarboxylation (PDC) of ω-phthalimidoalkyl carboxylates has been developed by Griesbeck and coworkers as a versatile pathway to medium- and large-ring heterocycles. Model reactions were further realized on macro- and micro-scales. We recently described PDC cyclizations of ω-phthalimidoalkynoates to produce macrocyclic alkynes with ring-sizes up to 17. In recent study, we expanded the portfolio of this reaction and investigated the photochemistry of related aryl-linked phthalimides in Scheme 1. Based on these approaches, we demonstrated that ω-phthalimido-ortho/meta-phenoxy carboxylates undergo efficient PDC cyclizations. While the yields of ω-phthalimido-ortho-phenoxy carboxylates steadily decreased with increasing chain-length and the maximum yield of the 6-membered product was obtained in 75%, the yields of meta-phenoxy carboxylates steadily increased with increasing chain-length and the extended 16-membered product was subsequently obtained in 48% yield.

Experimental models of autoimmune inflammatory ocular diseases

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Fabio Gasparin

2012-04-01

Full Text Available Ocular inflammation is one of the leading causes of blindness and loss of vision. Human uveitis is a complex and heterogeneous group of diseases characterized by inflammation of intraocular tissues. The eye may be the only organ involved, or uveitis may be part of a systemic disease. A significant number of cases are of unknown etiology and are labeled idiopathic. Animal models have been developed to the study of the physiopathogenesis of autoimmune uveitis due to the difficulty in obtaining human eye inflamed tissues for experiments. Most of those models are induced by injection of specific photoreceptors proteins (e.g., S-antigen, interphotoreceptor retinoid-binding protein, rhodopsin, recoverin, phosducin. Non-retinal antigens, including melanin-associated proteins and myelin basic protein, are also good inducers of uveitis in animals. Understanding the basic mechanisms and pathogenesis of autoimmune ocular diseases are essential for the development of new treatment approaches and therapeutic agents. The present review describes the main experimental models of autoimmune ocular inflammatory diseases.

Gene coexpression network analysis as a source of functional annotation for rice genes.

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Kevin L Childs

Full Text Available With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional

The drug target genes show higher evolutionary conservation than non-target genes.

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Lv, Wenhua; Xu, Yongdeng; Guo, Yiying; Yu, Ziqi; Feng, Guanglong; Liu, Panpan; Luan, Meiwei; Zhu, Hongjie; Liu, Guiyou; Zhang, Mingming; Lv, Hongchao; Duan, Lian; Shang, Zhenwei; Li, Jin; Jiang, Yongshuai; Zhang, Ruijie

2016-01-26

Although evidence indicates that drug target genes share some common evolutionary features, there have been few studies analyzing evolutionary features of drug targets from an overall level. Therefore, we conducted an analysis which aimed to investigate the evolutionary characteristics of drug target genes. We compared the evolutionary conservation between human drug target genes and non-target genes by combining both the evolutionary features and network topological properties in human protein-protein interaction network. The evolution rate, conservation score and the percentage of orthologous genes of 21 species were included in our study. Meanwhile, four topological features including the average shortest path length, betweenness centrality, clustering coefficient and degree were considered for comparison analysis. Then we got four results as following: compared with non-drug target genes, 1) drug target genes had lower evolutionary rates; 2) drug target genes had higher conservation scores; 3) drug target genes had higher percentages of orthologous genes and 4) drug target genes had a tighter network structure including higher degrees, betweenness centrality, clustering coefficients and lower average shortest path lengths. These results demonstrate that drug target genes are more evolutionarily conserved than non-drug target genes. We hope that our study will provide valuable information for other researchers who are interested in evolutionary conservation of drug targets.

Identifying potential maternal genes of Bombyx mori using digital gene expression profiling

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Xu, Pingzhen

2018-01-01

Maternal genes present in mature oocytes play a crucial role in the early development of silkworm. Although maternal genes have been widely studied in many other species, there has been limited research in Bombyx mori. High-throughput next generation sequencing provides a practical method for gene discovery on a genome-wide level. Herein, a transcriptome study was used to identify maternal-related genes from silkworm eggs. Unfertilized eggs from five different stages of early development were used to detect the changing situation of gene expression. The expressed genes showed different patterns over time. Seventy-six maternal genes were annotated according to homology analysis with Drosophila melanogaster. More than half of the differentially expressed maternal genes fell into four expression patterns, while the expression patterns showed a downward trend over time. The functional annotation of these material genes was mainly related to transcription factor activity, growth factor activity, nucleic acid binding, RNA binding, ATP binding, and ion binding. Additionally, twenty-two gene clusters including maternal genes were identified from 18 scaffolds. Altogether, we plotted a profile for the maternal genes of Bombyx mori using a digital gene expression profiling method. This will provide the basis for maternal-specific signature research and improve the understanding of the early development of silkworm. PMID:29462160

Novel gene sets improve set-level classification of prokaryotic gene expression data.

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Holec, Matěj; Kuželka, Ondřej; Železný, Filip

2015-10-28

Set-level classification of gene expression data has received significant attention recently. In this setting, high-dimensional vectors of features corresponding to genes are converted into lower-dimensional vectors of features corresponding to biologically interpretable gene sets. The dimensionality reduction brings the promise of a decreased risk of overfitting, potentially resulting in improved accuracy of the learned classifiers. However, recent empirical research has not confirmed this expectation. Here we hypothesize that the reported unfavorable classification results in the set-level framework were due to the adoption of unsuitable gene sets defined typically on the basis of the Gene ontology and the KEGG database of metabolic networks. We explore an alternative approach to defining gene sets, based on regulatory interactions, which we expect to collect genes with more correlated expression. We hypothesize that such more correlated gene sets will enable to learn more accurate classifiers. We define two families of gene sets using information on regulatory interactions, and evaluate them on phenotype-classification tasks using public prokaryotic gene expression data sets. From each of the two gene-set families, we first select the best-performing subtype. The two selected subtypes are then evaluated on independent (testing) data sets against state-of-the-art gene sets and against the conventional gene-level approach. The novel gene sets are indeed more correlated than the conventional ones, and lead to significantly more accurate classifiers. The novel gene sets are indeed more correlated than the conventional ones, and lead to significantly more accurate classifiers. Novel gene sets defined on the basis of regulatory interactions improve set-level classification of gene expression data. The experimental scripts and other material needed to reproduce the experiments are available at http://ida.felk.cvut.cz/novelgenesets.tar.gz.

Personality disorders among Danish alcoholics attending outpatient treatment

DEFF Research Database (Denmark)

Nordholm, Dorte; Nielsen, Bent

2007-01-01

of the Addiction Severity Index. A+PDC had significantly more serious medical problems than A-PD, while the A+PDB group had significantly more employment, drug use and social problems than the A-PD. As for psychiatric status, A-PD had significantly different scores compared with A+PDB and A+PDC. A+PDB were younger...... at the outpatient alcohol clinic at Odense University Hospital, Denmark. It was possible to re-interview 276 (76%) patients 1 year after onset of treatment. Of the 363 patients, 87% were alcohol-dependent (ICD-10) and 34% fulfilled the ICD-10-R criteria for PDs. The basic interviews focused on the seven main areas...

Polymer-Derived Silicon Oxycarbide Ceramics as Promising Next-Generation Sustainable Thermoelectrics.

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Kousaalya, Adhimoolam Bakthavachalam; Zeng, Xiaoyu; Karakaya, Mehmet; Tritt, Terry; Pilla, Srikanth; Rao, Apparao M

2018-01-24

We demonstrate the potential of polymer-derived ceramics (PDC) as next-generation sustainable thermoelectrics. Thermoelectric behavior of polymer-derived silicon oxycarbide (SiOC) ceramics (containing hexagonal boron nitride (h-BN) as filler) was studied as a function of measurement temperature. SiOC, sintered at 1300 °C exhibited invariant low thermal conductivity (∼1.5 W/(m·K)) over 30-600 °C, coupled with a small increase in both Seebeck coefficient and electrical conductivity, with increase in measurement temperature (30-150 °C). SiOC ceramics containing 1 wt % h-BN showed the highest Seebeck coefficient (-33 μV/K) for any PDC thus far.

Study of pyruvate decarboxylase and thiamine kinase from brewer's yeast by SERS

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Maskevich, Sergei A.; Chernikevich, Ivan P.; Gachko, Gennedy A.; Kivach, Leonid N.; Strekal, Nataliya D.

1993-06-01

The Surface Enhanced Raman Scattering (SERS) spectra of holopyruvate decarboxylase (PDC) and thiamine kinase (ThK) adsorbed on silver electrode were obtained. In contrast to the Raman, the SERS spectrum of PDC contained no modes of tryptophan residues, it indicates a removal of this moiety from the surface. In the SERS spectrum of ThK the bands belonging to ligands bound to the protein were observed. A correlation between the SERS signal intensity and the enzymatic activity of the ThK separate fraction and found. The influence of amino acids on SERS spectra of thiamine (Th) was studied to determine the possible composition on microsurrounding of coenzyme.

[Gene doping: gene transfer and possible molecular detection].

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Argüelles, Carlos Francisco; Hernández-Zamora, Edgar

2007-01-01

The use of illegal substances in sports to enhance athletic performance during competition has caused international sports organizations such as the COI and WADA to take anti doping measures. A new doping method know as gene doping is defined as "the non-therapeutic use of genes, genetic elements and/or cells that have the capacity to enhance athletic performance". However, gene doping in sports is not easily identified and can cause serious consequences. Molecular biology techniques are needed in order to distinguish the difference between a "normal" and an "altered" genome. Further, we need to develop new analytic methods and biological molecular techniques in anti-doping laboratories, and design programs that avoid the non therapeutic use of genes.

Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets.

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Springer, Mark S; Gatesy, John

2018-02-26

coalescence methods have emerged as a popular alternative for inferring species trees with large genomic datasets, because these methods explicitly account for incomplete lineage sorting. However, statistical consistency of summary coalescence methods is not guaranteed unless several model assumptions are true, including the critical assumption that recombination occurs freely among but not within coalescence genes (c-genes), which are the fundamental units of analysis for these methods. Each c-gene has a single branching history, and large sets of these independent gene histories should be the input for genome-scale coalescence estimates of phylogeny. By contrast, numerous studies have reported the results of coalescence analyses in which complete protein-coding sequences are treated as c-genes even though exons for these loci can span more than a megabase of DNA. Empirical estimates of recombination breakpoints suggest that c-genes may be much shorter, especially when large clades with many species are the focus of analysis. Although this idea has been challenged recently in the literature, the inverse relationship between c-gene size and increased taxon sampling in a dataset-the 'recombination ratchet'-is a fundamental property of c-genes. For taxonomic groups characterized by genes with long intron sequences, complete protein-coding sequences are likely not valid c-genes and are inappropriate units of analysis for summary coalescence methods unless they occur in recombination deserts that are devoid of incomplete lineage sorting (ILS). Finally, it has been argued that coalescence methods are robust when the no-recombination within loci assumption is violated, but recombination must matter at some scale because ILS, a by-product of recombination, is the raison d'etre for coalescence methods. That is, extensive recombination is required to yield the large number of independently segregating c-genes used to infer a species tree. If coalescent methods are powerful

Gene therapy of cancer and development of therapeutic target gene

Energy Technology Data Exchange (ETDEWEB)

Kim, Chang Min; Kwon, Hee Chung

1998-04-01

We applied HSV-tk/GCV strategy to orthotopic rat hepatoma model and showed anticancer effects of hepatoma. The increased expression of Lac Z gene after adenovirus-mediated gene delivery throughout hepatic artery was thought that is increased the possibility of gene therapy for curing hepatoma. With the construction of kGLP-laboratory, it is possible to produce a good quantity and quality of adenovirus in lage-scale production and purification of adenovirus vector. Also, the analysis of hepatoma related genes by PCR-LOH could be used for the diagnosis of patients and the development of therapeutic gene.

Gene therapy of cancer and development of therapeutic target gene

International Nuclear Information System (INIS)

Kim, Chang Min; Kwon, Hee Chung

1998-04-01

We applied HSV-tk/GCV strategy to orthotopic rat hepatoma model and showed anticancer effects of hepatoma. The increased expression of Lac Z gene after adenovirus-mediated gene delivery throughout hepatic artery was thought that is increased the possibility of gene therapy for curing hepatoma. With the construction of kGLP-laboratory, it is possible to produce a good quantity and quality of adenovirus in lage-scale production and purification of adenovirus vector. Also, the analysis of hepatoma related genes by PCR-LOH could be used for the diagnosis of patients and the development of therapeutic gene

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

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Baseler Michael W

2007-11-01

Full Text Available Abstract Background Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis. Description The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner. Conclusion The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/.

Evolutionary dynamics of human autoimmune disease genes and malfunctioned immunological genes

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Podder Soumita

2012-01-01

Full Text Available Abstract Background One of the main issues of molecular evolution is to divulge the principles in dictating the evolutionary rate differences among various gene classes. Immunological genes have received considerable attention in evolutionary biology as candidates for local adaptation and for studying functionally important polymorphisms. The normal structure and function of immunological genes will be distorted when they experience mutations leading to immunological dysfunctions. Results Here, we examined the fundamental differences between the genes which on mutation give rise to autoimmune or other immune system related diseases and the immunological genes that do not cause any disease phenotypes. Although the disease genes examined are analogous to non-disease genes in product, expression, function, and pathway affiliation, a statistically significant decrease in evolutionary rate has been found in autoimmune disease genes relative to all other immune related diseases and non-disease genes. Possible ways of accumulation of mutation in the three steps of the central dogma (DNA-mRNA-Protein have been studied to trace the mutational effects predisposed to disease consequence and acquiring higher selection pressure. Principal Component Analysis and Multivariate Regression Analysis have established the predominant role of single nucleotide polymorphisms in guiding the evolutionary rate of immunological disease and non-disease genes followed by m-RNA abundance, paralogs number, fraction of phosphorylation residue, alternatively spliced exon, protein residue burial and protein disorder. Conclusions Our study provides an empirical insight into the etiology of autoimmune disease genes and other immunological diseases. The immediate utility of our study is to help in disease gene identification and may also help in medicinal improvement of immune related disease.

Carboxylesterase 1 genes

DEFF Research Database (Denmark)

Rasmussen, Henrik Berg; Madsen, Majbritt Busk

2018-01-01

The carboxylesterase 1 gene (CES1) encodes a hydrolase that metabolizes commonly used drugs. The CES1-related pseudogene, carboxylesterase 1 pseudogene 1 (CES1P1), has been implicated in gene exchange with CES1 and in the formation of hybrid genes including the carboxylesterase 1A2 gene (CES1A2...

Bayesian assignment of gene ontology terms to gene expression experiments

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Sykacek, P.

2012-01-01

Motivation: Gene expression assays allow for genome scale analyses of molecular biological mechanisms. State-of-the-art data analysis provides lists of involved genes, either by calculating significance levels of mRNA abundance or by Bayesian assessments of gene activity. A common problem of such approaches is the difficulty of interpreting the biological implication of the resulting gene lists. This lead to an increased interest in methods for inferring high-level biological information. A common approach for representing high level information is by inferring gene ontology (GO) terms which may be attributed to the expression data experiment. Results: This article proposes a probabilistic model for GO term inference. Modelling assumes that gene annotations to GO terms are available and gene involvement in an experiment is represented by a posterior probabilities over gene-specific indicator variables. Such probability measures result from many Bayesian approaches for expression data analysis. The proposed model combines these indicator probabilities in a probabilistic fashion and provides a probabilistic GO term assignment as a result. Experiments on synthetic and microarray data suggest that advantages of the proposed probabilistic GO term inference over statistical test-based approaches are in particular evident for sparsely annotated GO terms and in situations of large uncertainty about gene activity. Provided that appropriate annotations exist, the proposed approach is easily applied to inferring other high level assignments like pathways. Availability: Source code under GPL license is available from the author. Contact: peter.sykacek@boku.ac.at PMID:22962488

Bayesian assignment of gene ontology terms to gene expression experiments.

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Sykacek, P

2012-09-15

Gene expression assays allow for genome scale analyses of molecular biological mechanisms. State-of-the-art data analysis provides lists of involved genes, either by calculating significance levels of mRNA abundance or by Bayesian assessments of gene activity. A common problem of such approaches is the difficulty of interpreting the biological implication of the resulting gene lists. This lead to an increased interest in methods for inferring high-level biological information. A common approach for representing high level information is by inferring gene ontology (GO) terms which may be attributed to the expression data experiment. This article proposes a probabilistic model for GO term inference. Modelling assumes that gene annotations to GO terms are available and gene involvement in an experiment is represented by a posterior probabilities over gene-specific indicator variables. Such probability measures result from many Bayesian approaches for expression data analysis. The proposed model combines these indicator probabilities in a probabilistic fashion and provides a probabilistic GO term assignment as a result. Experiments on synthetic and microarray data suggest that advantages of the proposed probabilistic GO term inference over statistical test-based approaches are in particular evident for sparsely annotated GO terms and in situations of large uncertainty about gene activity. Provided that appropriate annotations exist, the proposed approach is easily applied to inferring other high level assignments like pathways. Source code under GPL license is available from the author. peter.sykacek@boku.ac.at.

Targeting the human lysozyme gene on bovine αs1- casein gene ...

African Journals Online (AJOL)

Targeting an exogenous gene into a favorable gene locus and for expression under endogenous regulators is an ideal method in mammary gland bioreactor research. For this purpose, a gene targeting vector was constructed to targeting the human lysozyme gene on bovine αs1-casein gene locus. In this case, the ...

A powerful score-based test statistic for detecting gene-gene co-association.

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Xu, Jing; Yuan, Zhongshang; Ji, Jiadong; Zhang, Xiaoshuai; Li, Hongkai; Wu, Xuesen; Xue, Fuzhong; Liu, Yanxun

2016-01-29

The genetic variants identified by Genome-wide association study (GWAS) can only account for a small proportion of the total heritability for complex disease. The existence of gene-gene joint effects which contains the main effects and their co-association is one of the possible explanations for the "missing heritability" problems. Gene-gene co-association refers to the extent to which the joint effects of two genes differ from the main effects, not only due to the traditional interaction under nearly independent condition but the correlation between genes. Generally, genes tend to work collaboratively within specific pathway or network contributing to the disease and the specific disease-associated locus will often be highly correlated (e.g. single nucleotide polymorphisms (SNPs) in linkage disequilibrium). Therefore, we proposed a novel score-based statistic (SBS) as a gene-based method for detecting gene-gene co-association. Various simulations illustrate that, under different sample sizes, marginal effects of causal SNPs and co-association levels, the proposed SBS has the better performance than other existed methods including single SNP-based and principle component analysis (PCA)-based logistic regression model, the statistics based on canonical correlations (CCU), kernel canonical correlation analysis (KCCU), partial least squares path modeling (PLSPM) and delta-square (δ (2)) statistic. The real data analysis of rheumatoid arthritis (RA) further confirmed its advantages in practice. SBS is a powerful and efficient gene-based method for detecting gene-gene co-association.

Prediction of regulatory gene pairs using dynamic time warping and gene ontology.

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Yang, Andy C; Hsu, Hui-Huang; Lu, Ming-Da; Tseng, Vincent S; Shih, Timothy K

2014-01-01

Selecting informative genes is the most important task for data analysis on microarray gene expression data. In this work, we aim at identifying regulatory gene pairs from microarray gene expression data. However, microarray data often contain multiple missing expression values. Missing value imputation is thus needed before further processing for regulatory gene pairs becomes possible. We develop a novel approach to first impute missing values in microarray time series data by combining k-Nearest Neighbour (KNN), Dynamic Time Warping (DTW) and Gene Ontology (GO). After missing values are imputed, we then perform gene regulation prediction based on our proposed DTW-GO distance measurement of gene pairs. Experimental results show that our approach is more accurate when compared with existing missing value imputation methods on real microarray data sets. Furthermore, our approach can also discover more regulatory gene pairs that are known in the literature than other methods.

The Drosophila melanogaster methuselah gene: a novel gene with ancient functions.

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Ana Rita Araújo

Full Text Available The Drosophila melanogaster G protein-coupled receptor gene, methuselah (mth, has been described as a novel gene that is less than 10 million years old. Nevertheless, it shows a highly specific expression pattern in embryos, larvae, and adults, and has been implicated in larval development, stress resistance, and in the setting of adult lifespan, among others. Although mth belongs to a gene subfamily with 16 members in D. melanogaster, there is no evidence for functional redundancy in this subfamily. Therefore, it is surprising that a novel gene influences so many traits. Here, we explore the alternative hypothesis that mth is an old gene. Under this hypothesis, in species distantly related to D. melanogaster, there should be a gene with features similar to those of mth. By performing detailed phylogenetic, synteny, protein structure, and gene expression analyses we show that the D. virilis GJ12490 gene is the orthologous of mth in species distantly related to D. melanogaster. We also show that, in D. americana (a species of the virilis group of Drosophila, a common amino acid polymorphism at the GJ12490 orthologous gene is significantly associated with developmental time, size, and lifespan differences. Our results imply that GJ12490 orthologous genes are candidates for developmental time and lifespan differences in Drosophila in general.

Constructing an integrated gene similarity network for the identification of disease genes.

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Tian, Zhen; Guo, Maozu; Wang, Chunyu; Xing, LinLin; Wang, Lei; Zhang, Yin

2017-09-20

Discovering novel genes that are involved human diseases is a challenging task in biomedical research. In recent years, several computational approaches have been proposed to prioritize candidate disease genes. Most of these methods are mainly based on protein-protein interaction (PPI) networks. However, since these PPI networks contain false positives and only cover less half of known human genes, their reliability and coverage are very low. Therefore, it is highly necessary to fuse multiple genomic data to construct a credible gene similarity network and then infer disease genes on the whole genomic scale. We proposed a novel method, named RWRB, to infer causal genes of interested diseases. First, we construct five individual gene (protein) similarity networks based on multiple genomic data of human genes. Then, an integrated gene similarity network (IGSN) is reconstructed based on similarity network fusion (SNF) method. Finally, we employee the random walk with restart algorithm on the phenotype-gene bilayer network, which combines phenotype similarity network, IGSN as well as phenotype-gene association network, to prioritize candidate disease genes. We investigate the effectiveness of RWRB through leave-one-out cross-validation methods in inferring phenotype-gene relationships. Results show that RWRB is more accurate than state-of-the-art methods on most evaluation metrics. Further analysis shows that the success of RWRB is benefited from IGSN which has a wider coverage and higher reliability comparing with current PPI networks. Moreover, we conduct a comprehensive case study for Alzheimer's disease and predict some novel disease genes that supported by literature. RWRB is an effective and reliable algorithm in prioritizing candidate disease genes on the genomic scale. Software and supplementary information are available at http://nclab.hit.edu.cn/~tianzhen/RWRB/ .

Evolutionary signatures amongst disease genes permit novel methods for gene prioritization and construction of informative gene-based networks.

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Nolan Priedigkeit

2015-02-01

Full Text Available Genes involved in the same function tend to have similar evolutionary histories, in that their rates of evolution covary over time. This coevolutionary signature, termed Evolutionary Rate Covariation (ERC, is calculated using only gene sequences from a set of closely related species and has demonstrated potential as a computational tool for inferring functional relationships between genes. To further define applications of ERC, we first established that roughly 55% of genetic diseases posses an ERC signature between their contributing genes. At a false discovery rate of 5% we report 40 such diseases including cancers, developmental disorders and mitochondrial diseases. Given these coevolutionary signatures between disease genes, we then assessed ERC's ability to prioritize known disease genes out of a list of unrelated candidates. We found that in the presence of an ERC signature, the true disease gene is effectively prioritized to the top 6% of candidates on average. We then apply this strategy to a melanoma-associated region on chromosome 1 and identify MCL1 as a potential causative gene. Furthermore, to gain global insight into disease mechanisms, we used ERC to predict molecular connections between 310 nominally distinct diseases. The resulting "disease map" network associates several diseases with related pathogenic mechanisms and unveils many novel relationships between clinically distinct diseases, such as between Hirschsprung's disease and melanoma. Taken together, these results demonstrate the utility of molecular evolution as a gene discovery platform and show that evolutionary signatures can be used to build informative gene-based networks.

Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life.

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Kannan, Lavanya; Li, Hua; Rubinstein, Boris; Mushegian, Arcady

2013-12-19

The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes, assign the probability that its ancestral gene was present in the genome of their last common ancestor. We have developed a family of models of gene gain and gene loss in evolution, and applied the maximum-likelihood approach that uses phylogenetic tree of prokaryotes and the record of orthologous relationships between their genes to infer the gene content of LUCA, the Last Universal Common Ancestor of all currently living cellular organisms. The crucial parameter, the ratio of gene losses and gene gains, was estimated from the data and was higher in models that take account of the number of in-paralogs in genomes than in models that treat gene presences and absences as a binary trait. While the numbers of genes that are placed confidently into LUCA are similar in the ML methods and in previously published methods that use various parsimony-based approaches, the identities of genes themselves are different. Most of the models of either kind treat the genes found in many existing genomes in a similar way, assigning to them high probabilities of being ancestral ("high ancestrality"). The ML models are more likely than others to assign high ancestrality to the genes that are relatively rare in the present-day genomes.

Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization

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McDonald Karen

2011-08-01

Full Text Available Abstract Background Direct gene synthesis is becoming more popular owing to decreases in gene synthesis pricing. Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific applications. In order to facilitate gene optimization, we have developed a stand-alone software called Visual Gene Developer. Results The software not only provides general functions for gene analysis and optimization along with an interactive user-friendly interface, but also includes unique features such as programming capability, dedicated mRNA secondary structure prediction, artificial neural network modeling, network & multi-threaded computing, and user-accessible programming modules. The software allows a user to analyze and optimize a sequence using main menu functions or specialized module windows. Alternatively, gene optimization can be initiated by designing a gene construct and configuring an optimization strategy. A user can choose several predefined or user-defined algorithms to design a complicated strategy. The software provides expandable functionality as platform software supporting module development using popular script languages such as VBScript and JScript in the software programming environment. Conclusion Visual Gene Developer is useful for both researchers who want to quickly analyze and optimize genes, and those who are interested in developing and testing new algorithms in bioinformatics. The software is available for free download at http://www.visualgenedeveloper.net.

Gene delivery to the lungs: pulmonary gene therapy for cystic fibrosis.

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Villate-Beitia, Ilia; Zarate, Jon; Puras, Gustavo; Pedraz, José Luis

2017-07-01

Cystic fibrosis (CF) is a monogenic autosomal recessive disorder where the defective gene, the cystic fibrosis transmembrane conductance regulator (CFTR), is well identified. Moreover, the respiratory tract can be targeted through noninvasive aerosolized formulations for inhalation. Therefore, gene therapy is considered a plausible strategy to address this disease. Conventional gene therapy strategies rely on the addition of a correct copy of the CFTR gene into affected cells in order to restore the channel activity. In recent years, genome correction strategies have emerged, such as zinc-finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeats associated to Cas9 nucleases. These gene editing tools aim to repair the mutated gene at its original genomic locus with high specificity. Besides, the success of gene therapy critically depends on the nucleic acids carriers. To date, several clinical studies have been carried out to add corrected copies of the CFTR gene into target cells using viral and non-viral vectors, some of them with encouraging results. Regarding genome editing systems, preliminary in vitro studies have been performed in order to repair the CFTR gene. In this review, after briefly introducing the basis of CF, we discuss the up-to-date gene therapy strategies to address the disease. The review focuses on the main factors to take into consideration when developing gene delivery strategies, such as the design of vectors and plasmid DNA, in vitro/in vivo tests, translation to human use, administration methods, manufacturing conditions and regulatory issues.

Iron homeostasis in Arabidopsis thaliana: transcriptomic analyses reveal novel FIT-regulated genes, iron deficiency marker genes and functional gene networks.

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Mai, Hans-Jörg; Pateyron, Stéphanie; Bauer, Petra

2016-10-03

FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) is the central regulator of iron uptake in Arabidopsis thaliana roots. We performed transcriptome analyses of six day-old seedlings and roots of six week-old plants using wild type, a fit knock-out mutant and a FIT over-expression line grown under iron-sufficient or iron-deficient conditions. We compared genes regulated in a FIT-dependent manner depending on the developmental stage of the plants. We assembled a high likelihood dataset which we used to perform co-expression and functional analysis of the most stably iron deficiency-induced genes. 448 genes were found FIT-regulated. Out of these, 34 genes were robustly FIT-regulated in root and seedling samples and included 13 novel FIT-dependent genes. Three hundred thirty-one genes showed differential regulation in response to the presence and absence of FIT only in the root samples, while this was the case for 83 genes in the seedling samples. We assembled a virtual dataset of iron-regulated genes based on a total of 14 transcriptomic analyses of iron-deficient and iron-sufficient wild-type plants to pinpoint the best marker genes for iron deficiency and analyzed this dataset in depth. Co-expression analysis of this dataset revealed 13 distinct regulons part of which predominantly contained functionally related genes. We could enlarge the list of FIT-dependent genes and discriminate between genes that are robustly FIT-regulated in roots and seedlings or only in one of those. FIT-regulated genes were mostly induced, few of them were repressed by FIT. With the analysis of a virtual dataset we could filter out and pinpoint new candidates among the most reliable marker genes for iron deficiency. Moreover, co-expression and functional analysis of this virtual dataset revealed iron deficiency-induced and functionally distinct regulons.

Intracellular delivery of potential therapeutic genes: prospects in cancer gene therapy.

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Bakhtiar, Athirah; Sayyad, Mustak; Rosli, Rozita; Maruyama, Atsushi; Chowdhury, Ezharul H

2014-01-01

Conventional therapies for malignant cancer such as chemotherapy and radiotherapy are associated with poor survival rates owing to the development of cellular resistance to cancer drugs and the lack of targetability, resulting in unwanted adverse effects on healthy cells and necessitating the lowering of therapeutic dose with consequential lower efficacy of the treatment. Gene therapy employing different types of viral and non-viral carriers to transport gene(s) of interest and facilitating production of the desirable therapeutic protein(s) has tremendous prospects in cancer treatments due to the high-level of specificity in therapeutic action of the expressed protein(s) with diminished off-target effects, although cancer cell-specific delivery of transgene(s) still poses some challenges to be addressed. Depending on the potential therapeutic target genes, cancer gene therapy could be categorized into tumor suppressor gene replacement therapy, immune gene therapy and enzyme- or prodrug-based therapy. This review would shed light on the current progress of delivery of potentially therapeutic genes into various cancer cells in vitro and animal models utilizing a variety of viral and non-viral vectors.

Divergence of gene body DNA methylation and evolution of plant duplicate genes.

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Jun Wang

Full Text Available It has been shown that gene body DNA methylation is associated with gene expression. However, whether and how deviation of gene body DNA methylation between duplicate genes can influence their divergence remains largely unexplored. Here, we aim to elucidate the potential role of gene body DNA methylation in the fate of duplicate genes. We identified paralogous gene pairs from Arabidopsis and rice (Oryza sativa ssp. japonica genomes and reprocessed their single-base resolution methylome data. We show that methylation in paralogous genes nonlinearly correlates with several gene properties including exon number/gene length, expression level and mutation rate. Further, we demonstrated that divergence of methylation level and pattern in paralogs indeed positively correlate with their sequence and expression divergences. This result held even after controlling for other confounding factors known to influence the divergence of paralogs. We observed that methylation level divergence might be more relevant to the expression divergence of paralogs than methylation pattern divergence. Finally, we explored the mechanisms that might give rise to the divergence of gene body methylation in paralogs. We found that exonic methylation divergence more closely correlates with expression divergence than intronic methylation divergence. We show that genomic environments (e.g., flanked by transposable elements and repetitive sequences of paralogs generated by various duplication mechanisms are associated with the methylation divergence of paralogs. Overall, our results suggest that the changes in gene body DNA methylation could provide another avenue for duplicate genes to develop differential expression patterns and undergo different evolutionary fates in plant genomes.

GeneTopics - interpretation of gene sets via literature-driven topic models

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2013-01-01

Background Annotation of a set of genes is often accomplished through comparison to a library of labelled gene sets such as biological processes or canonical pathways. However, this approach might fail if the employed libraries are not up to date with the latest research, don't capture relevant biological themes or are curated at a different level of granularity than is required to appropriately analyze the input gene set. At the same time, the vast biomedical literature offers an unstructured repository of the latest research findings that can be tapped to provide thematic sub-groupings for any input gene set. Methods Our proposed method relies on a gene-specific text corpus and extracts commonalities between documents in an unsupervised manner using a topic model approach. We automatically determine the number of topics summarizing the corpus and calculate a gene relevancy score for each topic allowing us to eliminate non-specific topics. As a result we obtain a set of literature topics in which each topic is associated with a subset of the input genes providing directly interpretable keywords and corresponding documents for literature research. Results We validate our method based on labelled gene sets from the KEGG metabolic pathway collection and the genetic association database (GAD) and show that the approach is able to detect topics consistent with the labelled annotation. Furthermore, we discuss the results on three different types of experimentally derived gene sets, (1) differentially expressed genes from a cardiac hypertrophy experiment in mice, (2) altered transcript abundance in human pancreatic beta cells, and (3) genes implicated by GWA studies to be associated with metabolite levels in a healthy population. In all three cases, we are able to replicate findings from the original papers in a quick and semi-automated manner. Conclusions Our approach provides a novel way of automatically generating meaningful annotations for gene sets that are directly

Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life

Science.gov (United States)

2013-01-01

Background The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes, assign the probability that its ancestral gene was present in the genome of their last common ancestor. Results We have developed a family of models of gene gain and gene loss in evolution, and applied the maximum-likelihood approach that uses phylogenetic tree of prokaryotes and the record of orthologous relationships between their genes to infer the gene content of LUCA, the Last Universal Common Ancestor of all currently living cellular organisms. The crucial parameter, the ratio of gene losses and gene gains, was estimated from the data and was higher in models that take account of the number of in-paralogs in genomes than in models that treat gene presences and absences as a binary trait. Conclusion While the numbers of genes that are placed confidently into LUCA are similar in the ML methods and in previously published methods that use various parsimony-based approaches, the identities of genes themselves are different. Most of the models of either kind treat the genes found in many existing genomes in a similar way, assigning to them high probabilities of being ancestral (“high ancestrality”). The ML models are more likely than others to assign high ancestrality to the genes that are relatively rare in the present-day genomes. Reviewers This article was reviewed by Martijn A Huynen, Toni Gabaldón and Fyodor Kondrashov. PMID:24354654

Gene therapy: An overview

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Sudip Indu

2013-01-01

Full Text Available Gene therapy "the use of genes as medicine" involves the transfer of a therapeutic or working copy of a gene into specific cells of an individual in order to repair a faulty gene copy. The technique may be used to replace a faulty gene, or to introduce a new gene whose function is to cure or to favorably modify the clinical course of a condition. The objective of gene therapy is to introduce new genetic material into target cells while causing no damage to the surrounding healthy cells and tissues, hence the treatment related morbidity is decreased. The delivery system includes a vector that delivers a therapeutic gene into the patient′s target cell. Functional proteins are created from the therapeutic gene causing the cell to return to a normal stage. The vectors used in gene therapy can be viral and non-viral. Gene therapy, an emerging field of biomedicine, is still at infancy and much research remains to be done before this approach to the treatment of condition will realize its full potential.

Gene doping in sports.

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Unal, Mehmet; Ozer Unal, Durisehvar

2004-01-01

Gene or cell doping is defined by the World Anti-Doping Agency (WADA) as "the non-therapeutic use of genes, genetic elements and/or cells that have the capacity to enhance athletic performance". New research in genetics and genomics will be used not only to diagnose and treat disease, but also to attempt to enhance human performance. In recent years, gene therapy has shown progress and positive results that have highlighted the potential misuse of this technology and the debate of 'gene doping'. Gene therapies developed for the treatment of diseases such as anaemia (the gene for erythropoietin), muscular dystrophy (the gene for insulin-like growth factor-1) and peripheral vascular diseases (the gene for vascular endothelial growth factor) are potential doping methods. With progress in gene technology, many other genes with this potential will be discovered. For this reason, it is important to develop timely legal regulations and to research the field of gene doping in order to develop methods of detection. To protect the health of athletes and to ensure equal competitive conditions, the International Olympic Committee, WADA and International Sports Federations have accepted performance-enhancing substances and methods as being doping, and have forbidden them. Nevertheless, the desire to win causes athletes to misuse these drugs and methods. This paper reviews the current status of gene doping and candidate performance enhancement genes, and also the use of gene therapy in sports medicine and ethics of genetic enhancement. Copyright 2004 Adis Data Information BV

Identifying key genes in rheumatoid arthritis by weighted gene co-expression network analysis.

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Ma, Chunhui; Lv, Qi; Teng, Songsong; Yu, Yinxian; Niu, Kerun; Yi, Chengqin

2017-08-01

This study aimed to identify rheumatoid arthritis (RA) related genes based on microarray data using the WGCNA (weighted gene co-expression network analysis) method. Two gene expression profile datasets GSE55235 (10 RA samples and 10 healthy controls) and GSE77298 (16 RA samples and seven healthy controls) were downloaded from Gene Expression Omnibus database. Characteristic genes were identified using metaDE package. WGCNA was used to find disease-related networks based on gene expression correlation coefficients, and module significance was defined as the average gene significance of all genes used to assess the correlation between the module and RA status. Genes in the disease-related gene co-expression network were subject to functional annotation and pathway enrichment analysis using Database for Annotation Visualization and Integrated Discovery. Characteristic genes were also mapped to the Connectivity Map to screen small molecules. A total of 599 characteristic genes were identified. For each dataset, characteristic genes in the green, red and turquoise modules were most closely associated with RA, with gene numbers of 54, 43 and 79, respectively. These genes were enriched in totally enriched in 17 Gene Ontology terms, mainly related to immune response (CD97, FYB, CXCL1, IKBKE, CCR1, etc.), inflammatory response (CD97, CXCL1, C3AR1, CCR1, LYZ, etc.) and homeostasis (C3AR1, CCR1, PLN, CCL19, PPT1, etc.). Two small-molecule drugs sanguinarine and papaverine were predicted to have a therapeutic effect against RA. Genes related to immune response, inflammatory response and homeostasis presumably have critical roles in RA pathogenesis. Sanguinarine and papaverine have a potential therapeutic effect against RA. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

Identification of suitable reference genes for gene expression studies of shoulder instability.

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Mariana Ferreira Leal

Full Text Available Shoulder instability is a common shoulder injury, and patients present with plastic deformation of the glenohumeral capsule. Gene expression analysis may be a useful tool for increasing the general understanding of capsule deformation, and reverse-transcription quantitative polymerase chain reaction (RT-qPCR has become an effective method for such studies. Although RT-qPCR is highly sensitive and specific, it requires the use of suitable reference genes for data normalization to guarantee meaningful and reproducible results. In the present study, we evaluated the suitability of a set of reference genes using samples from the glenohumeral capsules of individuals with and without shoulder instability. We analyzed the expression of six commonly used reference genes (ACTB, B2M, GAPDH, HPRT1, TBP and TFRC in the antero-inferior, antero-superior and posterior portions of the glenohumeral capsules of cases and controls. The stability of the candidate reference gene expression was determined using four software packages: NormFinder, geNorm, BestKeeper and DataAssist. Overall, HPRT1 was the best single reference gene, and HPRT1 and B2M composed the best pair of reference genes from different analysis groups, including simultaneous analysis of all tissue samples. GenEx software was used to identify the optimal number of reference genes to be used for normalization and demonstrated that the accumulated standard deviation resulting from the use of 2 reference genes was similar to that resulting from the use of 3 or more reference genes. To identify the optimal combination of reference genes, we evaluated the expression of COL1A1. Although the use of different reference gene combinations yielded variable normalized quantities, the relative quantities within sample groups were similar and confirmed that no obvious differences were observed when using 2, 3 or 4 reference genes. Consequently, the use of 2 stable reference genes for normalization, especially

The Pathway From Genes to Gene Therapy in Glaucoma: A Review of Possibilities for Using Genes as Glaucoma Drugs.

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Borrás, Teresa

2017-01-01

Treatment of diseases with gene therapy is advancing rapidly. The use of gene therapy has expanded from the original concept of re-placing the mutated gene causing the disease to the use of genes to con-trol nonphysiological levels of expression or to modify pathways known to affect the disease. Genes offer numerous advantages over conventional drugs. They have longer duration of action and are more specific. Genes can be delivered to the target site by naked DNA, cells, nonviral, and viral vectors. The enormous progress of the past decade in molecular bi-ology and delivery systems has provided ways for targeting genes to the intended cell/tissue and safe, long-term vectors. The eye is an ideal organ for gene therapy. It is easily accessible and it is an immune-privileged site. Currently, there are clinical trials for diseases affecting practically every tissue of the eye, including those to restore vision in patients with Leber congenital amaurosis. However, the number of eye trials compared with those for systemic diseases is quite low (1.8%). Nevertheless, judg-ing by the vast amount of ongoing preclinical studies, it is expected that such number will increase considerably in the near future. One area of great need for eye gene therapy is glaucoma, where a long-term gene drug would eliminate daily applications and compliance issues. Here, we review the current state of gene therapy for glaucoma and the possibilities for treating the trabecular meshwork to lower intraocular pressure and the retinal ganglion cells to protect them from neurodegeneration. Copyright© 2017 Asia-Pacific Academy of Ophthalmology.

Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity

Energy Technology Data Exchange (ETDEWEB)

Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu; Tratz, Stephen C.; Gregory, Michelle L.

2006-06-08

With the rising influence of the Gene On-tology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associ-ated with them. So far, these approaches have solely relied on the knowledge en-coded in the Gene Ontology and the gene annotations associated with the Gene On-tology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.

UniGene Tabulator: a full parser for the UniGene format.

Science.gov (United States)

Lenzi, Luca; Frabetti, Flavia; Facchin, Federica; Casadei, Raffaella; Vitale, Lorenza; Canaider, Silvia; Carinci, Paolo; Zannotti, Maria; Strippoli, Pierluigi

2006-10-15

UniGene Tabulator 1.0 provides a solution for full parsing of UniGene flat file format; it implements a structured graphical representation of each data field present in UniGene following import into a common database managing system usable in a personal computer. This database includes related tables for sequence, protein similarity, sequence-tagged site (STS) and transcript map interval (TXMAP) data, plus a summary table where each record represents a UniGene cluster. UniGene Tabulator enables full local management of UniGene data, allowing parsing, querying, indexing, retrieving, exporting and analysis of UniGene data in a relational database form, usable on Macintosh (OS X 10.3.9 or later) and Windows (2000, with service pack 4, XP, with service pack 2 or later) operating systems-based computers. The current release, including both the FileMaker runtime applications, is freely available at http://apollo11.isto.unibo.it/software/

Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks.

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Vipin Narang

Full Text Available Human gene regulatory networks (GRN can be difficult to interpret due to a tangle of edges interconnecting thousands of genes. We constructed a general human GRN from extensive transcription factor and microRNA target data obtained from public databases. In a subnetwork of this GRN that is active during estrogen stimulation of MCF-7 breast cancer cells, we benchmarked automated algorithms for identifying core regulatory genes (transcription factors and microRNAs. Among these algorithms, we identified K-core decomposition, pagerank and betweenness centrality algorithms as the most effective for discovering core regulatory genes in the network evaluated based on previously known roles of these genes in MCF-7 biology as well as in their ability to explain the up or down expression status of up to 70% of the remaining genes. Finally, we validated the use of K-core algorithm for organizing the GRN in an easier to interpret layered hierarchy where more influential regulatory genes percolate towards the inner layers. The integrated human gene and miRNA network and software used in this study are provided as supplementary materials (S1 Data accompanying this manuscript.

Maximum Gene-Support Tree

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Yunfeng Shan

2008-01-01

Full Text Available Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees available. In this study, we generated single gene trees of seven yeast species as well as single gene trees of nine baculovirus species using all the orthologous genes among the species compared. Homologous genes among seven known plants were used for validation of the finding. Four algorithms—maximum parsimony (MP, minimum evolution (ME, maximum likelihood (ML, and neighbor-joining (NJ—were used. Trees were reconstructed before and after weighting the DNA and protein sequence lengths among genes. Rarely a gene can always generate the “true tree” by all the four algorithms. However, the most frequent gene tree, termed “maximum gene-support tree” (MGS tree, or WMGS tree for the weighted one, in yeasts, baculoviruses, or plants was consistently found to be the “true tree” among the species. The results provide insights into the overall degree of divergence of orthologous genes of the genomes analyzed and suggest the following: 1 The true tree relationship among the species studied is still maintained by the largest group of orthologous genes; 2 There are usually more orthologous genes with higher similarities between genetically closer species than between genetically more distant ones; and 3 The maximum gene-support tree reflects the phylogenetic relationship among species in comparison.

Hydrothermal synthesis of Bismuth(III) coordination polymer and its transformation to nano α-Bi{sub 2}O{sub 3} for photocatalytic degradation

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Huang, Ya-Jing; Zheng, Yue-Qing, E-mail: zhengnbu@163.com; Zhu, Hong-Lin; Wang, Jin-Jian

2016-07-15

A new Bi(III) coordination polymer Bi{sub 2}(Hpdc){sub 2}(pdc){sub 2}·2H{sub 2}O (H{sub 2}pdc=pyridine-2,6-dicarboxylic acid) was synthesized by hydrothermal method. Solid state thermal decomposition of this complex under 500 °C for 1 h led to the foliated Bi{sub 2}O{sub 3} nanoparticles, which were then characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM). Comparative study on their photocatalytic activity toward the degradation of rhodamine B (RhB), methylene blue (MB) and methyl orange (MO) in polluted water was explored, and the mechanism of these photocatalytic degradation was discussed. These results provided some interesting insights into their photocatalytic applications. - Graphical abstract: We regard Bi{sub 2}(Hpdc){sub 2}(pdc){sub 2}·2H{sub 2}O with 1D chain structures as the precursor, then calcinate the complex to prepare nano-powder α-Bi{sub 2}O{sub 3}. The photochemical experiment indicates that Bi{sub 2}(Hpdc){sub 2}(pdc){sub 2}·2H{sub 2}O can be used as an efficient photocatalyst for the degradation of RhB and MB. Interestingly, nano α-Bi{sub 2}O{sub 3} shows higher activity than the commercial Bi{sub 2}O{sub 3} for the degradation of RhB, MB or MO. Display Omitted - Highlights: • A novel dinuclear Bi(III) coordination polymer is hydrothermally synthesized. • Calcinating the precursor Bi-CP will result in the nano Bi{sub 2}O{sub 3} with foliated morphology. • Nano Bi{sub 2}O{sub 3} shows higher activity than the commercial Bi{sub 2}O{sub 3} for the degradation of dyes.

A comparison of reactive plasma pre-treatments on PET substrates by Cu and Ti pulsed-DC and HIPIMS discharges

Energy Technology Data Exchange (ETDEWEB)

Audronis, M., E-mail: m.audronis@yahoo.co.uk [Gencoa Ltd, Physics Road, Speke, Liverpool, L24 9HP (United Kingdom); Hinder, S.J. [The Surface Analysis Laboratory, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, GU2 7XH (United Kingdom); Mack, P. [ThermoFisher Scientific Ltd, Imberhorne Lane, East Grinstead, Sussex, RH19 1UB (United Kingdom); Bellido-Gonzalez, V. [Gencoa Ltd, Physics Road, Speke, Liverpool, L24 9HP (United Kingdom); Bussey, D.; Matthews, A. [Department of Engineering Materials, University of Sheffield, Sheffield S1 3JD (United Kingdom); Baker, M.A. [The Surface Analysis Laboratory, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, GU2 7XH (United Kingdom)

2011-12-30

PET web samples have been treated by magnetically enhanced glow discharges powered using either medium frequency pulse direct current (p-DC) or low frequency high power pulse (HIPIMS) sources. The plasma pre-treatment processes were carried out in an Ar-O{sub 2} atmosphere using either Cu or Ti sputter targets. XPS, AFM and sessile drop water contact angle measurements have been employed to examine changes in surface chemistry and morphology for different pre-treatment process parameters. Deposition of metal oxide onto the PET surface is observed as a result of the sputter magnetron-based glow discharge web treatment. Using the Cu target, both the p-DC and HIPIMS processes result in the formation of a thin CuO layer (with a thickness between 1 and 11 nm) being deposited onto the PET surface. Employing the Ti target, both p-DC and HIPIMS processes give rise to a much lower concentration of Ti (< 5 at.%), in the form of TiO{sub 2} on the PET treated surface. The TiO{sub 2} is probably distributed as an island-like distribution covering the PET surface. Presence of Cu and Ti oxide constituents on the treated PET is beneficial in aiding the adhesion but alone (i.e. without oxygen plasma activation) is not enough to provide very high levels of hydrophilicity as is clear from sessile drop water contact angle measurements on aged samples. Exposure to the plasma treatments leads to a small amount of roughening of the substrate surface, but the average surface roughness in all cases is below 2.5 nm. The PET structure at the interface with a coating is mostly or wholly preserved. The oxygen plasma treatment, metal oxide deposition and surface roughening resulting from the HIPIMS and p-DC treatments will promote adhesion to any subsequent thin film that is deposited immediately following the plasma treatment.

Caregiver outcomes of partners in dementia care: effect of a care coordination program for veterans with dementia and their family members and friends.

Science.gov (United States)

Bass, David M; Judge, Katherine S; Snow, A Lynn; Wilson, Nancy L; Morgan, Robert; Looman, Wendy J; McCarthy, Catherine A; Maslow, Katie; Moye, Jennifer A; Randazzo, Ronda; Garcia-Maldonado, Maurilio; Elbein, Richard; Odenheimer, Germaine; Kunik, Mark E

2013-08-01

The objective is to test the effectiveness of Partners in Dementia Care (PDC), a care-coordination program that integrates and improves access to medical and nonmedical services, while strengthening the informal care network and providing information, coaching, and emotional support. PDC was delivered via a partnership between Veterans Affairs (VA) Medical Centers (VAMCs) and Alzheimer's Association chapters, for caregivers of veterans with dementia living in the community and receiving primary care from the VA. The initial sample was 486 caregivers of 508 veterans with diagnosed dementia. Outcomes were evaluated for 394 and 324 caregivers who completed 6- and 12- month follow-up, respectively. PDC had a standardized protocol that included assessment and reassessment, action planning, and ongoing monitoring. It was delivered by telephone and e-mail for cost efficiency and the ability to handle caseloads of 100 to 125. Care coordinators from VAMCs and Alzheimer's Association chapters worked as a team using a shared computerized record. A variety of caregiver outcomes was measured after 6 and 12 months. Intervention group caregivers had significant improvements in outcomes representing unmet needs, three types of caregiver strains, depression, and two support resources. Most improvements were evident after 6 months, with more-limited improvements from Months 6 to 12. Some outcomes improved for all caregivers, whereas some improved for caregivers experiencing more initial difficulties or caring for veterans with more-severe impairments. PDC is a promising model that improves linkages between healthcare services and community services, which is a goal of several new national initiatives such as the National Plan to Address Alzheimer's Disease and a proposed amendment to the Older Americans Act. © 2013, Copyright the Authors Journal compilation © 2013, The American Geriatrics Society.

Interactive visualization of gene regulatory networks with associated gene expression time series data

NARCIS (Netherlands)

Westenberg, M.A.; Hijum, van S.A.F.T.; Lulko, A.T.; Kuipers, O.P.; Roerdink, J.B.T.M.; Linsen, L.; Hagen, H.; Hamann, B.

2008-01-01

We present GENeVis, an application to visualize gene expression time series data in a gene regulatory network context. This is a network of regulator proteins that regulate the expression of their respective target genes. The networks are represented as graphs, in which the nodes represent genes,

Using gene expression noise to understand gene regulation

NARCIS (Netherlands)

Munsky, B.; Neuert, G.; van Oudenaarden, A.

2012-01-01

Phenotypic variation is ubiquitous in biology and is often traceable to underlying genetic and environmental variation. However, even genetically identical cells in identical environments display variable phenotypes. Stochastic gene expression, or gene expression "noise," has been suggested as a

Gene Conversion in Angiosperm Genomes with an Emphasis on Genes Duplicated by Polyploidization

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Xi-Yin Wang

2011-01-01

Full Text Available Angiosperm genomes differ from those of mammals by extensive and recursive polyploidizations. The resulting gene duplication provides opportunities both for genetic innovation, and for concerted evolution. Though most genes may escape conversion by their homologs, concerted evolution of duplicated genes can last for millions of years or longer after their origin. Indeed, paralogous genes on two rice chromosomes duplicated an estimated 60–70 million years ago have experienced gene conversion in the past 400,000 years. Gene conversion preserves similarity of paralogous genes, but appears to accelerate their divergence from orthologous genes in other species. The mutagenic nature of recombination coupled with the buffering effect provided by gene redundancy, may facilitate the evolution of novel alleles that confer functional innovations while insulating biological fitness of affected plants. A mixed evolutionary model, characterized by a primary birth-and-death process and occasional homoeologous recombination and gene conversion, may best explain the evolution of multigene families.

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

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Lemay Danielle G

2012-09-01

Full Text Available Abstract Background In previous studies, gene neighborhoods—spatial clusters of co-expressed genes in the genome—have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level. In the current study, we developed a Gene Neighborhood Scoring Tool (G-NEST which combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all possible window sizes simultaneously. Results Using G-NEST on atlases of mouse and human tissue expression data, we found that large neighborhoods of ten or more genes are extremely rare in mammalian genomes. When they do occur, neighborhoods are typically composed of families of related genes. Both the highest scoring and the largest neighborhoods in mammalian genomes are formed by tandem gene duplication. Mammalian gene neighborhoods contain highly and variably expressed genes. Co-localized noisy gene pairs exhibit lower evolutionary conservation of their adjacent genome locations, suggesting that their shared transcriptional background may be disadvantageous. Genes that are essential to mammalian survival and reproduction are less likely to occur in neighborhoods, although neighborhoods are enriched with genes that function in mitosis. We also found that gene orientation and protein-protein interactions are partially responsible for maintenance of gene neighborhoods. Conclusions Our experiments using G-NEST confirm that tandem gene duplication is the primary driver of non-random gene order in mammalian genomes. Non-essentiality, co-functionality, gene orientation, and protein-protein interactions are additional forces that maintain gene neighborhoods, especially those formed by tandem duplicates. We expect G-NEST to be useful for other applications such as the identification of core regulatory modules, common transcriptional backgrounds, and chromatin domains. The

The Cumulative Effect of Gene-Gene and Gene-Environment Interactions on the Risk of Prostate Cancer in Chinese Men

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Ming Liu

2016-01-01

Full Text Available Prostate cancer (PCa is a multifactorial disease involving complex genetic and environmental factors interactions. Gene-gene and gene-environment interactions associated with PCa in Chinese men are less studied. We explored the association between 36 SNPs and PCa in 574 subjects from northern China. Body mass index (BMI, smoking, and alcohol consumption were determined through self-administered questionnaires in 134 PCa patients. Then gene-gene and gene-environment interactions among the PCa-associated SNPs were analyzed using the generalized multifactor dimensionality reduction (GMDR and logistic regression methods. Allelic and genotypic association analyses showed that six variants were associated with PCa and the cumulative effect suggested men who carried any combination of 1, 2, or ≥3 risk genotypes had a gradually increased PCa risk (odds ratios (ORs = 1.79–4.41. GMDR analysis identified the best gene-gene interaction model with scores of 10 for both the cross-validation consistency and sign tests. For gene-environment interactions, rs6983561 CC and rs16901966 GG in individuals with a BMI ≥ 28 had ORs of 7.66 (p = 0.032 and 5.33 (p = 0.046, respectively. rs7679673 CC + CA and rs12653946 TT in individuals that smoked had ORs of 2.77 (p = 0.007 and 3.11 (p = 0.024, respectively. rs7679673 CC in individuals that consumed alcohol had an OR of 4.37 (p = 0.041. These results suggest that polymorphisms, either individually or by interacting with other genes or environmental factors, contribute to an increased risk of PCa.

Primetime for Learning Genes.

Science.gov (United States)

Keifer, Joyce

2017-02-11

Learning genes in mature neurons are uniquely suited to respond rapidly to specific environmental stimuli. Expression of individual learning genes, therefore, requires regulatory mechanisms that have the flexibility to respond with transcriptional activation or repression to select appropriate physiological and behavioral responses. Among the mechanisms that equip genes to respond adaptively are bivalent domains. These are specific histone modifications localized to gene promoters that are characteristic of both gene activation and repression, and have been studied primarily for developmental genes in embryonic stem cells. In this review, studies of the epigenetic regulation of learning genes in neurons, particularly the brain-derived neurotrophic factor gene ( BDNF ), by methylation/demethylation and chromatin modifications in the context of learning and memory will be highlighted. Because of the unique function of learning genes in the mature brain, it is proposed that bivalent domains are a characteristic feature of the chromatin landscape surrounding their promoters. This allows them to be "poised" for rapid response to activate or repress gene expression depending on environmental stimuli.

Characterization of Genes for Beef Marbling Based on Applying Gene Coexpression Network

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Dajeong Lim

2014-01-01

Full Text Available Marbling is an important trait in characterization beef quality and a major factor for determining the price of beef in the Korean beef market. In particular, marbling is a complex trait and needs a system-level approach for identifying candidate genes related to the trait. To find the candidate gene associated with marbling, we used a weighted gene coexpression network analysis from the expression value of bovine genes. Hub genes were identified; they were topologically centered with large degree and BC values in the global network. We performed gene expression analysis to detect candidate genes in M. longissimus with divergent marbling phenotype (marbling scores 2 to 7 using qRT-PCR. The results demonstrate that transmembrane protein 60 (TMEM60 and dihydropyrimidine dehydrogenase (DPYD are associated with increasing marbling fat. We suggest that the network-based approach in livestock may be an important method for analyzing the complex effects of candidate genes associated with complex traits like marbling or tenderness.

Simple Comparative Analyses of Differentially Expressed Gene Lists May Overestimate Gene Overlap.

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Lawhorn, Chelsea M; Schomaker, Rachel; Rowell, Jonathan T; Rueppell, Olav

2018-04-16

Comparing the overlap between sets of differentially expressed genes (DEGs) within or between transcriptome studies is regularly used to infer similarities between biological processes. Significant overlap between two sets of DEGs is usually determined by a simple test. The number of potentially overlapping genes is compared to the number of genes that actually occur in both lists, treating every gene as equal. However, gene expression is controlled by transcription factors that bind to a variable number of transcription factor binding sites, leading to variation among genes in general variability of their expression. Neglecting this variability could therefore lead to inflated estimates of significant overlap between DEG lists. With computer simulations, we demonstrate that such biases arise from variation in the control of gene expression. Significant overlap commonly arises between two lists of DEGs that are randomly generated, assuming that the control of gene expression is variable among genes but consistent between corresponding experiments. More overlap is observed when transcription factors are specific to their binding sites and when the number of genes is considerably higher than the number of different transcription factors. In contrast, overlap between two DEG lists is always lower than expected when the genetic architecture of expression is independent between the two experiments. Thus, the current methods for determining significant overlap between DEGs are potentially confounding biologically meaningful overlap with overlap that arises due to variability in control of expression among genes, and more sophisticated approaches are needed.

The second iteration of the Systems Prioritization Method: A systems prioritization and decision-aiding tool for the Waste Isolation Pilot Plant: Volume 3, Analysis for final programmatic recommendations

International Nuclear Information System (INIS)

Prindle, N.H.; Boak, D.M.; Weiner, R.F.

1996-05-01

Systems Prioritization Method (SPM) is a decision-aiding tool developed by Sandia National Laboratories for the US DOE Carlsbad Area Office (DOE/CAO). This tool provides an analytical basis for programmatic decision making for the Waste Isolation Pilot Plant (WIPP). SPM integrates decision-analysis techniques, performance,a nd risk-assessment tools, and advanced information technology. Potential outcomes of proposed activities and combination of activities are used to calculate a probability of demonstrating compliance (PDC) with selected regulations. The results are presented in a decision matrix showing cost, duration, and maximum PDC for all activities in a given cost and duration category. This is the third and final volume in the series which presents the analysis for final programmatic recommendations

The second iteration of the Systems Prioritization Method: A systems prioritization and decision-aiding tool for the Waste Isolation Pilot Plant: Volume 3, Analysis for final programmatic recommendations

Energy Technology Data Exchange (ETDEWEB)

Prindle, N.H.; Boak, D.M.; Weiner, R.F. [and others

1996-05-01

Systems Prioritization Method (SPM) is a decision-aiding tool developed by Sandia National Laboratories for the US DOE Carlsbad Area Office (DOE/CAO). This tool provides an analytical basis for programmatic decision making for the Waste Isolation Pilot Plant (WIPP). SPM integrates decision-analysis techniques, performance,a nd risk-assessment tools, and advanced information technology. Potential outcomes of proposed activities and combination of activities are used to calculate a probability of demonstrating compliance (PDC) with selected regulations. The results are presented in a decision matrix showing cost, duration, and maximum PDC for all activities in a given cost and duration category. This is the third and final volume in the series which presents the analysis for final programmatic recommendations.

Pd Nanoparticles-Supported Carbon Nanotube-Encapsulated NiO/MgO Composite as an Enhanced Electrocatalyst for Ethanol Electrooxidation in Alkaline Medium

DEFF Research Database (Denmark)

Mahendiran, Chinnathambi; Rajesh, Dhanushkotti; Maiyalagan, Thandavarayan

2017-01-01

/(NiO/MgO-CNT) catalysts exhibit superior electrochemical performance compare to the commercial Pd/C catalysts. The current densities of the main anodic peak of electrooxidation of ethanol increases sharply for the Pd/(NiO/MgO-CNT) (98.20 mA/cm2), which are ∼2.1 times as large as that of Pd/C (47 mA/cm2). The excellent......In this work, an easy method is developed to prepare well-dispersed palladium nanoparticles into the carbon nanotube (CNT) encapsulated NiO/MgO nanocomposite by the chemical reduction method. CNT encapsulated NiO/MgO nanocomposite were prepared by autogenous pressure at elevated temperature (RAPET...

Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function.

Science.gov (United States)

Di, Chao; Xu, Wenying; Su, Zhen; Yuan, Joshua S

2010-10-07

PHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes. PHB genes are ubiquitously present in divergent species from prokaryotes to eukaryotes. Human PHB genes have been found to be associated with various diseases. Recent studies by our group and others have shown diverse function of PHB genes in plants for development, senescence, defence, and others. Despite the importance of the PHB gene family, no comprehensive gene family analysis has been carried to evaluate the relatedness of PHB genes across different species. In order to better guide the gene function analysis and understand the evolution of the PHB gene family, we therefore carried out the comparative genome analysis of the PHB genes across different kingdoms. The relatedness, motif distribution, and intron/exon distribution all indicated that PHB genes is a relatively conserved gene family. The PHB genes can be classified into 5 classes and each class have a very deep evolutionary origin. The PHB genes within the class maintained the same motif patterns during the evolution. With Arabidopsis as the model species, we found that PHB gene intron/exon structure and domains are also conserved during the evolution. Despite being a conserved gene family, various gene duplication events led to the expansion of the PHB genes. Both segmental and tandem gene duplication were involved in Arabidopsis PHB gene family expansion. However, segmental duplication is predominant in Arabidopsis. Moreover, most of the duplicated genes experienced neofunctionalization. The results highlighted that PHB genes might be involved in important functions so that the duplicated genes are under the evolutionary pressure to derive new function. PHB gene family is a conserved gene family and accounts for diverse but important biological functions based on the similar molecular mechanisms. The highly diverse biological function indicated that more research needs to be carried out

Genes and Hearing Loss

Science.gov (United States)

... ENTCareers Marketplace Find an ENT Doctor Near You Genes and Hearing Loss Genes and Hearing Loss Patient ... mutation may only have dystopia canthorum. How Do Genes Work? Genes are a road map for the ...

Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing.

Science.gov (United States)

Seoane-Zonjic, Pedro; Cañas, Rafael A; Bautista, Rocío; Gómez-Maldonado, Josefa; Arrillaga, Isabel; Fernández-Pozo, Noé; Claros, M Gonzalo; Cánovas, Francisco M; Ávila, Concepción

2016-02-27

In the era of DNA throughput sequencing, assembling and understanding gymnosperm mega-genomes remains a challenge. Although drafts of three conifer genomes have recently been published, this number is too low to understand the full complexity of conifer genomes. Using techniques focused on specific genes, gene models can be established that can aid in the assembly of gene-rich regions, and this information can be used to compare genomes and understand functional evolution. In this study, gene capture technology combined with BAC isolation and sequencing was used as an experimental approach to establish de novo gene structures without a reference genome. Probes were designed for 866 maritime pine transcripts to sequence genes captured from genomic DNA. The gene models were constructed using GeneAssembler, a new bioinformatic pipeline, which reconstructed over 82% of the gene structures, and a high proportion (85%) of the captured gene models contained sequences from the promoter regulatory region. In a parallel experiment, the P. pinaster BAC library was screened to isolate clones containing genes whose cDNA sequence were already available. BAC clones containing the asparagine synthetase, sucrose synthase and xyloglucan endotransglycosylase gene sequences were isolated and used in this study. The gene models derived from the gene capture approach were compared with the genomic sequences derived from the BAC clones. This combined approach is a particularly efficient way to capture the genomic structures of gene families with a small number of members. The experimental approach used in this study is a valuable combined technique to study genomic gene structures in species for which a reference genome is unavailable. It can be used to establish exon/intron boundaries in unknown gene structures, to reconstruct incomplete genes and to obtain promoter sequences that can be used for transcriptional studies. A bioinformatics algorithm (GeneAssembler) is also provided as a

Mining tissue specificity, gene connectivity and disease association to reveal a set of genes that modify the action of disease causing genes

Directory of Open Access Journals (Sweden)

Reverter Antonio

2008-09-01

Full Text Available Abstract Background The tissue specificity of gene expression has been linked to a number of significant outcomes including level of expression, and differential rates of polymorphism, evolution and disease association. Recent studies have also shown the importance of exploring differential gene connectivity and sequence conservation in the identification of disease-associated genes. However, no study relates gene interactions with tissue specificity and disease association. Methods We adopted an a priori approach making as few assumptions as possible to analyse the interplay among gene-gene interactions with tissue specificity and its subsequent likelihood of association with disease. We mined three large datasets comprising expression data drawn from massively parallel signature sequencing across 32 tissues, describing a set of 55,606 true positive interactions for 7,197 genes, and microarray expression results generated during the profiling of systemic inflammation, from which 126,543 interactions among 7,090 genes were reported. Results Amongst the myriad of complex relationships identified between expression, disease, connectivity and tissue specificity, some interesting patterns emerged. These include elevated rates of expression and network connectivity in housekeeping and disease-associated tissue-specific genes. We found that disease-associated genes are more likely to show tissue specific expression and most frequently interact with other disease genes. Using the thresholds defined in these observations, we develop a guilt-by-association algorithm and discover a group of 112 non-disease annotated genes that predominantly interact with disease-associated genes, impacting on disease outcomes. Conclusion We conclude that parameters such as tissue specificity and network connectivity can be used in combination to identify a group of genes, not previously confirmed as disease causing, that are involved in interactions with disease causing

AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data

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Xia Yuannan

2006-12-01

Full Text Available Abstract Background DNA microarrays are a powerful tool for monitoring the expression of tens of thousands of genes simultaneously. With the advance of microarray technology, the challenge issue becomes how to analyze a large amount of microarray data and make biological sense of them. Affymetrix GeneChips are widely used microarrays, where a variety of statistical algorithms have been explored and used for detecting significant genes in the experiment. These methods rely solely on the quantitative data, i.e., signal intensity; however, qualitative data are also important parameters in detecting differentially expressed genes. Results AffyMiner is a tool developed for detecting differentially expressed genes in Affymetrix GeneChip microarray data and for associating gene annotation and gene ontology information with the genes detected. AffyMiner consists of the functional modules, GeneFinder for detecting significant genes in a treatment versus control experiment and GOTree for mapping genes of interest onto the Gene Ontology (GO space; and interfaces to run Cluster, a program for clustering analysis, and GenMAPP, a program for pathway analysis. AffyMiner has been used for analyzing the GeneChip data and the results were presented in several publications. Conclusion AffyMiner fills an important gap in finding differentially expressed genes in Affymetrix GeneChip microarray data. AffyMiner effectively deals with multiple replicates in the experiment and takes into account both quantitative and qualitative data in identifying significant genes. AffyMiner reduces the time and effort needed to compare data from multiple arrays and to interpret the possible biological implications associated with significant changes in a gene's expression.

Gene therapy in periodontics.

Science.gov (United States)

Chatterjee, Anirban; Singh, Nidhi; Saluja, Mini

2013-03-01

GENES are made of DNA - the code of life. They are made up of two types of base pair from different number of hydrogen bonds AT, GC which can be turned into instruction. Everyone inherits genes from their parents and passes them on in turn to their children. Every person's genes are different, and the changes in sequence determine the inherited differences between each of us. Some changes, usually in a single gene, may cause serious diseases. Gene therapy is 'the use of genes as medicine'. It involves the transfer of a therapeutic or working gene copy into specific cells of an individual in order to repair a faulty gene copy. Thus it may be used to replace a faulty gene, or to introduce a new gene whose function is to cure or to favorably modify the clinical course of a condition. It has a promising era in the field of periodontics. Gene therapy has been used as a mode of tissue engineering in periodontics. The tissue engineering approach reconstructs the natural target tissue by combining four elements namely: Scaffold, signaling molecules, cells and blood supply and thus can help in the reconstruction of damaged periodontium including cementum, gingival, periodontal ligament and bone.

Norrie disease gene is distinct from the monoamine oxidase genes.

Science.gov (United States)

Sims, K B; Ozelius, L; Corey, T; Rinehart, W B; Liberfarb, R; Haines, J; Chen, W J; Norio, R; Sankila, E; de la Chapelle, A

1989-09-01

The genes for MAO-A and MAO-B appear to be very close to the Norrie disease gene, on the basis of loss and/or disruption of the MAO genes and activities in atypical Norrie disease patients deleted for the DXS7 locus; linkage among the MAO genes, the Norrie disease gene, and the DXS7 locus; and mapping of all these loci to the chromosomal region Xp11. The present study provides evidence that the MAO genes are not disrupted in "classic" Norrie disease patients. Genomic DNA from these "nondeletion" Norrie disease patients did not show rearrangements at the MAOA or DXS7 loci. Normal levels of MAO-A activities, as well as normal amounts and size of the MAO-A mRNA, were observed in cultured skin fibroblasts from these patients, and MAO-B activity in their platelets was normal. Catecholamine metabolites evaluated in plasma and urine were in the control range. Thus, although some atypical Norrie disease patients lack both MAO-A and MAO-B activities, MAO does not appear to be an etiologic factor in classic Norrie disease.

Gene profile analysis of osteoblast genes differentially regulated by histone deacetylase inhibitors

Directory of Open Access Journals (Sweden)

Lamblin Anne-Francoise

2007-10-01

Full Text Available Abstract Background Osteoblast differentiation requires the coordinated stepwise expression of multiple genes. Histone deacetylase inhibitors (HDIs accelerate the osteoblast differentiation process by blocking the activity of histone deacetylases (HDACs, which alter gene expression by modifying chromatin structure. We previously demonstrated that HDIs and HDAC3 shRNAs accelerate matrix mineralization and the expression of osteoblast maturation genes (e.g. alkaline phosphatase, osteocalcin. Identifying other genes that are differentially regulated by HDIs might identify new pathways that contribute to osteoblast differentiation. Results To identify other osteoblast genes that are altered early by HDIs, we incubated MC3T3-E1 preosteoblasts with HDIs (trichostatin A, MS-275, or valproic acid for 18 hours in osteogenic conditions. The promotion of osteoblast differentiation by HDIs in this experiment was confirmed by osteogenic assays. Gene expression profiles relative to vehicle-treated cells were assessed by microarray analysis with Affymetrix GeneChip 430 2.0 arrays. The regulation of several genes by HDIs in MC3T3-E1 cells and primary osteoblasts was verified by quantitative real-time PCR. Nine genes were differentially regulated by at least two-fold after exposure to each of the three HDIs and six were verified by PCR in osteoblasts. Four of the verified genes (solute carrier family 9 isoform 3 regulator 1 (Slc9a3r1, sorbitol dehydrogenase 1, a kinase anchor protein, and glutathione S-transferase alpha 4 were induced. Two genes (proteasome subunit, beta type 10 and adaptor-related protein complex AP-4 sigma 1 were suppressed. We also identified eight growth factors and growth factor receptor genes that are significantly altered by each of the HDIs, including Frizzled related proteins 1 and 4, which modulate the Wnt signaling pathway. Conclusion This study identifies osteoblast genes that are regulated early by HDIs and indicates pathways that

Acute Vhl gene inactivation induces cardiac HIF-dependent erythropoietin gene expression.

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Marta Miró-Murillo

Full Text Available Von Hippel Lindau (Vhl gene inactivation results in embryonic lethality. The consequences of its inactivation in adult mice, and of the ensuing activation of the hypoxia-inducible factors (HIFs, have been explored mainly in a tissue-specific manner. This mid-gestation lethality can be also circumvented by using a floxed Vhl allele in combination with an ubiquitous tamoxifen-inducible recombinase Cre-ER(T2. Here, we characterize a widespread reduction in Vhl gene expression in Vhl(floxed-UBC-Cre-ER(T2 adult mice after dietary tamoxifen administration, a convenient route of administration that has yet to be fully characterized for global gene inactivation. Vhl gene inactivation rapidly resulted in a marked splenomegaly and skin erythema, accompanied by renal and hepatic induction of the erythropoietin (Epo gene, indicative of the in vivo activation of the oxygen sensing HIF pathway. We show that acute Vhl gene inactivation also induced Epo gene expression in the heart, revealing cardiac tissue to be an extra-renal source of EPO. Indeed, primary cardiomyocytes and HL-1 cardiac cells both induce Epo gene expression when exposed to low O(2 tension in a HIF-dependent manner. Thus, as well as demonstrating the potential of dietary tamoxifen administration for gene inactivation studies in UBC-Cre-ER(T2 mouse lines, this data provides evidence of a cardiac oxygen-sensing VHL/HIF/EPO pathway in adult mice.

Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data

OpenAIRE

Ezer, Daphne; Moignard, Victoria; G?ttgens, Berthold; Adryan, Boris

2016-01-01

Many genes are expressed in bursts, which can contribute to cell-to-cell heterogeneity. It is now possible to measure this heterogeneity with high throughput single cell gene expression assays (single cell qPCR and RNA-seq). These experimental approaches generate gene expression distributions which can be used to estimate the kinetic parameters of gene expression bursting, namely the rate that genes turn on, the rate that genes turn off, and the rate of transcription. We construct a complete ...

Discovering genes underlying QTL

Energy Technology Data Exchange (ETDEWEB)

Vanavichit, Apichart [Kasetsart University, Kamphaengsaen, Nakorn Pathom (Thailand)

2002-02-01

A map-based approach has allowed scientists to discover few genes at a time. In addition, the reproductive barrier between cultivated rice and wild relatives has prevented us from utilizing the germ plasm by a map-based approach. Most genetic traits important to agriculture or human diseases are manifested as observable, quantitative phenotypes called Quantitative Trait Loci (QTL). In many instances, the complexity of the phenotype/genotype interaction and the general lack of clearly identifiable gene products render the direct molecular cloning approach ineffective, thus additional strategies like genome mapping are required to identify the QTL in question. Genome mapping requires no prior knowledge of the gene function, but utilizes statistical methods to identify the most likely gene location. To completely characterize genes of interest, the initially mapped region of a gene location will have to be narrowed down to a size that is suitable for cloning and sequencing. Strategies for gene identification within the critical region have to be applied after the sequencing of a potentially large clone or set of clones that contains this gene(s). Tremendous success of positional cloning has been shown for cloning many genes responsible for human diseases, including cystic fibrosis and muscular dystrophy as well as plant disease resistance genes. Genome and QTL mapping, positional cloning: the pre-genomics era, comparative approaches to gene identification, and positional cloning: the genomics era are discussed in the report. (M. Suetake)

GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity.

Science.gov (United States)

Kim, Hyunjin; Choi, Sang-Min; Park, Sanghyun

2018-01-01

When a gene shows varying levels of expression among normal people but similar levels in disease patients or shows similar levels of expression among normal people but different levels in disease patients, we can assume that the gene is associated with the disease. By utilizing this gene expression heterogeneity, we can obtain additional information that abets discovery of disease-associated genes. In this study, we used collaborative filtering to calculate the degree of gene expression heterogeneity between classes and then scored the genes on the basis of the degree of gene expression heterogeneity to find "differentially predicted" genes. Through the proposed method, we discovered more prostate cancer-associated genes than 10 comparable methods. The genes prioritized by the proposed method are potentially significant to biological processes of a disease and can provide insight into them.

Validation of reference genes for quantifying changes in gene expression in virus-infected tobacco.

Science.gov (United States)

Baek, Eseul; Yoon, Ju-Yeon; Palukaitis, Peter

2017-10-01

To facilitate quantification of gene expression changes in virus-infected tobacco plants, eight housekeeping genes were evaluated for their stability of expression during infection by one of three systemically-infecting viruses (cucumber mosaic virus, potato virus X, potato virus Y) or a hypersensitive-response-inducing virus (tobacco mosaic virus; TMV) limited to the inoculated leaf. Five reference-gene validation programs were used to establish the order of the most stable genes for the systemically-infecting viruses as ribosomal protein L25 > β-Tubulin > Actin, and the least stable genes Ubiquitin-conjugating enzyme (UCE) genes were EF1α > Cysteine protease > Actin, and the least stable genes were GAPDH genes, three defense responsive genes were examined to compare their relative changes in gene expression caused by each virus. Copyright © 2017 Elsevier Inc. All rights reserved.

Human gene therapy: novel approaches to improve the current gene delivery systems.

Science.gov (United States)

Cucchiarini, Magali

2016-06-01

Even though gene therapy made its way through the clinics to treat a number of human pathologies since the early years of experimental research and despite the recent approval of the first gene-based product (Glybera) in Europe, the safe and effective use of gene transfer vectors remains a challenge in human gene therapy due to the existence of barriers in the host organism. While work is under active investigation to improve the gene transfer systems themselves, the use of controlled release approaches may offer alternative, convenient tools of vector delivery to achieve a performant gene transfer in vivo while overcoming the various physiological barriers that preclude its wide use in patients. This article provides an overview of the most significant contributions showing how the principles of controlled release strategies may be adapted for human gene therapy.

From gene engineering to gene modulation and manipulation: can we prevent or detect gene doping in sports?

Science.gov (United States)

Fischetto, Giuseppe; Bermon, Stéphane

2013-10-01

During the last 2 decades, progress in deciphering the human gene map as well as the discovery of specific defective genes encoding particular proteins in some serious human diseases have resulted in attempts to treat sick patients with gene therapy. There has been considerable focus on human recombinant proteins which were gene-engineered and produced in vitro (insulin, growth hormone, insulin-like growth factor-1, erythropoietin). Unfortunately, these substances and methods also became improper tools for unscrupulous athletes. Biomedical research has focused on the possible direct insertion of gene material into the body, in order to replace some defective genes in vivo and/or to promote long-lasting endogenous synthesis of deficient proteins. Theoretically, diabetes, anaemia, muscular dystrophies, immune deficiency, cardiovascular diseases and numerous other illnesses could benefit from such innovative biomedical research, though much work remains to be done. Considering recent findings linking specific genotypes and physical performance, it is tempting to submit the young athletic population to genetic screening or, alternatively, to artificial gene expression modulation. Much research is already being conducted in order to achieve a safe transfer of genetic material to humans. This is of critical importance since uncontrolled production of the specifically coded protein, with serious secondary adverse effects (polycythaemia, acute cardiovascular problems, cancer, etc.), could occur. Other unpredictable reactions (immunogenicity of vectors or DNA-vector complex, autoimmune anaemia, production of wild genetic material) also remain possible at the individual level. Some new substances (myostatin blockers or anti-myostatin antibodies), although not gene material, might represent a useful and well-tolerated treatment to prevent progression of muscular dystrophies. Similarly, other molecules, in the roles of gene or metabolic activators [5-aminoimidazole-4

Genetic Dissociation of Glycolysis and the TCA Cycle Affects Neither Normal nor Neoplastic Proliferation.

Science.gov (United States)

Jackson, Laura E; Kulkarni, Sucheta; Wang, Huabo; Lu, Jie; Dolezal, James M; Bharathi, Sivakama S; Ranganathan, Sarangarajan; Patel, Mulchand S; Deshpande, Rahul; Alencastro, Frances; Wendell, Stacy G; Goetzman, Eric S; Duncan, Andrew W; Prochownik, Edward V

2017-11-01

Rapidly proliferating cells increase glycolysis at the expense of oxidative phosphorylation (oxphos) to generate sufficient levels of glycolytic intermediates for use as anabolic substrates. The pyruvate dehydrogenase complex (PDC) is a critical mitochondrial enzyme that catalyzes pyruvate's conversion to acetyl coenzyme A (AcCoA), thereby connecting these two pathways in response to complex energetic, enzymatic, and metabolic cues. Here we utilized a mouse model of hepatocyte-specific PDC inactivation to determine the need for this metabolic link during normal hepatocyte regeneration and malignant transformation. In PDC "knockout" (KO) animals, the long-term regenerative potential of hepatocytes was unimpaired, and growth of aggressive experimental hepatoblastomas was only modestly slowed in the face of 80%-90% reductions in AcCoA and significant alterations in the levels of key tricarboxylic acid (TCA) cycle intermediates and amino acids. Overall, oxphos activity in KO livers and hepatoblastoma was comparable with that of control counterparts, with evidence that metabolic substrate abnormalities were compensated for by increased mitochondrial mass. These findings demonstrate that the biochemical link between glycolysis and the TCA cycle can be completely severed without affecting normal or neoplastic proliferation, even under the most demanding circumstances. Cancer Res; 77(21); 5795-807. ©2017 AACR . ©2017 American Association for Cancer Research.

A model of gene-gene and gene-environment interactions and its implications for targeting environmental interventions by genotype

Directory of Open Access Journals (Sweden)

Wallace Helen M

2006-10-01

Full Text Available Abstract Background The potential public health benefits of targeting environmental interventions by genotype depend on the environmental and genetic contributions to the variance of common diseases, and the magnitude of any gene-environment interaction. In the absence of prior knowledge of all risk factors, twin, family and environmental data may help to define the potential limits of these benefits in a given population. However, a general methodology to analyze twin data is required because of the potential importance of gene-gene interactions (epistasis, gene-environment interactions, and conditions that break the 'equal environments' assumption for monozygotic and dizygotic twins. Method A new model for gene-gene and gene-environment interactions is developed that abandons the assumptions of the classical twin study, including Fisher's (1918 assumption that genes act as risk factors for common traits in a manner necessarily dominated by an additive polygenic term. Provided there are no confounders, the model can be used to implement a top-down approach to quantifying the potential utility of genetic prediction and prevention, using twin, family and environmental data. The results describe a solution space for each disease or trait, which may or may not include the classical twin study result. Each point in the solution space corresponds to a different model of genotypic risk and gene-environment interaction. Conclusion The results show that the potential for reducing the incidence of common diseases using environmental interventions targeted by genotype may be limited, except in special cases. The model also confirms that the importance of an individual's genotype in determining their risk of complex diseases tends to be exaggerated by the classical twin studies method, owing to the 'equal environments' assumption and the assumption of no gene-environment interaction. In addition, if phenotypes are genetically robust, because of epistasis

Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes.

Science.gov (United States)

Osato, Naoki

2018-01-19

Transcriptional target genes show functional enrichment of genes. However, how many and how significantly transcriptional target genes include functional enrichments are still unclear. To address these issues, I predicted human transcriptional target genes using open chromatin regions, ChIP-seq data and DNA binding sequences of transcription factors in databases, and examined functional enrichment and gene expression level of putative transcriptional target genes. Gene Ontology annotations showed four times larger numbers of functional enrichments in putative transcriptional target genes than gene expression information alone, independent of transcriptional target genes. To compare the number of functional enrichments of putative transcriptional target genes between cells or search conditions, I normalized the number of functional enrichment by calculating its ratios in the total number of transcriptional target genes. With this analysis, native putative transcriptional target genes showed the largest normalized number of functional enrichments, compared with target genes including 5-60% of randomly selected genes. The normalized number of functional enrichments was changed according to the criteria of enhancer-promoter interactions such as distance from transcriptional start sites and orientation of CTCF-binding sites. Forward-reverse orientation of CTCF-binding sites showed significantly higher normalized number of functional enrichments than the other orientations. Journal papers showed that the top five frequent functional enrichments were related to the cellular functions in the three cell types. The median expression level of transcriptional target genes changed according to the criteria of enhancer-promoter assignments (i.e. interactions) and was correlated with the changes of the normalized number of functional enrichments of transcriptional target genes. Human putative transcriptional target genes showed significant functional enrichments. Functional

Conditional gene expression in the mouse using a Sleeping Beauty gene-trap transposon

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Hackett Perry B

2006-06-01

Full Text Available Abstract Background Insertional mutagenesis techniques with transposable elements have been popular among geneticists studying model organisms from E. coli to Drosophila and, more recently, the mouse. One such element is the Sleeping Beauty (SB transposon that has been shown in several studies to be an effective insertional mutagen in the mouse germline. SB transposon vector studies have employed different functional elements and reporter molecules to disrupt and report the expression of endogenous mouse genes. We sought to generate a transposon system that would be capable of reporting the expression pattern of a mouse gene while allowing for conditional expression of a gene of interest in a tissue- or temporal-specific pattern. Results Here we report the systematic development and testing of a transposon-based gene-trap system incorporating the doxycycline-repressible Tet-Off (tTA system that is capable of activating the expression of genes under control of a Tet response element (TRE promoter. We demonstrate that the gene trap system is fully functional in vitro by introducing the "gene-trap tTA" vector into human cells by transposition and identifying clones that activate expression of a TRE-luciferase transgene in a doxycycline-dependent manner. In transgenic mice, we mobilize gene-trap tTA vectors, discover parameters that can affect germline mobilization rates, and identify candidate gene insertions to demonstrate the in vivo functionality of the vector system. We further demonstrate that the gene-trap can act as a reporter of endogenous gene expression and it can be coupled with bioluminescent imaging to identify genes with tissue-specific expression patterns. Conclusion Akin to the GAL4/UAS system used in the fly, we have made progress developing a tool for mutating and revealing the expression of mouse genes by generating the tTA transactivator in the presence of a secondary TRE-regulated reporter molecule. A vector like the gene

Essential Bacillus subtilis genes

DEFF Research Database (Denmark)

Kobayashi, K.; Ehrlich, S.D.; Albertini, A.

2003-01-01

To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among approximate to4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were...... predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related...... to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from...

Integrative characterization of germ cell-specific genes from mouse spermatocyte UniGene library

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Eddy Edward M

2007-07-01

Full Text Available Abstract Background The primary regulator of spermatogenesis, a highly ordered and tightly regulated developmental process, is an intrinsic genetic program involving male germ cell-specific genes. Results We analyzed the mouse spermatocyte UniGene library containing 2155 gene-oriented transcript clusters. We predict that 11% of these genes are testis-specific and systematically identified 24 authentic genes specifically and abundantly expressed in the testis via in silico and in vitro approaches. Northern blot analysis disclosed various transcript characteristics, such as expression level, size and the presence of isoform. Expression analysis revealed developmentally regulated and stage-specific expression patterns in all of the genes. We further analyzed the genes at the protein and cellular levels. Transfection assays performed using GC-2 cells provided information on the cellular characteristics of the gene products. In addition, antibodies were generated against proteins encoded by some of the genes to facilitate their identification and characterization in spermatogenic cells and sperm. Our data suggest that a number of the gene products are implicated in transcriptional regulation, nuclear integrity, sperm structure and motility, and fertilization. In particular, we found for the first time that Mm.333010, predicted to contain a trypsin-like serine protease domain, is a sperm acrosomal protein. Conclusion We identify 24 authentic genes with spermatogenic cell-specific expression, and provide comprehensive information about the genes. Our findings establish a new basis for future investigation into molecular mechanisms underlying male reproduction.

Genome-wide identification of key modulators of gene-gene interaction networks in breast cancer.

Science.gov (United States)

Chiu, Yu-Chiao; Wang, Li-Ju; Hsiao, Tzu-Hung; Chuang, Eric Y; Chen, Yidong

2017-10-03

With the advances in high-throughput gene profiling technologies, a large volume of gene interaction maps has been constructed. A higher-level layer of gene-gene interaction, namely modulate gene interaction, is composed of gene pairs of which interaction strengths are modulated by (i.e., dependent on) the expression level of a key modulator gene. Systematic investigations into the modulation by estrogen receptor (ER), the best-known modulator gene, have revealed the functional and prognostic significance in breast cancer. However, a genome-wide identification of key modulator genes that may further unveil the landscape of modulated gene interaction is still lacking. We proposed a systematic workflow to screen for key modulators based on genome-wide gene expression profiles. We designed four modularity parameters to measure the ability of a putative modulator to perturb gene interaction networks. Applying the method to a dataset of 286 breast tumors, we comprehensively characterized the modularity parameters and identified a total of 973 key modulator genes. The modularity of these modulators was verified in three independent breast cancer datasets. ESR1, the encoding gene of ER, appeared in the list, and abundant novel modulators were illuminated. For instance, a prognostic predictor of breast cancer, SFRP1, was found the second modulator. Functional annotation analysis of the 973 modulators revealed involvements in ER-related cellular processes as well as immune- and tumor-associated functions. Here we present, as far as we know, the first comprehensive analysis of key modulator genes on a genome-wide scale. The validity of filtering parameters as well as the conservativity of modulators among cohorts were corroborated. Our data bring new insights into the modulated layer of gene-gene interaction and provide candidates for further biological investigations.

A new type of gene-disruption cassette with a rescue gene for Pichia pastoris.

Science.gov (United States)

Shibui, Tatsuro; Hara, Hiroyoshi

2017-09-01

Pichia pastoris has been used for the production of many recombinant proteins, and many useful mutant strains have been created. However, the efficiency of mutant isolation by gene-targeting is usually low and the procedure is difficult for those inexperienced in yeast genetics. In order to overcome these issues, we developed a new gene-disruption system with a rescue gene using an inducible Cre/mutant-loxP system. With only short homology regions, the gene-disruption cassette of the system replaces its target-gene locus containing a mutation with a compensatory rescue gene. As the cassette contains the AOX1 promoter-driven Cre gene, when targeted strains are grown on media containing methanol, the DNA fragment, i.e., the marker, rescue and Cre genes, between the mutant-loxP sequences in the cassette is excised, leaving only the remaining mutant-loxP sequence in the genome, and consequently a target gene-disrupted mutant can be isolated. The system was initially validated on ADE2 gene disruption, where the disruption can easily be detected by color-change of the colonies. Then, the system was applied for knocking-out URA3 and OCH1 genes, reported to be difficult to accomplish by conventional gene-targeting methods. All three gene-disruption cassettes with their rescue genes replaced their target genes, and the Cre/mutant-loxP system worked well to successfully isolate their knock-out mutants. This study identified a new gene-disruption system that could be used to effectively and strategically knock out genes of interest, especially whose deletion is detrimental to growth, without using special strains, e.g., deficient in nonhomologous end-joining, in P. pastoris. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1201-1208, 2017. © 2017 American Institute of Chemical Engineers.

A recently transferred cluster of bacterial genes in Trichomonas vaginalis - lateral gene transfer and the fate of acquired genes

Science.gov (United States)

2014-01-01

Background Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome. Results A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation. Conclusions We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes. PMID:24898731

Gene-based Association Approach Identify Genes Across Stress Traits in Fruit Flies

DEFF Research Database (Denmark)

Rohde, Palle Duun; Edwards, Stefan McKinnon; Sarup, Pernille Merete

Identification of genes explaining variation in quantitative traits or genetic risk factors of human diseases requires both good phenotypic- and genotypic data, but also efficient statistical methods. Genome-wide association studies may reveal association between phenotypic variation and variation...... approach grouping variants accordingly to gene position, thus lowering the number of statistical tests performed and increasing the probability of identifying genes with small to moderate effects. Using this approach we identify numerous genes associated with different types of stresses in Drosophila...... melanogaster, but also identify common genes that affects the stress traits....

Gene doping.

Science.gov (United States)

Haisma, H J; de Hon, O

2006-04-01

Together with the rapidly increasing knowledge on genetic therapies as a promising new branch of regular medicine, the issue has arisen whether these techniques might be abused in the field of sports. Previous experiences have shown that drugs that are still in the experimental phases of research may find their way into the athletic world. Both the World Anti-Doping Agency (WADA) and the International Olympic Committee (IOC) have expressed concerns about this possibility. As a result, the method of gene doping has been included in the list of prohibited classes of substances and prohibited methods. This review addresses the possible ways in which knowledge gained in the field of genetic therapies may be misused in elite sports. Many genes are readily available which may potentially have an effect on athletic performance. The sporting world will eventually be faced with the phenomena of gene doping to improve athletic performance. A combination of developing detection methods based on gene arrays or proteomics and a clear education program on the associated risks seems to be the most promising preventive method to counteract the possible application of gene doping.

Systematic study of association of four GABAergic genes: glutamic acid decarboxylase 1 gene, glutamic acid decarboxylase 2 gene, GABA(B) receptor 1 gene and GABA(A) receptor subunit beta2 gene, with schizophrenia using a universal DNA microarray.

Science.gov (United States)

Zhao, Xu; Qin, Shengying; Shi, Yongyong; Zhang, Aiping; Zhang, Jing; Bian, Li; Wan, Chunling; Feng, Guoyin; Gu, Niufan; Zhang, Guangqi; He, Guang; He, Lin

2007-07-01

Several studies have suggested the dysfunction of the GABAergic system as a risk factor in the pathogenesis of schizophrenia. In the present study, case-control association analysis was conducted in four GABAergic genes: two glutamic acid decarboxylase genes (GAD1 and GAD2), a GABA(A) receptor subunit beta2 gene (GABRB2) and a GABA(B) receptor 1 gene (GABBR1). Using a universal DNA microarray procedure we genotyped a total of 20 SNPs on the above four genes in a study involving 292 patients and 286 controls of Chinese descent. Statistically significant differences were observed in the allelic frequencies of the rs187269C/T polymorphism in the GABRB2 gene (P=0.0450, chi(2)=12.40, OR=1.65) and the -292A/C polymorphism in the GAD1 gene (P=0.0450, chi(2)=14.64 OR=1.77). In addition, using an electrophoretic mobility shift assay (EMSA), we discovered differences in the U251 nuclear protein binding to oligonucleotides representing the -292 SNP on the GAD1 gene, which suggests that the -292C allele has reduced transcription factor binding efficiency compared with the 292A allele. Using the multifactor-dimensionality reduction method (MDR), we found that the interactions among the rs187269C/T polymorphism in the GABRB2 gene, the -243A/G polymorphism in the GAD2 gene and the 27379C/T and 661C/T polymorphisms in the GAD1 gene revealed a significant association with schizophrenia (Pschizophrenia in the Chinese population.

Exploring the key genes and pathways in enchondromas using a gene expression microarray.

Science.gov (United States)

Shi, Zhongju; Zhou, Hengxing; Pan, Bin; Lu, Lu; Kang, Yi; Liu, Lu; Wei, Zhijian; Feng, Shiqing

2017-07-04

Enchondromas are the most common primary benign osseous neoplasms that occur in the medullary bone; they can undergo malignant transformation into chondrosarcoma. However, enchondromas are always undetected in patients, and the molecular mechanism is unclear. To identify key genes and pathways associated with the occurrence and development of enchondromas, we downloaded the gene expression dataset GSE22855 and obtained the differentially expressed genes (DEGs) by analyzing high-throughput gene expression in enchondromas. In total, 635 genes were identified as DEGs. Of these, 225 genes (35.43%) were up-regulated, and the remaining 410 genes (64.57%) were down-regulated. We identified the predominant gene ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were significantly over-represented in the enchondromas samples compared with the control samples. Subsequently the top 10 core genes were identified from the protein-protein interaction (PPI) network. The enrichment analyses of the genes mainly involved in two significant modules showed that the DEGs were principally related to ribosomes, protein digestion and absorption, ECM-receptor interaction, focal adhesion, amoebiasis and the PI3K-Akt signaling pathway.Together, these data elucidate the molecular mechanisms underlying the occurrence and development of enchondromas and provide promising candidates for therapeutic intervention and prognostic evaluation. However, further experimental studies are needed to confirm these results.

Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life

OpenAIRE

Kannan, Lavanya; Li, Hua; Rubinstein, Boris; Mushegian, Arcady

2013-01-01

Background The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes, assign the probability that its ancestral gene was present in the genome of their last common ancestor. Results We have developed a family of models of gene gain and gene loss in evolution, and applied the maximum-likelihood approach that uses phylogenetic tree of prokaryotes...

Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks.

Science.gov (United States)

Saik, Olga V; Demenkov, Pavel S; Ivanisenko, Timofey V; Bragina, Elena Yu; Freidin, Maxim B; Goncharova, Irina A; Dosenko, Victor E; Zolotareva, Olga I; Hofestaedt, Ralf; Lavrik, Inna N; Rogaev, Evgeny I; Ivanisenko, Vladimir A

2018-02-13

Hypertension and bronchial asthma are a major issue for people's health. As of 2014, approximately one billion adults, or ~ 22% of the world population, have had hypertension. As of 2011, 235-330 million people globally have been affected by asthma and approximately 250,000-345,000 people have died each year from the disease. The development of the effective treatment therapies against these diseases is complicated by their comorbidity features. This is often a major problem in diagnosis and their treatment. Hence, in this study the bioinformatical methodology for the analysis of the comorbidity of these two diseases have been developed. As such, the search for candidate genes related to the comorbid conditions of asthma and hypertension can help in elucidating the molecular mechanisms underlying the comorbid condition of these two diseases, and can also be useful for genotyping and identifying new drug targets. Using ANDSystem, the reconstruction and analysis of gene networks associated with asthma and hypertension was carried out. The gene network of asthma included 755 genes/proteins and 62,603 interactions, while the gene network of hypertension - 713 genes/proteins and 45,479 interactions. Two hundred and five genes/proteins and 9638 interactions were shared between asthma and hypertension. An approach for ranking genes implicated in the comorbid condition of two diseases was proposed. The approach is based on nine criteria for ranking genes by their importance, including standard methods of gene prioritization (Endeavor, ToppGene) as well as original criteria that take into account the characteristics of an associative gene network and the presence of known polymorphisms in the analysed genes. According to the proposed approach, the genes IL10, TLR4, and CAT had the highest priority in the development of comorbidity of these two diseases. Additionally, it was revealed that the list of top genes is enriched with apoptotic genes and genes involved in

Tumor targeted gene therapy

International Nuclear Information System (INIS)

Kang, Joo Hyun

2006-01-01

Knowledge of molecular mechanisms governing malignant transformation brings new opportunities for therapeutic intervention against cancer using novel approaches. One of them is gene therapy based on the transfer of genetic material to an organism with the aim of correcting a disease. The application of gene therapy to the cancer treatment had led to the development of new experimental approaches such as suicidal gene therapy, inhibition of oncogenes and restoration of tumor-suppressor genes. Suicidal gene therapy is based on the expression in tumor cells of a gene encoding an enzyme that converts a prodrug into a toxic product. Representative suicidal genes are Herpes simplex virus type 1 thymidine kinase (HSV1-tk) and cytosine deaminase (CD). Especially, physicians and scientists of nuclear medicine field take an interest in suicidal gene therapy because they can monitor the location and magnitude, and duration of expression of HSV1-tk and CD by PET scanner

PCR-based detection of gene transfer vectors: application to gene doping surveillance.

Science.gov (United States)

Perez, Irene C; Le Guiner, Caroline; Ni, Weiyi; Lyles, Jennifer; Moullier, Philippe; Snyder, Richard O

2013-12-01

Athletes who illicitly use drugs to enhance their athletic performance are at risk of being banned from sports competitions. Consequently, some athletes may seek new doping methods that they expect to be capable of circumventing detection. With advances in gene transfer vector design and therapeutic gene transfer, and demonstrations of safety and therapeutic benefit in humans, there is an increased probability of the pursuit of gene doping by athletes. In anticipation of the potential for gene doping, assays have been established to directly detect complementary DNA of genes that are top candidates for use in doping, as well as vector control elements. The development of molecular assays that are capable of exposing gene doping in sports can serve as a deterrent and may also identify athletes who have illicitly used gene transfer for performance enhancement. PCR-based methods to detect foreign DNA with high reliability, sensitivity, and specificity include TaqMan real-time PCR, nested PCR, and internal threshold control PCR.

Evolutionary genomics of plant genes encoding N-terminal-TM-C2 domain proteins and the similar FAM62 genes and synaptotagmin genes of metazoans

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Craxton Molly

2007-07-01

Full Text Available Abstract Background Synaptotagmin genes are found in animal genomes and are known to function in the nervous system. Genes with a similar domain architecture as well as sequence similarity to synaptotagmin C2 domains have also been found in plant genomes. The plant genes share an additional region of sequence similarity with a group of animal genes named FAM62. FAM62 genes also have a similar domain architecture. Little is known about the functions of the plant genes and animal FAM62 genes. Indeed, many members of the large and diverse Syt gene family await functional characterization. Understanding the evolutionary relationships among these genes will help to realize the full implications of functional studies and lead to improved genome annotation. Results I collected and compared plant Syt-like sequences from the primary nucleotide sequence databases at NCBI. The collection comprises six groups of plant genes conserved in embryophytes: NTMC2Type1 to NTMC2Type6. I collected and compared metazoan FAM62 sequences and identified some similar sequences from other eukaryotic lineages. I found evidence of RNA editing and alternative splicing. I compared the intron patterns of Syt genes. I also compared Rabphilin and Doc2 genes. Conclusion Genes encoding proteins with N-terminal-transmembrane-C2 domain architectures resembling synaptotagmins, are widespread in eukaryotes. A collection of these genes is presented here. The collection provides a resource for studies of intron evolution. I have classified the collection into homologous gene families according to distinctive patterns of sequence conservation and intron position. The evolutionary histories of these gene families are traceable through the appearance of family members in different eukaryotic lineages. Assuming an intron-rich eukaryotic ancestor, the conserved intron patterns distinctive of individual gene families, indicate independent origins of Syt, FAM62 and NTMC2 genes. Resemblances

Inferring Gene Regulatory Networks Using Conditional Regulation Pattern to Guide Candidate Genes.

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Fei Xiao

Full Text Available Combining path consistency (PC algorithms with conditional mutual information (CMI are widely used in reconstruction of gene regulatory networks. CMI has many advantages over Pearson correlation coefficient in measuring non-linear dependence to infer gene regulatory networks. It can also discriminate the direct regulations from indirect ones. However, it is still a challenge to select the conditional genes in an optimal way, which affects the performance and computation complexity of the PC algorithm. In this study, we develop a novel conditional mutual information-based algorithm, namely RPNI (Regulation Pattern based Network Inference, to infer gene regulatory networks. For conditional gene selection, we define the co-regulation pattern, indirect-regulation pattern and mixture-regulation pattern as three candidate patterns to guide the selection of candidate genes. To demonstrate the potential of our algorithm, we apply it to gene expression data from DREAM challenge. Experimental results show that RPNI outperforms existing conditional mutual information-based methods in both accuracy and time complexity for different sizes of gene samples. Furthermore, the robustness of our algorithm is demonstrated by noisy interference analysis using different types of noise.

A review for detecting gene-gene interactions using machine learning methods in genetic epidemiology.

Science.gov (United States)

Koo, Ching Lee; Liew, Mei Jing; Mohamad, Mohd Saberi; Salleh, Abdul Hakim Mohamed

2013-01-01

Recently, the greatest statistical computational challenge in genetic epidemiology is to identify and characterize the genes that interact with other genes and environment factors that bring the effect on complex multifactorial disease. These gene-gene interactions are also denoted as epitasis in which this phenomenon cannot be solved by traditional statistical method due to the high dimensionality of the data and the occurrence of multiple polymorphism. Hence, there are several machine learning methods to solve such problems by identifying such susceptibility gene which are neural networks (NNs), support vector machine (SVM), and random forests (RFs) in such common and multifactorial disease. This paper gives an overview on machine learning methods, describing the methodology of each machine learning methods and its application in detecting gene-gene and gene-environment interactions. Lastly, this paper discussed each machine learning method and presents the strengths and weaknesses of each machine learning method in detecting gene-gene interactions in complex human disease.

A Review for Detecting Gene-Gene Interactions Using Machine Learning Methods in Genetic Epidemiology

Directory of Open Access Journals (Sweden)

Ching Lee Koo

2013-01-01

Full Text Available Recently, the greatest statistical computational challenge in genetic epidemiology is to identify and characterize the genes that interact with other genes and environment factors that bring the effect on complex multifactorial disease. These gene-gene interactions are also denoted as epitasis in which this phenomenon cannot be solved by traditional statistical method due to the high dimensionality of the data and the occurrence of multiple polymorphism. Hence, there are several machine learning methods to solve such problems by identifying such susceptibility gene which are neural networks (NNs, support vector machine (SVM, and random forests (RFs in such common and multifactorial disease. This paper gives an overview on machine learning methods, describing the methodology of each machine learning methods and its application in detecting gene-gene and gene-environment interactions. Lastly, this paper discussed each machine learning method and presents the strengths and weaknesses of each machine learning method in detecting gene-gene interactions in complex human disease.

Reference Gene Screening for Analyzing Gene Expression Across Goat Tissue

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Yu Zhang

2013-12-01

Full Text Available Real-time quantitative PCR (qRT-PCR is one of the important methods for investigating the changes in mRNA expression levels in cells and tissues. Selection of the proper reference genes is very important when calibrating the results of real-time quantitative PCR. Studies on the selection of reference genes in goat tissues are limited, despite the economic importance of their meat and dairy products. We used real-time quantitative PCR to detect the expression levels of eight reference gene candidates (18S, TBP, HMBS, YWHAZ, ACTB, HPRT1, GAPDH and EEF1A2 in ten tissues types sourced from Boer goats. The optimal reference gene combination was selected according to the results determined by geNorm, NormFinder and Bestkeeper software packages. The analyses showed that tissue is an important variability factor in genes expression stability. When all tissues were considered, 18S, TBP and HMBS is the optimal reference combination for calibrating quantitative PCR analysis of gene expression from goat tissues. Dividing data set by tissues, ACTB was the most stable in stomach, small intestine and ovary, 18S in heart and spleen, HMBS in uterus and lung, TBP in liver, HPRT1 in kidney and GAPDH in muscle. Overall, this study provided valuable information about the goat reference genes that can be used in order to perform a proper normalisation when relative quantification by qRT-PCR studies is undertaken.

Refining discordant gene trees.

Science.gov (United States)

Górecki, Pawel; Eulenstein, Oliver

2014-01-01

Evolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees, including the well-established Robinson-Foulds, gene duplication, and deep coalescence costs. While these costs have provided credible results for binary rooted gene trees, corresponding cost definitions for non-binary unrooted gene trees, which are frequently occurring in practice, are challenged by biological realism. We propose a natural extension of the well-established costs for comparing unrooted and non-binary gene trees with rooted binary species trees using a binary refinement model. For the duplication cost we describe an efficient algorithm that is based on a linear time reduction and also computes an optimal rooted binary refinement of the given gene tree. Finally, we show that similar reductions lead to solutions for computing the deep coalescence and the Robinson-Foulds costs. Our binary refinement of Robinson-Foulds, gene duplication, and deep coalescence costs for unrooted and non-binary gene trees together with the linear time reductions provided here for computing these costs significantly extends the range of trees that can be incorporated into approaches dealing with discordance.

The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.

Directory of Open Access Journals (Sweden)

Marion Ouedraogo

Full Text Available BACKGROUND: There has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the same sequence, duplicated genes can diverge strongly over evolution and take on different functions or regulated expression. However, information on the function and expression of duplicated genes remains sparse. Identifying groups of duplicated genes in different genomes and characterizing their expression and function would therefore be of great interest to the research community. The 'Duplicated Genes Database' (DGD was developed for this purpose. METHODOLOGY: Nine species were included in the DGD. For each species, BLAST analyses were conducted on peptide sequences corresponding to the genes mapped on a same chromosome. Groups of duplicated genes were defined based on these pairwise BLAST comparisons and the genomic location of the genes. For each group, Pearson correlations between gene expression data and semantic similarities between functional GO annotations were also computed when the relevant information was available. CONCLUSIONS: The Duplicated Gene Database provides a list of co-localised and duplicated genes for several species with the available gene co-expression level and semantic similarity value of functional annotation. Adding these data to the groups of duplicated genes provides biological information that can prove useful to gene expression analyses. The Duplicated Gene Database can be freely accessed through the DGD website at http://dgd.genouest.org.

[Key effect genes responding to nerve injury identified by gene ontology and computer pattern recognition].

Science.gov (United States)

Pan, Qian; Peng, Jin; Zhou, Xue; Yang, Hao; Zhang, Wei

2012-07-01

In order to screen out important genes from large gene data of gene microarray after nerve injury, we combine gene ontology (GO) method and computer pattern recognition technology to find key genes responding to nerve injury, and then verify one of these screened-out genes. Data mining and gene ontology analysis of gene chip data GSE26350 was carried out through MATLAB software. Cd44 was selected from screened-out key gene molecular spectrum by comparing genes' different GO terms and positions on score map of principal component. Function interferences were employed to influence the normal binding of Cd44 and one of its ligands, chondroitin sulfate C (CSC), to observe neurite extension. Gene ontology analysis showed that the first genes on score map (marked by red *) mainly distributed in molecular transducer activity, receptor activity, protein binding et al molecular function GO terms. Cd44 is one of six effector protein genes, and attracted us with its function diversity. After adding different reagents into the medium to interfere the normal binding of CSC and Cd44, varying-degree remissions of CSC's inhibition on neurite extension were observed. CSC can inhibit neurite extension through binding Cd44 on the neuron membrane. This verifies that important genes in given physiological processes can be identified by gene ontology analysis of gene chip data.

Radiopharmaceuticals to monitor the expression of transferred genes in gene transfer therapy

International Nuclear Information System (INIS)

Wiebe, L. I.

1997-01-01

The development and application of radiopharmaceuticals has, in many instances, been based on the pharmacological properties of therapeutic agents. The molecular biology-biotechnology revolution has had an important impact on treatment of diseases, in part through the reduced toxicity of 'biologicals', in part because of their specificity for interaction at unique molecular sites and in part because of their selective delivery to the target site. Immunotherapeutic approaches include the use of monoclonal antibodies (MABs), MAB-fragments and chemotactic peptides. Such agents currently form the basis of both diagnostic and immunotherapeutic radiopharmaceuticals. More recently, gene transfer techniques have been advanced to the point that a new molecular approach, gene therapy, has become a reality. Gene therapy offers an opportunity to attack disease at its most fundamental level. The therapeutic mechanism is based on the expression of a specific gene or genes, the product of which will invoke immunological, receptor-based or enzyme-based therapeutic modalities. Several approaches to gene therapy of cancer have been envisioned, the most clinically-advanced concepts involving the introduction of genes that will encode for molecular targets nor normally found in healthy mammalian cells. A number of gene therapy clinical trials are based on the introduction of the Herpes simplex virus type-1 (HSV-1) gene that encodes for viral thymidine kinase (tk+). Once HSV-1 tk+ is expressed in the target (cancer) cell, therapy can be effected by the administration of a highly molecularly-targeted and systemically non-toxic antiviral drug such as ganciclovir. The development of radiodiagnostic imaging in gene therapy will be reviewed, using HSV-1 tk+ and radioiodinated IVFRU as a basis for development of the theme. Molecular targets that could be exploited in gene therapy, other than tk+, will be identified

Radiopharmaceuticals to monitor the expression of transferred genes in gene transfer therapy

Energy Technology Data Exchange (ETDEWEB)

Wiebe, L I [University of Alberta, Edmonton (Canada). Noujaim Institute for Pharmaceutical Oncology Research

1997-10-01

The development and application of radiopharmaceuticals has, in many instances, been based on the pharmacological properties of therapeutic agents. The molecular biology-biotechnology revolution has had an important impact on treatment of diseases, in part through the reduced toxicity of `biologicals`, in part because of their specificity for interaction at unique molecular sites and in part because of their selective delivery to the target site. Immunotherapeutic approaches include the use of monoclonal antibodies (MABs), MAB-fragments and chemotactic peptides. Such agents currently form the basis of both diagnostic and immunotherapeutic radiopharmaceuticals. More recently, gene transfer techniques have been advanced to the point that a new molecular approach, gene therapy, has become a reality. Gene therapy offers an opportunity to attack disease at its most fundamental level. The therapeutic mechanism is based on the expression of a specific gene or genes, the product of which will invoke immunological, receptor-based or enzyme-based therapeutic modalities. Several approaches to gene therapy of cancer have been envisioned, the most clinically-advanced concepts involving the introduction of genes that will encode for molecular targets nor normally found in healthy mammalian cells. A number of gene therapy clinical trials are based on the introduction of the Herpes simplex virus type-1 (HSV-1) gene that encodes for viral thymidine kinase (tk+). Once HSV-1 tk+ is expressed in the target (cancer) cell, therapy can be effected by the administration of a highly molecularly-targeted and systemically non-toxic antiviral drug such as ganciclovir. The development of radiodiagnostic imaging in gene therapy will be reviewed, using HSV-1 tk+ and radioiodinated IVFRU as a basis for development of the theme. Molecular targets that could be exploited in gene therapy, other than tk+, will be identified

Environ: E00167 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available PD:C01530], Benzoxazinones, Polysaccharide, Protein Coix lacryma-jobi [TAX:714458] Same as: D06798 Poaceae (grass family) Coicis semen Major component: Coixenolide [CPD:C17566] ...

Identification of a Transcriptionally Forward α Gene and Two υ Genes within the Pigeon (Columba livia) IgH Gene Locus.

Science.gov (United States)

Huang, Tian; Wang, Xifeng; Si, Run; Chi, Hao; Han, Binyue; Han, Haitang; Cao, Gengsheng; Zhao, Yaofeng

2018-06-01

Compared with mammals, the bird Ig genetic system relies on gene conversion to create an Ab repertoire, with inversion of the IgA-encoding gene and very few cases of Ig subclass diversification. Although gene conversion has been studied intensively, class-switch recombination, a mechanism by which the IgH C region is exchanged, has rarely been investigated in birds. In this study, based on the published genome of pigeon ( Columba livia ) and high-throughput transcriptome sequencing of immune-related tissues, we identified a transcriptionally forward α gene and found that the pigeon IgH gene locus is arranged as μ-α-υ1-υ2. In this article, we show that both DNA deletion and inversion may result from IgA and IgY class switching, and similar junction patterns were observed for both types of class-switch recombination. We also identified two subclasses of υ genes in pigeon, which share low sequence identity. Phylogenetic analysis suggests that divergence of the two pigeon υ genes occurred during the early stage of bird evolution. The data obtained in this study provide new insight into class-switch recombination and Ig gene evolution in birds. Copyright © 2018 by The American Association of Immunologists, Inc.

Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models.

Science.gov (United States)

Mahony, Shaun; McInerney, James O; Smith, Terry J; Golden, Aaron

2004-03-05

Many current gene prediction methods use only one model to represent protein-coding regions in a genome, and so are less likely to predict the location of genes that have an atypical sequence composition. It is likely that future improvements in gene finding will involve the development of methods that can adequately deal with intra-genomic compositional variation. This work explores a new approach to gene-prediction, based on the Self-Organizing Map, which has the ability to automatically identify multiple gene models within a genome. The current implementation, named RescueNet, uses relative synonymous codon usage as the indicator of protein-coding potential. While its raw accuracy rate can be less than other methods, RescueNet consistently identifies some genes that other methods do not, and should therefore be of interest to gene-prediction software developers and genome annotation teams alike. RescueNet is recommended for use in conjunction with, or as a complement to, other gene prediction methods.

Evaluation of Appropriate Reference Genes for Gene Expression Normalization during Watermelon Fruit Development.

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Qiusheng Kong

Full Text Available Gene expression analysis in watermelon (Citrullus lanatus fruit has drawn considerable attention with the availability of genome sequences to understand the regulatory mechanism of fruit development and to improve its quality. Real-time quantitative reverse-transcription PCR (qRT-PCR is a routine technique for gene expression analysis. However, appropriate reference genes for transcript normalization in watermelon fruits have not been well characterized. The aim of this study was to evaluate the appropriateness of 12 genes for their potential use as reference genes in watermelon fruits. Expression variations of these genes were measured in 48 samples obtained from 12 successive developmental stages of parthenocarpic and fertilized fruits of two watermelon genotypes by using qRT-PCR analysis. Considering the effects of genotype, fruit setting method, and developmental stage, geNorm determined clathrin adaptor complex subunit (ClCAC, β-actin (ClACT, and alpha tubulin 5 (ClTUA5 as the multiple reference genes in watermelon fruit. Furthermore, ClCAC alone or together with SAND family protein (ClSAND was ranked as the single or two best reference genes by NormFinder. By using the top-ranked reference genes to normalize the transcript abundance of phytoene synthase (ClPSY1, a good correlation between lycopene accumulation and ClPSY1 expression pattern was observed in ripening watermelon fruit. These validated reference genes will facilitate the accurate measurement of gene expression in the studies on watermelon fruit biology.

Evaluation of Appropriate Reference Genes for Gene Expression Normalization during Watermelon Fruit Development.

Science.gov (United States)

Kong, Qiusheng; Yuan, Jingxian; Gao, Lingyun; Zhao, Liqiang; Cheng, Fei; Huang, Yuan; Bie, Zhilong

2015-01-01

Gene expression analysis in watermelon (Citrullus lanatus) fruit has drawn considerable attention with the availability of genome sequences to understand the regulatory mechanism of fruit development and to improve its quality. Real-time quantitative reverse-transcription PCR (qRT-PCR) is a routine technique for gene expression analysis. However, appropriate reference genes for transcript normalization in watermelon fruits have not been well characterized. The aim of this study was to evaluate the appropriateness of 12 genes for their potential use as reference genes in watermelon fruits. Expression variations of these genes were measured in 48 samples obtained from 12 successive developmental stages of parthenocarpic and fertilized fruits of two watermelon genotypes by using qRT-PCR analysis. Considering the effects of genotype, fruit setting method, and developmental stage, geNorm determined clathrin adaptor complex subunit (ClCAC), β-actin (ClACT), and alpha tubulin 5 (ClTUA5) as the multiple reference genes in watermelon fruit. Furthermore, ClCAC alone or together with SAND family protein (ClSAND) was ranked as the single or two best reference genes by NormFinder. By using the top-ranked reference genes to normalize the transcript abundance of phytoene synthase (ClPSY1), a good correlation between lycopene accumulation and ClPSY1 expression pattern was observed in ripening watermelon fruit. These validated reference genes will facilitate the accurate measurement of gene expression in the studies on watermelon fruit biology.

Gene composer: database software for protein construct design, codon engineering, and gene synthesis.

Science.gov (United States)

Lorimer, Don; Raymond, Amy; Walchli, John; Mixon, Mark; Barrow, Adrienne; Wallace, Ellen; Grice, Rena; Burgin, Alex; Stewart, Lance

2009-04-21

To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease

Gene Composer: database software for protein construct design, codon engineering, and gene synthesis

Directory of Open Access Journals (Sweden)

Mixon Mark

2009-04-01

Full Text Available Abstract Background To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. Results An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. Conclusion We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene

Evaluation of suitable reference genes for gene expression studies in bovine muscular tissue

Directory of Open Access Journals (Sweden)

Dunner Susana

2008-09-01

Full Text Available Abstract Background Real-time reverse transcriptase quantitative polymerase chain reaction (real-time RTqPCR is a technique used to measure mRNA species copy number as a way to determine key genes involved in different biological processes. However, the expression level of these key genes may vary among tissues or cells not only as a consequence of differential expression but also due to different factors, including choice of reference genes to normalize the expression levels of the target genes; thus the selection of reference genes is critical for expression studies. For this purpose, ten candidate reference genes were investigated in bovine muscular tissue. Results The value of stability of ten candidate reference genes included in three groups was estimated: the so called 'classical housekeeping' genes (18S, GAPDH and ACTB, a second set of genes used in expression studies conducted on other tissues (B2M, RPII, UBC and HMBS and a third set of novel genes (SF3A1, EEF1A2 and CASC3. Three different statistical algorithms were used to rank the genes by their stability measures as produced by geNorm, NormFinder and Bestkeeper. The three methods tend to agree on the most stably expressed genes and the least in muscular tissue. EEF1A2 and HMBS followed by SF3A1, ACTB, and CASC3 can be considered as stable reference genes, and B2M, RPII, UBC and GAPDH would not be appropriate. Although the rRNA-18S stability measure seems to be within the range of acceptance, its use is not recommended because its synthesis regulation is not representative of mRNA levels. Conclusion Based on geNorm algorithm, we propose the use of three genes SF3A1, EEF1A2 and HMBS as references for normalization of real-time RTqPCR in muscle expression studies.

Ageing genes

DEFF Research Database (Denmark)

Rattan, Suresh

2018-01-01

The idea of gerontogenes is in line with the evolutionary explanation of ageing as being an emergent phenomenon as a result of the imperfect maintenance and repair systems. Although evolutionary processes did not select for any specific ageing genes that restrict and determine the lifespan...... of an individual, the term ‘gerontogenes’ primarily refers to any genes that may seem to influence ageing and longevity, without being specifically selected for that role. Such genes can also be called ‘virtual gerontogenes’ by virtue of their indirect influence on the rate and process of ageing. More than 1000...... virtual gerontogenes have been associated with ageing and longevity in model organisms and humans. The ‘real’ genes, which do influence the essential lifespan of a species, and have been selected for in accordance with the evolutionary life history of the species, are known as the longevity assurance...

Correlating Information Contents of Gene Ontology Terms to Infer Semantic Similarity of Gene Products

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Mingxin Gan

2014-01-01

Full Text Available Successful applications of the gene ontology to the inference of functional relationships between gene products in recent years have raised the need for computational methods to automatically calculate semantic similarity between gene products based on semantic similarity of gene ontology terms. Nevertheless, existing methods, though having been widely used in a variety of applications, may significantly overestimate semantic similarity between genes that are actually not functionally related, thereby yielding misleading results in applications. To overcome this limitation, we propose to represent a gene product as a vector that is composed of information contents of gene ontology terms annotated for the gene product, and we suggest calculating similarity between two gene products as the relatedness of their corresponding vectors using three measures: Pearson’s correlation coefficient, cosine similarity, and the Jaccard index. We focus on the biological process domain of the gene ontology and annotations of yeast proteins to study the effectiveness of the proposed measures. Results show that semantic similarity scores calculated using the proposed measures are more consistent with known biological knowledge than those derived using a list of existing methods, suggesting the effectiveness of our method in characterizing functional relationships between gene products.

Compressibilidade de um Argissolo sob plantio direto escarificado e compactado Compressibility of a Paleudalf chisel plough and compacted under no-tillage