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Sample records for cell-free microtiter plate

  1. The Spheroplast Lysis Assay for Yeast in Microtiter Plate Format

    Science.gov (United States)

    Ovalle, Rafael; Spencer, Moyah; Thiwanont, Monthiwa; Lipke, Peter N.

    1999-01-01

    A yeast lysis assay in the microtiter plate format improved precision and throughput and led to an improved algorithm for estimating lag time. The assay reproducibly revealed differences of 10% or greater in the maximal lysis rate and 50% or greater in the lag time. Clonal differences were determined to be the major source of variation. Microtiter-based assays should be useful for screening for drug susceptibility and for analyzing mutant phenotypes. PMID:10427014

  2. Microtiter plate-based antibody microarrays for bacteria and toxins

    Science.gov (United States)

    Research has focused on the development of rapid biosensor-based, high-throughput, and multiplexed detection of pathogenic bacteria in foods. Specifically, antibody microarrays in 96-well microtiter plates have been generated for the purpose of selective detection of Shiga toxin-producing E. coli (...

  3. 96-well microtiter plates for biofouling simulation in biomedical settings.

    Science.gov (United States)

    Gomes, L C; Moreira, J M R; Teodósio, J S; Araújo, J D P; Miranda, J M; Simões, M; Melo, L F; Mergulhão, F J

    2014-01-01

    Microtiter plates with 96 wells are routinely used in biofilm research mainly because they enable high-throughput assays. These platforms are used in a variety of conditions ranging from static to dynamic operation using different shaking frequencies and orbital diameters. The main goals of this work were to assess the influence of nutrient concentration and flow conditions on biofilm formation by Escherichia coli in microtiter plates and to define the operational conditions to be used in order to simulate relevant biomedical scenarios. Assays were performed in static mode and in incubators with distinct orbital diameters using different concentrations of glucose, peptone and yeast extract. Computational fluid dynamics (CFD) was used to simulate the flow inside the wells for shaking frequencies ranging from 50 to 200 rpm and orbital diameters from 25 to 100 mm. Higher glucose concentrations enhanced adhesion of E. coli in the first 24 h, but variation in peptone and yeast extract concentration had no significant impact on biofilm formation. Numerical simulations indicate that 96-well microtiter plates can be used to simulate a variety of biomedical scenarios if the operating conditions are carefully set.

  4. Scale-down of vinegar production into microtiter plates using a custom-made lid.

    Science.gov (United States)

    Schlepütz, Tino; Büchs, Jochen

    2014-04-01

    As an important food preservative and condiment, vinegar is widely produced in industry by submerged acetic acid bacteria cultures. Although vinegar production is established on the large scale, up to now suitable microscale cultivation methods, e.g. using microtiter plates, are missing to enable high-throughput cultivation and to optimize fermentation conditions. In order to minimize evaporation losses of ethanol and acetic acid in a 48-well microtiter plate during vinegar production a new custom-made lid was developed. A diffusion model was used to calculate the dimensions of a hole in the lid to guarantee a suitable oxygen supply and level of ventilation. Reference fermentation was conducted in a 9-L bioreactor to enable the calculation of the proper cultivation conditions in the microtiter plate. The minimum dissolved oxygen tensions in the microtiter plate were between 7.5% and 23% of air saturation and in the same range as in the 9-L bioreactor. Evaporation losses of ethanol and acetic acid were less than 5% after 47 h and considerably reduced compared to those of microtiter plate fermentations with a conventional gas-permeable seal. Furthermore, cultivation times in the microtiter plate were with about 40 h as long as in the 9-L bioreactor. In conclusion, microtiter plate cultivations with the new custom-made lid provide a platform for high-throughput studies on vinegar production. Results are comparable to those in the 9-L bioreactor.

  5. Plasma-based surface modification of polystyrene microtiter plates for covalent immobilization of biomolecules.

    Science.gov (United States)

    North, Stella H; Lock, Evgeniya H; Cooper, Candace J; Franek, James B; Taitt, Chris R; Walton, Scott G

    2010-10-01

    In recent years, polymer surfaces have become increasingly popular for biomolecule attachment because of their relatively low cost and desirable bulk physicochemical characteristics. However, the chemical inertness of some polymer surfaces poses an obstacle to more expansive implementation of polymer materials in bioanalytical applications. We describe use of argon plasma to generate reactive hydroxyl moieties at the surface of polystyrene microtiter plates. The plates are then selectively functionalized with silanes and cross-linkers suitable for the covalent immobilization of biomolecules. This plasma-based method for microtiter plate functionalization was evaluated after each step by X-ray photoelectron spectroscopy, water contact angle analysis, atomic force microscopy, and bioimmobilization efficacy. We further demonstrate that the plasma treatment followed by silane derivatization supports direct, covalent immobilization of biomolecules on microtiter plates and thus overcomes challenging issues typically associated with simple physisorption. Importantly, biomolecules covalently immobilized onto microtiter plates using this plasma-based method retained functionality and demonstrated attachment efficiency comparable to commercial preactivated microtiter plates.

  6. Comparative evaluation of phototrophic microtiter plate cultivation against laboratory-scale photobioreactors.

    Science.gov (United States)

    Morschett, Holger; Schiprowski, Danny; Rohde, Jannis; Wiechert, Wolfgang; Oldiges, Marco

    2017-01-18

    Extended cultivation times, rendering phototrophic bioprocess development time inefficient, resulted in the recent development of micro-photobioreactors enabling accelerated process development. However, especially for laboratory photobioreactors, only little is known concerning the influence of design on process performance. Thus, the aim of the present investigation was to evaluate the scalability of a microtiter plate-based parallelized micro-photobioreactor against a representative set of established laboratory photobioreactors. Lipid production by Chlorella vulgaris was used as a model system. During exponential growth, the microtiter plate cultures achieved maximal growth rates of ca. 1.44 ± 0.02 day(-1) being in good agreement with the larger systems. Moreover, cultures in the micro-photobioreactor could be kept in the exponential phase up to the highest biomass concentrations most probably due to the beneficial light supply at this scale. Compared to the shake flask and test tube cultures, microtiter plate cultivation achieved an equivalent biomass yield, lipid content, and lipid fingerprint. In contrast, the flat-panel process resulted only in marginal productivity due to insufficient light supply. Thus, microtiter plates showed good scalability to the investigated laboratory photobioreactors as overall differences were rather small taking the differing scales into account.

  7. A Simple Method of Detecting Chlamydia Trachomatis Using Enzymatically Amplified DNA and Immobilized Probes on Microtiter Plate

    Institute of Scientific and Technical Information of China (English)

    王仁礼; 熊艳; 张龙兴; 蒋秀蓉; 张忠恕

    1998-01-01

    We have developed a simple and economical method for Chlamydia trachomatis detecting, called microtiter plate hybridization (PCR-MPtt) , which may replace standard PCR. This method is similar to that of an ELISA. Briefly, the PCR products labeled at the 5' termini with biotin were hybridized with probes immobilized on a microtiter well

  8. Mitigation of microtiter plate positioning effects using a block randomization scheme.

    Science.gov (United States)

    Roselle, Christopher; Verch, Thorsten; Shank-Retzlaff, Mary

    2016-06-01

    Microtiter plate-based assays are a common tool in biochemical and analytical labs. Despite widespread use, results generated in microtiter plate-based assays are often impacted by positional bias, in which variability in raw signal measurements are not uniform in all regions of the plate. Since small positional effects can disproportionately affect assay results and the reliability of the data, an effective mitigation strategy is critical. Commonly used mitigation strategies include avoiding the use of outer regions of the plate, replicating treatments within and between plates, and randomizing placement of treatments within and between plates. These strategies often introduce complexity while only partially mitigating positional effects and significantly reducing assay throughput. To reduce positional bias more effectively, we developed a novel block-randomized plate layout. Unlike a completely randomized layout, the block randomization scheme coordinates placement of specific curve regions into pre-defined blocks on the plate based on key experimental findings and assumptions about the distribution of assay bias and variability. Using the block-randomized plate layout, we demonstrated a mean bias reduction of relative potency estimates from 6.3 to 1.1 % in a sandwich enzyme-linked immunosorbent assay (ELISA) used for vaccine release. In addition, imprecision in relative potency estimates decreased from 10.2 to 4.5 % CV. Using simulations, we also demonstrated the impact of assay bias on measurement confidence and its relation to replication strategies. We outlined the underlying concepts of the block randomization scheme to potentially apply to other microtiter-based assays.

  9. Development of Colorimetric Microtiter Plate Assay for Assessment of Antimicrobials against Acanthamoeba

    OpenAIRE

    McBride, James; Ingram, Paul R.; Henriquez, Fiona L.; Roberts, Craig W.

    2005-01-01

    We have developed and optimized a 96-well microtiter plate assay, based on the reduction of alamarBlue, to assess the efficacies of much needed new antimicrobials against Acanthamoeba species. This assay has been optimized for determination of drug efficacy against two potentially pathogenic species, Acanthamoeba castellanii and Acanthamoeba polyphaga, and has been validated by comparison of their relative susceptibilities to chlorhexidine, a drug widely used to treat Acanthamoeba keratitis. ...

  10. Automated high-throughput infusion ESI-MS with direct coupling to a microtiter plate.

    Science.gov (United States)

    Felten, C; Foret, F; Minarik, M; Goetzinger, W; Karger, B L

    2001-04-01

    This paper describes the design and application of instrumentation for automated high-throughput infusion ESI-mass spectrometry. The approach, based on a subatmospheric ESI interface, allows sample introduction from a commercially available microtiter plate without the need for a separate fluid delivery system. The microtiter plate was placed vertically on a three-dimensional translation stage in front of the sampling ESI interface. A single, 7-cm, 20-microm-i.d. fused-silica capillary (total volume, 70 nL), with a tapered tip, served as a combination of sample delivery and spraying capillary. The tapered tip of the capillary was enclosed in a subatmospheric chamber attached in front of the orifice of the mass spectrometer. The sample aspiration rate (flow rate) was regulated by computer-controlled pneumatic valves, which allowed fast switching of the pressure in the subatmospheric ESI chamber. A flow-through wash device was positioned between the microtiter plate and the ESI interface. This design allowed alternate filling of the capillary with (a) sample from the wells and (b) wash solution from the wash device. Sample turnaround times of 10 s/sample, with a 120-nL sample consumption/analysis, and a duty cycle (percentage of total analysis time spent acquiring data) of 40% were achieved. The infusion system was demonstrated in the analysis of preparative HPLC fractions from a small molecule combinatorial library.

  11. Quantification of biofilm in microtiter plates: overview of testing conditions and practical recommendations for assessment of biofilm production by staphylococci.

    Science.gov (United States)

    Stepanović, Srdjan; Vuković, Dragana; Hola, Veronika; Di Bonaventura, Giovanni; Djukić, Slobodanka; Cirković, Ivana; Ruzicka, Filip

    2007-08-01

    The details of all steps involved in the quantification of biofilm formation in microtiter plates are described. The presented protocol incorporates information on assessment of biofilm production by staphylococci, gained both by direct experience as well as by analysis of methods for assaying biofilm production. The obtained results should simplify quantification of biofilm formation in microtiter plates, and make it more reliable and comparable among different laboratories.

  12. Improvement and scale-down of a Trichoderma reesei shake flask protocol to microtiter plates enables high-throughput screening.

    Science.gov (United States)

    Giese, Heiner; Kruithof, Paulien; Meier, Kristina; Sieben, Michaela; Antonov, Elena; Hommes, Ronald W J; Büchs, Jochen

    2014-12-01

    Nowadays, high-throughput screening is essential for determining the best microbial strains and fermentation conditions. Although microtiter plates allow higher throughput in screening than shake flasks, they do not guarantee sufficient oxygen supply if operated at unsuitable conditions. This is especially the case in viscous fermentations, potentially leading to poor liquid movement and surface growth. Therefore, in this study, two aims were pursued. First, an industrial Trichoderma reesei shake flask protocol is improved with respect to oxygen supply and production. Second, this improved shake flask protocol is scaled down into microtiter plate under consideration of similar oxygen supply. For this purpose, the respiration activity monitoring system (RAMOS) was applied. An approach based on a sulfite system was introduced to ensure equal maximum oxygen transfer capacities (OTRmax) in microtiter plates and shake flasks. OTRmax-values of 250 mL shake flasks and 24-well microtiter plates were determined in a wide range of operating conditions. These sulfite datasets were used to identify operating conditions leading to the same oxygen supply for T. reesei in shake flasks and 24-well microtiter plates. For 24-well microtiter plates, the shake flask OTRmax of 20 mmol/L/h of an industrial protocol was obtained under the following optimal operating conditions: 1 mL filling volume per well, 200 rpm shaking frequency and 50 mm shaking diameter. With these conditions almost identical oxygen transfer rates and product concentrations were measured in both scales. The proposed approach is a fast and accurate means to scale-down established screening procedures into microtiter plates to achieve high-throughput.

  13. Quantitative comparison between microfluidic and microtiter plate formats for cell-based assays.

    Science.gov (United States)

    Yin, Huabing; Pattrick, Nicola; Zhang, Xunli; Klauke, Norbert; Cordingley, Hayley C; Haswell, Steven J; Cooper, Jonathan M

    2008-01-01

    In this paper, we compare a quantitative cell-based assay measuring the intracellular Ca2+ response to the agonist uridine 5'-triphosphate in Chinese hamster ovary cells, in both microfluidic and microtiter formats. The study demonstrates that, under appropriate hydrodynamic conditions, there is an excellent agreement between traditional well-plate assays and those obtained on-chip for both suspended immobilized cells and cultured adherent cells. We also demonstrate that the on-chip assay, using adherent cells, provides the possibility of faster screening protocols with the potential for resolving subcellular information about local Ca2+ flux.

  14. Optimization of Salmonella Typhi biofilm assay on polypropylene microtiter plates using response surface methodology.

    Science.gov (United States)

    Ganjali Dashti, M; Abdeshahian, P; Sudesh, K; Phua, K K

    2016-01-01

    The objective of this study was to develop an optimized assay for Salmonella Typhi biofilm that mimics the environment of the gallbladder as an experimental model for chronic typhoid fever. Multi-factorial assays are difficult to optimize using traditional one-factor-at-a-time optimization methods. Response surface methodology (RSM) was used to optimize six key variables involved in S. Typhi biofilm formation on cholesterol-coated polypropylene 96-well microtiter plates. The results showed that bile (1.22%), glucose (2%), cholesterol (0.05%) and potassium chloride (0.25%) were critical factors affecting the amount of biofilm produced, but agitation (275 rpm) and sodium chloride (0.5%) had antagonistic effects on each other. Under these optimum conditions the maximum OD reading for biofilm formation was 3.4 (λ600 nm), and the coefficients of variation for intra-plate and inter-plate assays were 3% (n = 20) and 5% (n = 8), respectively. These results showed that RSM is an effective approach for biofilm assay optimization.

  15. A cell-free microtiter plate screen for improved [FeFe] hydrogenases.

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    James A Stapleton

    Full Text Available BACKGROUND: [FeFe] hydrogenase enzymes catalyze the production and dissociation of H(2, a potential renewable fuel. Attempts to exploit these catalysts in engineered systems have been hindered by the biotechnologically inconvenient properties of the natural enzymes, including their extreme oxygen sensitivity. Directed evolution has been used to improve the characteristics of a range of natural catalysts, but has been largely unsuccessful for [FeFe] hydrogenases because of a lack of convenient screening platforms. METHODOLOGY/PRINCIPAL FINDINGS: Here we describe an in vitro screening technology for oxygen-tolerant and highly active [FeFe] hydrogenases. Despite the complexity of the protocol, we demonstrate a level of reproducibility that allows moderately improved mutants to be isolated. We have used the platform to identify a mutant of the Chlamydomonas reinhardtii [FeFe] hydrogenase HydA1 with a specific activity approximately 4 times that of the wild-type enzyme. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate the feasibility of using the screen presented here for large-scale efforts to identify improved biocatalysts for energy applications. The system is based on our ability to activate these complex enzymes in E. coli cell extracts, which allows unhindered access to the protein maturation and assay environment.

  16. Surface-activated microtiter-plate microarray for simultaneous CRP quantification and viral antibody detection.

    Science.gov (United States)

    Viitala, Sari M; Jääskeläinen, Anne J; Kelo, Eira; Sirola, Helena; Moilanen, Kirsi; Suni, Jukka; Vaheri, Antti; Vapalahti, Olli; Närvänen, Ale

    2013-02-01

    Microarrays are widely used in high-throughput DNA and RNA hybridization tests and recently adopted to protein and small molecule interaction studies in basic research and diagnostics. Parallel detection of serum antibodies and antigens has several potential applications in epidemiologic research, vaccine development, and in the diagnosis of allergies, autoimmunity, and infectious diseases. This study demonstrates an immobilization method for immunoassay-based microarray in conventional 96-well polystyrene plates for a serologic diagnostic method combined with quantitative C-reactive protein (CRP) assay. A synthetic peptide (HIV-1), a recombinant protein (Puumala hantavirus nucleocapsid), and purified virus preparations (Sindbis and adenoviruses) were used as antigens for virus-specific antibody detection and monoclonal anti-CRP antibody for antigen detection. The microarray was based on conventional enzyme immunoassays and densitometry from photographed results. Peptide and recombinant antigens functioned well, while whole virus antigens gave discrepant results in 1 out of 23 samples from the reference method, tested with human sera with various antibody responses. The CRP results were in concordance in the concentration range 0.5-150 mg/L with 2 commercially available CRP assays: ReaScan rapid test (R(2) = 0.9975) and Cobas 6000 analyzer (R(2) =0.9595). The results indicate that microtiter plates provide a promising platform for further development of microarrays for parallel antibody and antigen detection.

  17. A rapid sandwich immunoassay for human fetuin A using agarose-3-aminopropyltriethoxysilane modified microtiter plate.

    Science.gov (United States)

    Vashist, Sandeep Kumar; Schneider, E Marion; Luong, John H T

    2015-07-09

    A rapid sandwich immunoassay (IA) with enhanced signal response for human fetuin A (HFA) was developed by modifying the surface of a KOH-treated polystyrene microtiter plate (MTP) with agarose and 3-aminopropyltriethoxysilane (APTES). The agarose-APTES complex binds covalently to the hydroxyl moiety of the MTP plate to serve as a binding platform for bioconjugation of EDC-activated anti-HFA antibody (Ab) via carbodiimide coupling. The one-step kinetics-based sandwich enzyme-linked immunosorbent assay (ELISA) enabled the detection of HFA in 30 min with a limit of detection (LOD) and a linear range of 0.02 ng mL(-1) and 1-243 ng mL(-1), respectively. It detected HFA spiked in diluted human whole blood and serum, and HFA in ethylenediaminetetraacetic acid (EDTA)-plasma of patients with high precision similar to that of conventional ELISA. The anti-HFA Ab-bound agarose-functionalized MTPs retained their functional activity after 6 weeks of storage in 0.1 M PBS, pH 7.4 at 4 °C.

  18. Development of a fluorometric microtiter plate based enzyme assay for MPS IVA (Morquio type A) using dried blood spots.

    Science.gov (United States)

    Ullal, Anirudh J; Millington, David S; Bali, Deeksha S

    2014-01-01

    Mucopolysaccharidosis type IVA or Morquio type-A disease is a hereditary lysosomal storage disorder caused by deficient activity of the lysosomal enzyme N-acetylgalactosamine-6-sulfate sulfatase (GALNS). The disease is caused by lysosomal accumulation of unprocessed glycosaminoglycans (GAGs) that manifests with severe to mild skeletal and cardiopulmonary abnormalities. We have developed a modified microtiter plate-based enzyme activity assay using dried blood spots and a fluorescent substrate for measuring specific GALNS activity to identify patients with MPS IVA.

  19. Fully automated synthesis of (phosphopeptide arrays in microtiter plate wells provides efficient access to protein tyrosine kinase characterization

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    Goldstein David J

    2005-01-01

    Full Text Available Abstract Background Synthetic peptides have played a useful role in studies of protein kinase substrates and interaction domains. Synthetic peptide arrays and libraries, in particular, have accelerated the process. Several factors have hindered or limited the applicability of various techniques, such as the need for deconvolution of combinatorial libraries, the inability or impracticality of achieving full automation using two-dimensional or pin solid phases, the lack of convenient interfacing with standard analytical platforms, or the difficulty of compartmentalization of a planar surface when contact between assay components needs to be avoided. This paper describes a process for synthesis of peptides and phosphopeptides on microtiter plate wells that overcomes previous limitations and demonstrates utility in determination of the epitope of an autophosphorylation site phospho-motif antibody and utility in substrate utilization assays of the protein tyrosine kinase, p60c-src. Results The overall reproducibility of phospho-peptide synthesis and multiplexed EGF receptor (EGFR autophosphorylation site (pY1173 antibody ELISA (9H2 was within 5.5 to 8.0%. Mass spectrometric analyses of the released (phosphopeptides showed homogeneous peaks of the expected molecular weights. An overlapping peptide array of the complete EGFR cytoplasmic sequence revealed a high redundancy of 9H2 reactive sites. The eight reactive phospopeptides were structurally related and interestingly, the most conserved antibody reactive peptide motif coincided with a subset of other known EGFR autophosphorylation and SH2 binding motifs and an EGFR optimal substrate motif. Finally, peptides based on known substrate specificities of c-src and related enzymes were synthesized in microtiter plate array format and were phosphorylated by c-Src with the predicted specificities. The level of phosphorylation was proportional to c-Src concentration with sensitivities below 0.1 Units of

  20. A high-throughput microtiter plate based method for the determination of peracetic acid and hydrogen peroxide.

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    Karson S Putt

    Full Text Available Peracetic acid is gaining usage in numerous industries who have found a myriad of uses for its antimicrobial activity. However, rapid high throughput quantitation methods for peracetic acid and hydrogen peroxide are lacking. Herein, we describe the development of a high-throughput microtiter plate based assay based upon the well known and trusted titration chemical reactions. The adaptation of these titration chemistries to rapid plate based absorbance methods for the sequential determination of hydrogen peroxide specifically and the total amount of peroxides present in solution are described. The results of these methods were compared to those of a standard titration and found to be in good agreement. Additionally, the utility of the developed method is demonstrated through the generation of degradation curves of both peracetic acid and hydrogen peroxide in a mixed solution.

  1. A high-throughput microtiter plate based method for the determination of peracetic acid and hydrogen peroxide.

    Science.gov (United States)

    Putt, Karson S; Pugh, Randall B

    2013-01-01

    Peracetic acid is gaining usage in numerous industries who have found a myriad of uses for its antimicrobial activity. However, rapid high throughput quantitation methods for peracetic acid and hydrogen peroxide are lacking. Herein, we describe the development of a high-throughput microtiter plate based assay based upon the well known and trusted titration chemical reactions. The adaptation of these titration chemistries to rapid plate based absorbance methods for the sequential determination of hydrogen peroxide specifically and the total amount of peroxides present in solution are described. The results of these methods were compared to those of a standard titration and found to be in good agreement. Additionally, the utility of the developed method is demonstrated through the generation of degradation curves of both peracetic acid and hydrogen peroxide in a mixed solution.

  2. Robo-Lector – a novel platform for automated high-throughput cultivations in microtiter plates with high information content

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    Kensy Frank

    2009-08-01

    Full Text Available Abstract Background In industry and academic research, there is an increasing demand for flexible automated microfermentation platforms with advanced sensing technology. However, up to now, conventional platforms cannot generate continuous data in high-throughput cultivations, in particular for monitoring biomass and fluorescent proteins. Furthermore, microfermentation platforms are needed that can easily combine cost-effective, disposable microbioreactors with downstream processing and analytical assays. Results To meet this demand, a novel automated microfermentation platform consisting of a BioLector and a liquid-handling robot (Robo-Lector was sucessfully built and tested. The BioLector provides a cultivation system that is able to permanently monitor microbial growth and the fluorescence of reporter proteins under defined conditions in microtiter plates. Three examplary methods were programed on the Robo-Lector platform to study in detail high-throughput cultivation processes and especially recombinant protein expression. The host/vector system E. coli BL21(DE3 pRhotHi-2-EcFbFP, expressing the fluorescence protein EcFbFP, was hereby investigated. With the method 'induction profiling' it was possible to conduct 96 different induction experiments (varying inducer concentrations from 0 to 1.5 mM IPTG at 8 different induction times simultaneously in an automated way. The method 'biomass-specific induction' allowed to automatically induce cultures with different growth kinetics in a microtiter plate at the same biomass concentration, which resulted in a relative standard deviation of the EcFbFP production of only ± 7%. The third method 'biomass-specific replication' enabled to generate equal initial biomass concentrations in main cultures from precultures with different growth kinetics. This was realized by automatically transferring an appropiate inoculum volume from the different preculture microtiter wells to respective wells of the main

  3. Scale-up from microtiter plate to laboratory fermenter: evaluation by online monitoring techniques of growth and protein expression in Escherichia coli and Hansenula polymorpha fermentations

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    Engelbrecht Christoph

    2009-12-01

    Full Text Available Abstract Background In the past decade, an enormous number of new bioprocesses have evolved in the biotechnology industry. These bioprocesses have to be developed fast and at a maximum productivity. Up to now, only few microbioreactors were developed to fulfill these demands and to facilitate sample processing. One predominant reaction platform is the shaken microtiter plate (MTP, which provides high-throughput at minimal expenses in time, money and work effort. By taking advantage of this simple and efficient microbioreactor array, a new online monitoring technique for biomass and fluorescence, called BioLector, has been recently developed. The combination of high-throughput and high information content makes the BioLector a very powerful tool in bioprocess development. Nevertheless, the scalabilty of results from the micro-scale to laboratory or even larger scales is very important for short development times. Therefore, engineering parameters regarding the reactor design and its operation conditions play an important role even on a micro-scale. In order to evaluate the scale-up from a microtiter plate scale (200 μL to a stirred tank fermenter scale (1.4 L, two standard microbial expression systems, Escherichia coli and Hansenula polymorpha, were fermented in parallel at both scales and compared with regard to the biomass and protein formation. Results Volumetric mass transfer coefficients (kLa ranging from 100 to 350 1/h were obtained in 96-well microtiter plates. Even with a suboptimal mass transfer condition in the microtiter plate compared to the stirred tank fermenter (kLa = 370-600 1/h, identical growth and protein expression kinetics were attained in bacteria and yeast fermentations. The bioprocess kinetics were evaluated by optical online measurements of biomass and protein concentrations exhibiting the same fermentation times and maximum signal deviations below 10% between the scales. In the experiments, the widely applied green

  4. An immunoassay for dibutyl phthalate based on direct hapten linkage to the polystyrene surface of microtiter plates.

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    Chenxi Wei

    Full Text Available BACKGROUND: Dibutyl phthalate (DBP is predominantly used as a plasticizer inplastics to make them flexible. Extensive use of phthalates in both industrial processes and other consumer products has resulted in the ubiquitous presence of phthalates in the environment. In order to better determine the level of pollution in the environment and evaluate the potential adverse effects of exposure to DBP, immunoassay for DBP was developed. METHODOLOGY/PRINCIPAL FINDINGS: A monoclonal antibody specific to DBP was produced from a stable hybridoma cell line generated by lymphocyte hybridoma technique. An indirect competitive enzyme-linked immunosorbent assay (icELISA employing direct coating of hapten on polystyrene microtiter plates was established for the detection of DBP. Polystyrene surface was first oxidized by permanganate in dilute sulfuric acid to generate carboxyl groups. Then dibutyl 4-aminophthalate, which is an analogue of DBP, was covalently linked to the carboxyl groups of polystyrene surface with 1-ethyl-3-(3-dimethylaminopropyl carbodiimide hydrochloride (EDC. Compared with conjugate coated format (IC(50=106 ng/mL, the direct hapten coated format (IC(50=14.6 ng/mL improved assay sensitivity after careful optimization of assay conditions. The average recovery of DBP from spiked water sample was 104.4% and the average coefficient of variation was 9.95%. Good agreement of the results obtained by the hapten coated icELISA and gas chromatography-mass spectrometry further confirmed the reliability and accuracy of the icELISA for the detection of DBP in certain plastic and cosmetic samples. CONCLUSIONS/SIGNIFICANCE: The stable and efficient hybridoma cell line obtained is an unlimited source of sensitive and specific antibody to DBP. The hapten coated format is proposed as generally applicable because the carboxyl groups on modified microtiter plate surface enables stable immobilization of aminated or hydroxylated hapten with EDC. The developed

  5. Colorimetric microtiter plate receptor-binding assay for the detection of freshwater and marine neurotoxins targeting the nicotinic acetylcholine receptors

    Science.gov (United States)

    Rubio, Fernando; Kamp, Lisa; Carpino, Justin; Faltin, Erin; Loftin, Keith A.; Molgó, Jordi; Aráoz, Rómulo

    2014-01-01

    Anatoxin-a and homoanatoxin-a, produced by cyanobacteria, are agonists of nicotinic acetylcholine receptors (nAChRs). Pinnatoxins, spirolides, and gymnodimines, produced by dinoflagellates, are antagonists of nAChRs. In this study we describe the development and validation of a competitive colorimetric, high throughput functional assay based on the mechanism of action of freshwater and marine toxins against nAChRs. Torpedo electrocyte membranes (rich in muscle-type nAChR) were immobilized and stabilized on the surface of 96-well microtiter plates. Biotinylated α-bungarotoxin (the tracer) and streptavidin-horseradish peroxidase (the detector) enabled the detection and quantitation of anatoxin-a in surface waters and cyclic imine toxins in shellfish extracts that were obtained from different locations across the US. The method compares favorably to LC/MS/MS and provides accurate results for anatoxin-a and cyclic imine toxins monitoring. Study of common constituents at the concentrations normally found in drinking and environmental waters, as well as the tolerance to pH, salt, solvents, organic and inorganic compounds did not significantly affect toxin detection. The assay allowed the simultaneous analysis of up to 25 samples within 3.5 h and it is well suited for on-site or laboratory monitoring of low levels of toxins in drinking, surface, and ground water as well as in shellfish extracts.

  6. Comparison of a quantitative microtiter method, a quantitative automated method, and the plate-count method for determining microbial complement resistance.

    Science.gov (United States)

    Lee, M D; Wooley, R E; Brown, J; Spears, K R; Nolan, L K; Shotts, E B

    1991-01-01

    A quantitative microtiter method for determining the degree of complement resistance or sensitivity of microorganisms is described. The microtiter method is compared with a quantitative automated system and the standard plate-count technique. Data were accumulated from 30 avian Escherichia coli isolates incubated at 35 C with either chicken plasma or heat-inactivated chicken plasma. Analysis of data generated by the automated system and plate-count techniques resulted in a classification of the microorganisms into three groups: those sensitive to the action of complement; those of intermediate sensitivity to the action of complement; and those resistant to the action of complement. Although the three methods studied did not agree absolutely, there were statistically significant correlations among them.

  7. Antibody Microarray for E. coli O157:H7 and Shiga Toxin in Microtiter Plates

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    Andrew G. Gehring

    2015-12-01

    Full Text Available Antibody microarray is a powerful analytical technique because of its inherent ability to simultaneously discriminate and measure numerous analytes, therefore making the technique conducive to both the multiplexed detection and identification of bacterial analytes (i.e., whole cells, as well as associated metabolites and/or toxins. We developed a sandwich fluorescent immunoassay combined with a high-throughput, multiwell plate microarray detection format. Inexpensive polystyrene plates were employed containing passively adsorbed, array-printed capture antibodies. During sample reaction, centrifugation was the only strategy found to significantly improve capture, and hence detection, of bacteria (pathogenic Escherichia coli O157:H7 to planar capture surfaces containing printed antibodies. Whereas several other sample incubation techniques (e.g., static vs. agitation had minimal effect. Immobilized bacteria were labeled with a red-orange-fluorescent dye (Alexa Fluor 555 conjugated antibody to allow for quantitative detection of the captured bacteria with a laser scanner. Shiga toxin 1 (Stx1 could be simultaneously detected along with the cells, but none of the agitation techniques employed during incubation improved detection of the relatively small biomolecule. Under optimal conditions, the assay had demonstrated limits of detection of ~5.8 × 105 cells/mL and 110 ng/mL for E. coli O157:H7 and Stx1, respectively, in a ~75 min total assay time.

  8. Determination of glucose using a coupled-enzymatic reaction with new fluoride selective optical sensing polymeric film coated in microtiter plate wells.

    Science.gov (United States)

    Abd-Rabboh, Hisham S M; Meyerhoff, Mark E

    2007-05-15

    The determination of glucose in beverages is demonstrated using newly developed fluoride selective optical sensing polymeric film that contains aluminum (III) octaethylporphyrin (Al[OEP]) ionophore and the chromoionophore ETH7075 cast at the bottom of wells of a 96-well polypropylene microtiter plate. The method uses a dual enzymatic reaction involving glucose oxidase enzyme (GOD) and horseradish peroxidase (HRP), along with an organofluoro-substrate (4-fluorophenol) as the source of fluoride ions. The concentration of fluoride ions after enzymatic reaction is directly proportional to the glucose level in the sample. The method has a detection limit of 0.8 mmol L(-1), a linear range of 0.9- 40 mmol L(-1) and a sensitivity of 0.125 absorbance unit/decade of glucose concentration. Glucose levels in several beverage samples determined using the proposed method correlate well with a reference spectrophotometric enzyme method based on detection of hydrogen peroxide using bromopyrogallol red dye (BPR). The new method can also be used to determine H(2)O(2) concentrations in the 0.1 - 50 mmol L(-1) range using a single enzymatic reaction involving H(2)O(2) oxidation of 4-fluorophenol catalyzed by HRP. The methodology could potentially be used to detect a wide range of substrates for which selective oxidase enzymes exist (to generate H(2)O(2)), with the high throughput of simple microtiter plate detection scheme.

  9. High-throughput system for screening of high L-lactic acid-productivity strains in deep-well microtiter plates.

    Science.gov (United States)

    Lv, Xiangyun; Song, Jiali; Yu, Bo; Liu, Huilan; Li, Chao; Zhuang, Yingping; Wang, Yonghong

    2016-11-01

    For strain improvement, robust and scalable high-throughput cultivation systems as well as simple and rapid high-throughput detection methods are crucial. However, most of the screening methods for lactic acid bacteria (LAB) strains were conducted in shake flasks and detected by high-performance liquid chromatography (HPLC), making the screening program laborious, time-consuming and costly. In this study, an integrated strategy for high-throughput screening of high L-lactic acid-productivity strains by Bacillus coagulans in deep-well microtiter plates (MTPs) was developed. The good agreement of fermentation results obtained in the MTPs platform with shake flasks confirmed that 24-well U-bottom MTPs could well alternate shake flasks for cell cultivation as a scale-down tool. The high-throughput pH indicator (bromocresol green) and L-lactate oxidase (LOD) assays were subsequently developed to qualitatively and quantitatively analyze L-lactic acid concentration. Together with the color halos method, the pH indicator assay and LOD assay, the newly developed three-step screening strategy has greatly accelerated the screening process for LAB strains with low cost. As a result, two high L-lactic acid-productivity mutants, IH6 and IIIB5, were successfully screened out, which presented, respectively, 42.75 and 46.10 % higher productivities than that of the parent strain in a 5-L bioreactor.

  10. A 96-well microtiter plate assay for high-throughput screening of Mycobacterium tuberculosis dTDP-d-glucose 4,6-dehydratase inhibitors.

    Science.gov (United States)

    Shi, Xiaoxia; Sha, Shanshan; Liu, Likun; Li, Xin; Ma, Yufang

    2016-04-01

    Mycobacterium tuberculosis dTDP-d-glucose 4,6-dehydratase (RmlB) is the second enzyme for the biosynthesis of dTDP-l-rhamnose, which is a sugar donor to the synthesis of the cell wall linker, d-N-acetylglucosamine-l-rhamnose. RmlB is essential to mycobacterial growth and is not found in humans; therefore, it is a potential target for developing new anti-tuberculosis drugs. So far, there has been no suitable method for high-throughput screening of RmlB inhibitors. Here, the recombinant M. tuberculosis RmlB was purified and an absorbance-based microtiter plate assay was developed for RmlB activity. It could be used for high-throughput screening of RmlB inhibitors. The kinetic properties of M. tuberculosis RmlB, including optimal pH, optimal temperature, the effect of metal ions, and the kinetic parameters, were determined with this assay. The inhibitory effects of dTTP and dTDP on M. tuberculosis RmlB were also studied with the assay.

  11. Validation of a high-throughput fermentation system based on online monitoring of biomass and fluorescence in continuously shaken microtiter plates

    Directory of Open Access Journals (Sweden)

    Kensy Frank

    2009-06-01

    Full Text Available Abstract Background An advanced version of a recently reported high-throughput fermentation system with online measurement, called BioLector, and its validation is presented. The technology combines high-throughput screening and high-information content by applying online monitoring of scattered light and fluorescence intensities in continuously shaken microtiter plates. Various examples in calibration of the optical measurements, clone and media screening and promoter characterization are given. Results Bacterial and yeast biomass concentrations of up to 50 g/L cell dry weight could be linearly correlated to scattered light intensities. In media screening, the BioLector could clearly demonstrate its potential for detecting different biomass and product yields and deducing specific growth rates for quantitatively evaluating media and nutrients. Growth inhibition due to inappropriate buffer conditions could be detected by reduced growth rates and a temporary increase in NADH fluorescence. GFP served very well as reporter protein for investigating the promoter regulation under different carbon sources in yeast strains. A clone screening of 90 different GFP-expressing Hansenula polymorpha clones depicted the broad distribution of growth behavior and an even stronger distribution in GFP expression. The importance of mass transfer conditions could be demonstrated by varying filling volumes of an E. coli culture in 96 well MTP. The different filling volumes cause a deviation in the culture growth and acidification both monitored via scattered light intensities and the fluorescence of a pH indicator, respectively. Conclusion The BioLector technology is a very useful tool to perform quantitative microfermentations under engineered reaction conditions. With this technique, specific yields and rates can be directly deduced from online biomass and product concentrations, which is superior to existing technologies such as microplate readers or optode

  12. Kinetic Tetrazolium Microtiter Assay

    Science.gov (United States)

    Pierson, Duane L.; Stowe, Raymond; Koenig, David

    1993-01-01

    Kinetic tetrazolium microtiter assay (KTMA) involves use of tetrazolium salts and Triton X-100 (or equivalent), nontoxic, in vitro color developer solubilizing colored metabolite formazan without injuring or killing metabolizing cells. Provides for continuous measurement of metabolism and makes possible to determine rate of action of antimicrobial agent in real time as well as determines effective inhibitory concentrations. Used to monitor growth after addition of stimulatory compounds. Provides for kinetic determination of efficacy of biocide, greatly increasing reliability and precision of results. Also used to determine relative effectiveness of antimicrobial agent as function of time. Capability of generating results on day of test extremely important in treatment of water and waste, disinfection of hospital rooms, and in pharmaceutical, agricultural, and food-processing industries. Assay also used in many aspects of cell biology.

  13. Parallel microwave chemistry in silicon carbide microtiter platforms: a review.

    Science.gov (United States)

    Kappe, C Oliver; Damm, Markus

    2012-02-01

    In this review, applications of silicon carbide-based microtiter platforms designed for use in combination with dedicated multimode microwave reactors are described. These platforms are employed not only for the efficient parallel synthesis of compound libraries, but also in the context of high-throughput reaction screening/optimization and a number of other (bio)analytical and biomedical applications. Since the semiconducting plate material (silicon carbide) is strongly microwave absorbing and possesses high thermal conductivity, no temperature gradients across the microtiter plate exist. Therefore, many of the disadvantages experienced in attempting to perform microtiter plate chemistry under conventional microwave conditions can be eliminated. In general, the silicon carbide-based microtiter platforms allow sealed vessel processing (either directly in the well or in glass vials placed into the wells) of volumes ranging from 0.02-3.0 mL at a maximum temperature/pressure limit of 200°C/20 bar. Depending on the specific plate and rotor configuration, a maximum of 80-192 transformations can be carried out in parallel in a single microwave irradiation experiment under strict temperature control. A platform type utilizing HPLC/GC vials as reaction vessels allows analysis directly from the reaction vessel eliminating the need for a transfer step from the reaction to the analysis vial. The latter system is particularly useful for analytical applications as well as reaction optimization/screening.

  14. A novel microtiter plate radioimmunoassay of insulin autoantibody%胰岛素自身抗体微量平板放射免疫法的建立与应用

    Institute of Scientific and Technical Information of China (English)

    黄干; 李璋巍; 金河来; 王霞; 王建平; 周智广

    2009-01-01

    Objective Insulin autoantibody (IAA) is known to exist in sera of type 1 diabetes mellitus (T1DM) patients and pre-T1DM individuals. The aim of this study was to establish a novel microtiter plate radioimmunoassay (RIA) for IAA and evaluate its clinical value. Methods Diluted 125Ⅰ-insulin was mixed with 5 ul serum samples in a 96-well microtiter plate and then incubated for 72 h on an orbital plate shaker (4℃). The immunocomplexes were transferred to another protein a coated Millipore plate, and then the plate was washed with Tri-Buffered Saline Tween-20 (TBT) buffer. Counts per minute (CPM) was measured with liquid scintillation and luminescence counter. The positive cut-off point of IAA index was defined as ≥0.06 based on the 99-percentile of the distribution in 317 healthy individuals. The specificity and sensitivity of the assay were calculated from the samples provided by the fourth Diabetes Autoantibodies Standardization Program (DASP 2005). The IAA levels were determined in 71 T1 DM and 551 newly diagnosed type 2 diabetes (T2DM) patients, and 317 healthy controls. The t test, non-parametric test, x2 test and linear correlation analysis were performed on the data using SPSS 11.5 software. The concordance rate was estimated with Kappa value. Results (1) The optimized testing condition was described as 2×104 CPM of 125Ⅰ-insulin, 5 ul serum sample and slowly horizontal shaking for 72 h. (2) The intra-assay CV was 4.8%-8.9% and inter-assay CV was 6.4%-10.5%. Based on DASP 2005 samples, the specificity and sensitivity of the assay were 97% (97/100) and 50% (25/50), respectively. Ninety-six serum samples with different IAA levels were selected and tested to compare between our new method and a domestic IAA RIA kit. The results showed that the IAA indices from the two methods were positively correlated (r= 0.678, P0.05). Conclusions Our proposed microtiter plate RIA method for IAA is highly sensitive and specific, likely to be feasible for clinical

  15. A comparison of titers of anti-Brucella antibodies of naturally infected and healthy vaccinated cattle by standard tube agglutination test, microtiter plate agglutination test, indirect hemagglutination assay, and indirect enzyme-linked immunosorbent assay

    Directory of Open Access Journals (Sweden)

    Anju Mohan

    2016-07-01

    Full Text Available Aim: We determined the antibody response in cattle naturally infected with brucellosis and normal healthy adult cattle vaccinated during calf hood with strain 19. Materials and Methods: The antibody titers were measured by standard tube agglutination test (STAT, microtiter plate agglutination test (MAT, indirect hemagglutination assay (IHA, and indirect enzyme-linked immunosorbent assay (iELISA as per standard protocols. Results: The mean STAT titers were 1.963±0.345 in infected cattle and 1.200±0.155 in healthy vaccinated cattle. The difference was extremely significant (p<0.0001. The mean MAT titers were 2.244±0.727 in infected cattle and 1.200±0.155 in healthy vaccinated cattle. The difference was very significant (p<0.005. The mean IHA titers in infected cattle were 2.284±0.574, and those in healthy vaccinated cattle were 1.200±0.155. The difference was extremely significant (p=0.0002. However, the difference in mean iELISA titers of infected cattle (1.3678±0.014 and healthy vaccinated cattle (1.367±0.014 was non-significant. The infected animals showed very high titers of agglutinating antibodies compared to the vaccinated animals. However, it cannot be ascertained whether these antibodies are due to vaccine or response to infection. Since the infected animals had been vaccinated earlier, the current infection may suggest that vaccination was unable to induce protective levels of antibody. The heightened antibody response after infection may also indicate a secondary immune response to the antigens common to the vaccine strain and wild Brucella organisms. Conclusion: The brucellosis infected animals showed very high titers of agglutinating antibodies compared to the vaccinated animals.

  16. Cell-free synthesis and multifold screening of Candida antarctica lipase B (CalB) variants after combinatorial mutagenesis of hot spots.

    Science.gov (United States)

    Park, Chang-Gil; Kwon, Min-A; Song, Jae-Kwang; Kim, Dong-Myung

    2011-01-01

    We have developed a strategy for rapid and combinatorial optimization of the hot spot residues of enzymes. After combinatorial randomization of target locations in the Candida antarctica lipase B (CalB) gene, the individual variant genes isolated in the E.coli cells were expressed in the cell-free protein synthesis system to analyze different parameters of the resulting CalB variants. The enzymatic assays for the hydrolysis of para-nitrophenyl-ester (pNP-ester) and triglyceride, synthesis of wax ester, and thermal stability of the variant enzymes were carried out simultaneously in 96-well microtiter plates. From the 1,000 variant genes tested in each assay, we were able to identify a series of the variant enzymes having markedly improved hydrolytic, synthetic activity, or thermal stability. The improved traits of the cell-free selected CalB variants were well reproduced when the corresponding genes were expressed in Pichia pastoris. Therefore, we expect that the proposed strategy of cell-free expression screening can serve as a viable option for rapid and precise tuning of enzyme molecules, not only for analytical purposes but also for industrial applications through large scale production using microbial cells transformed with variant genes selected from the cell-free expression screening.

  17. Microtiter micromass cultures of limb-bud mesenchymal cells.

    Science.gov (United States)

    Paulsen, D F; Solursh, M

    1988-02-01

    A method is described for growing high-density micromass cultures of chick and mouse limb mesenchyme cells in 96-well microtiter plates (microT microM cultures). Rapid quantitative estimates of chondrogenic expression were obtained by automated spectrophotometric analysis of Alcian-blue-stained cartilage matrix extracts performed in the wells in which the cells had been grown. Quantitative estimates of myogenic expression were obtained similarly using anti-sarcomere myosin monoclonal antibody and modified ELISA techniques. This microT microM-ELISA method may be adapted for use with other antigens for which specific antibodies are available. These methods were used to compare cartilage and muscle differentiation in 1 to 4 d microT microM cultures grown in serum-containing (SCM) and defined (DM) media. The DM contains minimal additives (insulin, hydrocortisone, and in some cases, ascorbate or transferrin) and supports both chondrogenesis and myogenesis. The colorimetric analyses agree well with the morphologic appraisal of chondrogenesis and myogenesis. Similar numbers of cartilage nodules formed in all cultures, but in DM the nodules failed to enlarge; explaining the reduced matrix synthesis in DM as compared with SCM, and suggesting that nodule enlargement is a discrete, serum-dependent step. Studies of selected additives to DM show that transferrin enhances myogenesis, ascorbic acid enhances chondrogenesis, and retinoic acid inhibits chondrogenesis. Together, the microT microM system, in situ colorimetric assays of chondrogenesis and myogenesis, and DM will allow rapid prescreening of teratogens and screening of various bioactive compounds (e.g., hormones, growth factors, vitamins, adhesion factors) for effects on limb mesenchymal cell differentiation.

  18. Spontaneous and cytokine induced basophil adhesion evaluated by microtiter assay

    DEFF Research Database (Denmark)

    Quan, Sha; Poulsen, Lars K; Reimert, Claus Michael;

    2002-01-01

    We have developed a microtiter assay for evaluating basophil spontaneous adhesion to extracellular matrix (ECM) proteins exemplified by fibronectin and cytokine induced basophil adhesion to bovine serum albumin (BSA). The percentage of basophils adhering to either ECM or BSA was quantified...

  19. PLATE

    DEFF Research Database (Denmark)

    Kling, Joyce; Hjulmand, Lise-Lotte

    2008-01-01

    Copenhagen Business School (CBS) finds itself needing to address the issue of English-medium instruction for its increasing number of foreign exchange and full degree students. With internationalisation as a main pillar of the institution’s agenda, there are concerns whether the teaching faculty......’s level of English is sufficient for the increasing number of courses offered in English each semester. This paper addresses these concerns and describes a pilot project initiated in 2003 at CBS to gauge the overall English language proficiency of those teaching content courses in English. Through...... the Project in Language Assessment for Teaching in English (PLATE) language professionals from CBS’s Language Center observe teachers and provide feedback using evaluation criteria from the Common European Framework for Reference (CEFR) supplemented by some additional criteria which take the LSP nature...

  20. Microtiter plate based colorimetric assay for characterization of dehalogenation activity of GAC/Fe0 composite

    DEFF Research Database (Denmark)

    Hwang, Yuhoon; Salatas, Apostolos; Mines, Paul D.

    2015-01-01

    of nZVI and its composite with granular activated carbon (GAC). The assay focused on analysis of reaction products rather than its mother compounds, which gives more accurate quantification of reductive activity. The colorimetric assays were developed to quantify three reaction products, ammonia...

  1. Fluorescence assay for mitochondrial permeability transition in cardiomyocytes cultured in a microtiter plate

    DEFF Research Database (Denmark)

    Christensen, Marie Louise Muff; Braunstein, Thomas Hartig; Treiman, Marek

    2008-01-01

    by MPTP, as evidenced by inhibition in the presence of cyclosporin A (0.2-2 microM) and facilitation by pH 6.2. Delta F due to Delta Psi m-dissipating agent carbonyl cyanide p-trifluoromethoxyphenylhydrazone (FCCP) or alamethicin (10 microM) was insensitive to either pH or cyclosporin A. Inhibition of Ca......(2+)-induced (but not of FCCP- or alamethicin-induced) Delta F by glycogen synthase kinase 3beta (GSK3 beta) antagonist SB216763 and adenosine, acting at the level of intracellular signaling and plasma membrane receptors, respectively, is shown to illustrate potential applications of this assay...

  2. Maintaining Wolbachia in Cell-free Medium

    OpenAIRE

    Gamston, Courtney; Rasgon, Jason

    2007-01-01

    In this video protocol, procedures are demonstrated to (1) purify Wolbachia symbionts out of cultured mosquito cells, (2) use a fluorescent assay to ascertain the viability of the purified Wolbachia and (3) maintain the now extracellular Wolbachia in cell-free medium. Purified Wolbachia remain alive in the extracellular phase but do not replicate until re-inoculated into eukaryotic cells. Extracellular Wolbachia purified in this manner will remain viable for at least a week at ...

  3. Cell-free fetal DNA and cell-free total DNA levels in spontaneous abortion with fetal chromosomal aneuploidy.

    Directory of Open Access Journals (Sweden)

    Ji Hyae Lim

    Full Text Available BACKGROUND: Cell-free fetal DNA and cell-free total DNA in maternal circulation have been proposed as potential markers for noninvasive monitoring of the placental condition during the pregnancy. However, the correlation of and change in cell-free fetal DNA and cell-free total DNA in spontaneous abortion (SA with fetal chromosomal aneuploidy have not yet been reported. Therefore, we investigated cell-free fetal DNA and cell-free total DNA levels in SA women with fetal chromosomal aneuploidy. METHODOLOGY/PRINCIPAL FINDINGS: A nested case-control study was conducted with maternal plasma collected from 268 women in their first trimester of pregnancy. Subjects included 41 SA with normal fetal karyotype, 26 SA with fetal chromosomal aneuploidy, and 201 normal controls. The unmethylated PDE9A gene was used to measure the maternal plasma levels of cell-free fetal DNA. The GAPDH gene was used to measure the maternal plasma levels of cell-free total DNA. The diagnostic accuracy was measured using receiver-operating characteristic (ROC curves. Levels of cell-free fetal DNA and cell-free total DNA were significantly higher in both SA women with normal fetal karyotype and SA women with fetal chromosomal aneuploidy in comparison with the normal controls (P<0.001 in both. The correlation between cell-free fetal DNA and cell-free total DNA levels was stronger in the normal controls (r = 0.843, P<0.001 than in SA women with normal karyotype (r = 0.465, P = 0.002 and SA women with fetal chromosomal aneuploidy (r = 0.412, P = 0.037. The area under the ROC curve for cell-free fetal DNA and cell-free total DNA was 0.898 (95% CI, 0.852-0.945 and 0.939 (95% CI, 0.903-0.975, respectively. CONCLUSIONS: Significantly high levels of cell-free fetal DNA and cell-free total DNA were found in SA women with fetal chromosomal aneuploidy. Our findings suggest that cell-free fetal DNA and cell-free total DNA may be useful biomarkers for the prediction of SA

  4. The emerging age of cell-free synthetic biology.

    Science.gov (United States)

    Smith, Mark Thomas; Wilding, Kristen M; Hunt, Jeremy M; Bennett, Anthony M; Bundy, Bradley C

    2014-08-25

    The engineering of and mastery over biological parts has catalyzed the emergence of synthetic biology. This field has grown exponentially in the past decade. As increasingly more applications of synthetic biology are pursued, more challenges are encountered, such as delivering genetic material into cells and optimizing genetic circuits in vivo. An in vitro or cell-free approach to synthetic biology simplifies and avoids many of the pitfalls of in vivo synthetic biology. In this review, we describe some of the innate features that make cell-free systems compelling platforms for synthetic biology and discuss emerging improvements of cell-free technologies. We also select and highlight recent and emerging applications of cell-free synthetic biology.

  5. Cell-free synthetic biology for environmental sensing and remediation.

    Science.gov (United States)

    Karig, David K

    2017-02-19

    The fields of biosensing and bioremediation leverage the phenomenal array of sensing and metabolic capabilities offered by natural microbes. Synthetic biology provides tools for transforming these fields through complex integration of natural and novel biological components to achieve sophisticated sensing, regulation, and metabolic function. However, the majority of synthetic biology efforts are conducted in living cells, and concerns over releasing genetically modified organisms constitute a key barrier to environmental applications. Cell-free protein expression systems offer a path towards leveraging synthetic biology, while preventing the spread of engineered organisms in nature. Recent efforts in the areas of cell-free approaches for sensing, regulation, and metabolic pathway implementation, as well as for preserving and deploying cell-free expression components, embody key steps towards realizing the potential of cell-free systems for environmental sensing and remediation.

  6. Creating a completely "cell-free" system for protein synthesis.

    Science.gov (United States)

    Smith, Mark Thomas; Bennett, Anthony M; Hunt, Jeremy M; Bundy, Bradley C

    2015-01-01

    Cell-free protein synthesis is a promising tool to take biotechnology outside of the cell. A cell-free approach provides distinct advantages over in vivo systems including open access to the reaction environment and direct control over all chemical components for facile optimization and synthetic biology integration. Promising applications of cell-free systems include portable diagnostics, biotherapeutics expression, rational protein engineering, and biocatalyst production. The highest yielding and most economical cell-free systems use an extract composed of the soluble component of lysed Escherichia coli. Although E. coli lysis can be highly efficient (>99.999%), one persistent challenge is that the extract remains contaminated with up to millions of cells per mL. In this work, we examine the potential of multiple decontamination strategies to further reduce or eliminate bacteria in cell-free systems. Two strategies, sterile filtration and lyophilization, effectively eliminate contaminating cells while maintaining the systems' protein synthesis capabilities. Lyophilization provides the additional benefit of long-term stability at storage above freezing. Technologies for personalized, portable medicine and diagnostics can be expanded based on these foundational sterilized and completely "cell-free" systems.

  7. Cell-free synthetic biology: thinking outside the cell.

    Science.gov (United States)

    Hodgman, C Eric; Jewett, Michael C

    2012-05-01

    Cell-free synthetic biology is emerging as a powerful approach aimed to understand, harness, and expand the capabilities of natural biological systems without using intact cells. Cell-free systems bypass cell walls and remove genetic regulation to enable direct access to the inner workings of the cell. The unprecedented level of control and freedom of design, relative to in vivo systems, has inspired the rapid development of engineering foundations for cell-free systems in recent years. These efforts have led to programmed circuits, spatially organized pathways, co-activated catalytic ensembles, rational optimization of synthetic multi-enzyme pathways, and linear scalability from the micro-liter to the 100-liter scale. It is now clear that cell-free systems offer a versatile test-bed for understanding why nature's designs work the way they do and also for enabling biosynthetic routes to novel chemicals, sustainable fuels, and new classes of tunable materials. While challenges remain, the emergence of cell-free systems is poised to open the way to novel products that until now have been impractical, if not impossible, to produce by other means.

  8. Plasminogen activator activity and plasma-coagulum lysis measured by use of optimized fibrin gel structure preformed in microtiter plates

    DEFF Research Database (Denmark)

    Sidelmann, Johannes Jakobsen; Jespersen, J; Gram, J

    1995-01-01

    gel, and the absorbance of the gel was recorded at 405 nm. After incubation for 17 h at 25 degrees C, the absorbance was measured again. The difference in absorbance was proportional to the concentration of plasminogen activator, such that the dose-response curves were linear when the difference...

  9. Whole-cell microtiter plate screening assay for terminal hydroxylation of fatty acids by P450s.

    Science.gov (United States)

    Weissenborn, Martin J; Notonier, Sandra; Lang, Sarah-Luise; Otte, Konrad B; Herter, Susanne; Turner, Nicholas J; Flitsch, Sabine L; Hauer, Bernhard

    2016-05-04

    A readily available galactose oxidase (GOase) variant was used to develop a whole cell screening assay. This endpoint detection system was applied in a proof-of-concept approach by screening a focussed mutant library. This led to the discovery of the thus far most active P450 Marinobacter aquaeolei mutant catalysing the terminal hydroxylation of fatty acids.

  10. Tuning a 96-Well Microtiter Plate Fluorescence-Based Assay to Identify AGE Inhibitors in Crude Plant Extracts

    Directory of Open Access Journals (Sweden)

    Luc Séro

    2013-11-01

    Full Text Available Advanced glycation end-products (AGEs are involved in the pathogenesis of numerous diseases. Among them, cellular accumulation of AGEs contributes to vascular complications in diabetes. Besides using drugs to lower blood sugar, a balanced diet and the intake of herbal products potentially limiting AGE formation could be considered beneficial for patients’ health. The current paper presents a simple and cheap high-throughput screening (HTS assay based on AGE fluorescence and suitable for plant extract screening. We have already implemented an HTS assay based on vesperlysines-like fluorescing AGEs quickly (24 h formed from BSA and ribose under physiological conditions. However, interference was noted when fluorescent compounds and/or complex mixtures were tested. To overcome these problems and apply this HTS assay to plant extracts, we developed a technique for systematic quantification of both vesperlysines (λexc 370 nm; λem 440 nm and pentosidine-like (λexc 335 nm; λem 385 nm AGEs. In a batch of medicinal and food plant extracts, hits were selected as soon as fluorescence decreased under a fixed threshold for at least one wavelength. Hits revealed during this study appeared to contain well-known and powerful anti-AGE substances, thus demonstrating the suitability of this assay for screening crude extracts (0.1 mg/mL. Finally, quercetin was found to be a more powerful reference compound than aminoguanidine in such assay.

  11. Controls to validate plasma samples for cell free DNA quantification

    DEFF Research Database (Denmark)

    Pallisgaard, Niels; Spindler, Karen-Lise Garm; Andersen, Rikke Fredslund;

    2015-01-01

    Recent research has focused on the utility of cell free DNA (cfDNA) in serum and plasma for clinical application, especially in oncology. The literature holds promise of cfDNA as a valuable tumour marker to be used for treatment selection, monitoring and follow-up. The results, however, are diver...

  12. Cell-Free, De Nova Synthesis of Poliovirus

    Science.gov (United States)

    Molla, Akhteruzzaman; Paul, Aniko V.; Wimmer, Eckard

    1991-12-01

    Cell-free translation of poliovirus RNA in an extract of uninfected human (HeLa) cells yielded viral proteins through proteolysis of the polyprotein. In the extract, newly synthesized proteins catalyzed poliovirus-specific RNA synthesis, and formed infectious poliovirus de novo. Newly formed virions were neutralized by type-specific antiserum, and infection of human cells with them was prevented by poliovirus receptor-specific antibodies. Poliovirus synthesis was increased nearly 70-fold when nucleoside triphosphates were added, but it was abolished in the presence of inhibitors of translation or viral genome replication. The ability to conduct cell-free synthesis of poliovirus will aid in the study of picornavirus proliferation and in the search for the control of picornaviral disease.

  13. Rapid depletion of dissolved oxygen in 96 well microtitre plate Staphylococcus epidermidis biofilm assays promotes biofilm development and is influenced by inoculum cell concentration

    OpenAIRE

    Cotter, John J.; O'Gara, James P.; Casey, Eoin

    2009-01-01

    Biofilm-related research using 96-well microtiter plates involves static incubation of plates indiscriminate of environmental conditions, making oxygen availability an important variable which has not been considered to date. By directly measuring dissolved oxygen concentration over time we report here that dissolved oxygen is rapidly consumed in Staphylococcus epidermidis biofilm cultures grown in 96-well plates irrespective of the oxygen concentration in the gaseous environment in which the...

  14. Cell-Free Synthesis Meets Antibody Production: A Review

    Directory of Open Access Journals (Sweden)

    Marlitt Stech

    2015-01-01

    Full Text Available Engineered antibodies are key players in therapy, diagnostics and research. In addition to full size immunoglobulin gamma (IgG molecules, smaller formats of recombinant antibodies, such as single-chain variable fragments (scFv and antigen binding fragments (Fab, have emerged as promising alternatives since they possess different advantageous properties. Cell-based production technologies of antibodies and antibody fragments are well-established, allowing researchers to design and manufacture highly specific molecular recognition tools. However, as these technologies are accompanied by the drawbacks of being rather time-consuming and cost-intensive, efficient and powerful cell-free protein synthesis systems have been developed over the last decade as alternatives. So far, prokaryotic cell-free systems have been the focus of interest. Recently, eukaryotic in vitro translation systems have enriched the antibody production pipeline, as these systems are able to mimic the natural pathway of antibody synthesis in eukaryotic cells. This review aims to overview and summarize the advances made in the production of antibodies and antibody fragments in cell-free systems.

  15. Development of the nanotiter plate for use in antibody and cell array technologies

    Science.gov (United States)

    Ramdutt, Devin; Lui, Rodney; Davies, Kerrie; Boswell, Rod W.; dos Remedios, Cristobal G.; Charles, Christine; Bilek, Marcela M.; McKenzie, David R.

    2005-02-01

    The design and fabrication of biomedical tools using techniques common in microelectronics is becoming established procedure. In our research, we use gaseous plasma dry etching to form microstructures on silicon wafers. These are intended for use in capturing and binding antibodies and live cells in an array to be used in High Throughput Screening (HTS) and High Content Screening (HCS) of new pharmaceuticals. We call this new arraying plate the "Nanotiter" plate. The benefit of our design (100 x 100 wells in a 25 x 25 mm array) over current 96-, 384- and 1056-well microtiter plates are that the number of samples (wells) that can be tested in one plate scan can be substantially increased, the wells can be rapidly and effectively washed, and the well surfaces can be modified to modulate ligand binding. Simple crowding of wells on a plate can result in cross contamination of samples in adjacent wells during the washing. Furthermore, motile cells may migrate between the wells. 1056 microtiter plates currently cannot be washed, and washing 384 plates is problematic. Our design incorporates plasma-deposited polymers that functionally bind antibodies (or other proteins) in but not between wells. Furthermore, the wells can be shaped to minimize cell migration. Inverting the plate on a wash solution allows unbound cells to simply fall away under gravity thus minimising the contamination of adjacent wells. Thus, our Nanotiter plate represents a substantial improvement over existing technology.

  16. Cell-free DNA screening and sex chromosome aneuploidies.

    Science.gov (United States)

    Mennuti, Michael T; Chandrasekaran, Suchitra; Khalek, Nahla; Dugoff, Lorraine

    2015-10-01

    Cell-free DNA (cfDNA) testing is increasingly being used to screen pregnant women for fetal aneuploidies. This technology may also identify fetal sex and can be used to screen for sex chromosome aneuploidies (SCAs). Physicians offering this screening will need to be prepared to offer comprehensive prenatal counseling about these disorders to an increasing number of patients. The purpose of this article is to consider the source of information to use for counseling, factors in parental decision-making, and the performance characteristics of cfDNA testing in screening for SCAs. Discordance between ultrasound examination and cfDNA results regarding fetal sex is also discussed.

  17. Uses of cell free fetal DNA in maternal circulation.

    Science.gov (United States)

    Hill, Melissa; Barrett, Angela N; White, Helen; Chitty, Lyn S

    2012-10-01

    For over a decade, researchers have focused their attention on the development of non-invasive prenatal diagnosis tests based on cell-free fetal DNA circulating in maternal blood. With the possibility of earlier and safer testing, non-invasive prenatal diagnosis has the potential to bring many positive benefits to prenatal diagnosis. Non-invasive prenatal diagnosis for fetal sex determination for women who are carriers of sex-linked conditions is now firmly established in clinical practice. Other non-invasive prenatal diagnosis-based tests are set to follow, as future applications, such as the detection of single-gene disorders and chromosomal abnormalities, are now well within reach. Here, we review recent developments in non-invasive prenatal diagnosis for genetic conditions and chromosomal abnormalities, and provide an overview of research into ethical concerns, social issues and stakeholder view points.

  18. Improved cell-free RNA and protein synthesis system.

    Directory of Open Access Journals (Sweden)

    Jun Li

    Full Text Available Cell-free RNA and protein synthesis (CFPS is becoming increasingly used for protein production as yields increase and costs decrease. Advances in reconstituted CFPS systems such as the Protein synthesis Using Recombinant Elements (PURE system offer new opportunities to tailor the reactions for specialized applications including in vitro protein evolution, protein microarrays, isotopic labeling, and incorporating unnatural amino acids. In this study, using firefly luciferase synthesis as a reporter system, we improved PURE system productivity up to 5 fold by adding or adjusting a variety of factors that affect transcription and translation, including Elongation factors (EF-Ts, EF-Tu, EF-G, and EF4, ribosome recycling factor (RRF, release factors (RF1, RF2, RF3, chaperones (GroEL/ES, BSA and tRNAs. The work provides a more efficient defined in vitro transcription and translation system and a deeper understanding of the factors that limit the whole system efficiency.

  19. Trinucleotide repeat expansions catalyzed by human cell-free extracts

    Institute of Scientific and Technical Information of China (English)

    Jennifer R Stevens; Elaine E Lahue; Guo-Min Li; Robert S Lahue

    2013-01-01

    Trinucleotide repeat expansions cause 17 heritable human neurological disorders.In some diseases,somatic expansions occur in non-proliferating tissues such as brain where DNA replication is limited.This finding stimulated significant interest in replication-independent expansion mechanisms.Aberrant DNA repair is a likely source,based in part on mouse studies showing that somatic expansions are provoked by the DNA repair protein MutSβ (Msh2-Msh3complex).Biochemical studies to date used cell-free extracts or purified DNA repair proteins to yield partial reactions at triplet repeats.The findings included expansions on one strand but not the other,or processing of DNA hairpin structures thought to be important intermediates in the expansion process.However,it has been difficult to recapitulate complete expansions in vitro,and the biochemical role of MutSβ remains controversial.Here,we use a novel in vitro assay to show that human cell-free extracts catalyze expansions and contractions of trinucleotide repeats without the requirement for DNA replication.The extract promotes a size range of expansions that is similar to certain diseases,and triplet repeat length and sequence govern expansions in vitro as in vivo.MutSβ stimulates expansions in the extract,consistent with aberrant repair of endogenous DNA damage as a source of expansions.Overall,this biochemical system retains the key characteristics of somatic expansions in humans and mice,suggesting that this important mutagenic process can be restored in the test tube.

  20. Performance benchmarking of four cell-free protein expression systems.

    Science.gov (United States)

    Gagoski, Dejan; Polinkovsky, Mark E; Mureev, Sergey; Kunert, Anne; Johnston, Wayne; Gambin, Yann; Alexandrov, Kirill

    2016-02-01

    Over the last half century, a range of cell-free protein expression systems based on pro- and eukaryotic organisms have been developed and have found a range of applications, from structural biology to directed protein evolution. While it is generally accepted that significant differences in performance among systems exist, there is a paucity of systematic experimental studies supporting this notion. Here, we took advantage of the species-independent translation initiation sequence to express and characterize 87 N-terminally GFP-tagged human cytosolic proteins of different sizes in E. coli, wheat germ (WGE), HeLa, and Leishmania-based (LTE) cell-free systems. Using a combination of single-molecule fluorescence spectroscopy, SDS-PAGE, and Western blot analysis, we assessed the expression yields, the fraction of full-length translation product, and aggregation propensity for each of these systems. Our results demonstrate that the E. coli system has the highest expression yields. However, we observe that high expression levels are accompanied by production of truncated species-particularly pronounced in the case of proteins larger than 70 kDa. Furthermore, proteins produced in the E. coli system display high aggregation propensity, with only 10% of tested proteins being produced in predominantly monodispersed form. The WGE system was the most productive among eukaryotic systems tested. Finally, HeLa and LTE show comparable protein yields that are considerably lower than the ones achieved in the E. coli and WGE systems. The protein products produced in the HeLa system display slightly higher integrity, whereas the LTE-produced proteins have the lowest aggregation propensity among the systems analyzed. The high quality of HeLa- and LTE-produced proteins enable their analysis without purification and make them suitable for analysis of multi-domain eukaryotic proteins.

  1. Overview of cell-free protein synthesis: historic landmarks, commercial systems, and expanding applications.

    Science.gov (United States)

    Chong, Shaorong

    2014-10-01

    During the early days of molecular biology, cell-free protein synthesis played an essential role in deciphering the genetic code and contributed to our understanding of translation of protein from messenger RNA. Owing to several decades of major and incremental improvements, modern cell-free systems have achieved higher protein synthesis yields at lower production costs. Commercial cell-free systems are now available from a variety of material sources, ranging from "traditional" E. coli, rabbit reticulocyte lysate, and wheat germ extracts, to recent insect and human cell extracts, to defined systems reconstituted from purified recombinant components. Although each cell-free system has certain advantages and disadvantages, the diversity of the cell-free systems allows in vitro synthesis of a wide range of proteins for a variety of downstream applications. In the post-genomic era, cell-free protein synthesis has rapidly become the preferred approach for high-throughput functional and structural studies of proteins and a versatile tool for in vitro protein evolution and synthetic biology. This unit provides a brief history of cell-free protein synthesis and describes key advances in modern cell-free systems, practical differences between widely used commercial cell-free systems, and applications of this important technology.

  2. Adherence measured by microtiter assay as a virulence marker for Staphylococcus epidermidis infections.

    Science.gov (United States)

    Deighton, M A; Balkau, B

    1990-11-01

    Staphylococcus epidermidis strains isolated from clinical sources showed a wide range of abilities to adhere to glass and plastic materials. The degree of adherence depended on a number of factors, most notably, the composition of the growth medium. Adherence was enhanced by the addition of glucose or oleic acid to the growth medium and inhibited by serum. We have demonstrated a statistically significant association between the quantitative assessment of adherence to polystyrene tissue culture plates and clinical relevance. No such association was found when adherence was assessed by the qualitative adherence assay. Possible new approaches for assessing the clinical relevance of coagulase-negative staphylococcal isolates are discussed.

  3. Circulating Cell Free DNA in the Diagnosis of Trophoblastic Tumors

    Directory of Open Access Journals (Sweden)

    Mark R. Openshaw

    2016-02-01

    Full Text Available Gestational trophoblastic neoplasia (GTN represents a group of diseases characterized by production of human chorionic gonadotropin (hCG. Since non-gestational tumors may occasionally secrete hCG, histopathological diagnosis is important for appropriate clinical management. However, a histopathological diagnosis is not always available. We therefore investigated the feasibility of extracting cell free DNA (cfDNA from the plasma of women with GTN for use as a “liquid biopsy” in patients without histopathological diagnosis. cfDNA was prepared from the plasma of 20 women with a diagnosis of GTN and five with hCG-secreting tumors of unknown origin. Genotyping of cfDNA from the patient, genomic DNA from her and her partner and DNA from the tumor tissue identified circulating tumor DNA (ctDNA (from 9% to 53% of total cfDNA in 12 of 20 patients with GTN. In one case without a tissue diagnosis, ctDNA enabled a diagnosis of GTN originating in a non-molar conception and in another a diagnosis of non-gestational tumor, based on the high degree of allelic instability and loss of heterozygosity in the ctDNA. In summary ctDNA can be detected in the plasma of women with GTN and can facilitate the diagnosis of both gestational and non-gestational trophoblastic tumors in cases without histopathological diagnosis.

  4. Circulating Cell Free DNA in the Diagnosis of Trophoblastic Tumors

    Science.gov (United States)

    Openshaw, Mark R.; Harvey, Richard A.; Sebire, Neil J.; Kaur, Baljeet; Sarwar, Naveed; Seckl, Michael J.; Fisher, Rosemary A.

    2015-01-01

    Gestational trophoblastic neoplasia (GTN) represents a group of diseases characterized by production of human chorionic gonadotropin (hCG). Since non-gestational tumors may occasionally secrete hCG, histopathological diagnosis is important for appropriate clinical management. However, a histopathological diagnosis is not always available. We therefore investigated the feasibility of extracting cell free DNA (cfDNA) from the plasma of women with GTN for use as a “liquid biopsy” in patients without histopathological diagnosis. cfDNA was prepared from the plasma of 20 women with a diagnosis of GTN and five with hCG-secreting tumors of unknown origin. Genotyping of cfDNA from the patient, genomic DNA from her and her partner and DNA from the tumor tissue identified circulating tumor DNA (ctDNA) (from 9% to 53% of total cfDNA) in 12 of 20 patients with GTN. In one case without a tissue diagnosis, ctDNA enabled a diagnosis of GTN originating in a non-molar conception and in another a diagnosis of non-gestational tumor, based on the high degree of allelic instability and loss of heterozygosity in the ctDNA. In summary ctDNA can be detected in the plasma of women with GTN and can facilitate the diagnosis of both gestational and non-gestational trophoblastic tumors in cases without histopathological diagnosis. PMID:26981554

  5. Cell-free circulating tumor DNA in cancer

    Institute of Scientific and Technical Information of China (English)

    Zhen Qin; Vladimir A Ljubimov; Cuiqi Zhou; Yunguang Tong; Jimin Liang

    2016-01-01

    Cancer is a common cause of death worldwide. Despite significant advances in cancer treatments, the morbidity and mortality are still enormous. Tumor heterogeneity, especially intratumoral heterogeneity, is a significant reason under-lying difculties in tumor treatment and failure of a number of current therapeutic modalities, even of molecularly targeted therapies. The development of a virtually noninvasive“liquid biopsy”from the blood has been attempted to characterize tumor heterogeneity. This review focuses on cell-free circulating tumor DNA (ctDNA) in the bloodstream as a versatile biomarker. ctDNA analysis is an evolving field with many new methods being developed and optimized to be able to successfully extract and analyze ctDNA, which has vast clinical applications. ctDNA has the potential to accurately genotype the tumor and identify personalized genetic and epigenetic alterations of the entire tumor. In addition, ctDNA has the potential to accurately monitor tumor burden and treatment response, while also being able to monitor minimal residual disease, reducing the need for harmful adjuvant chemotherapy and allowing more rapid detection of relapse. There are still many challenges that need to be overcome prior to this biomarker getting wide adoption in the clinical world, including optimization, standardization, and large multicenter trials.

  6. Optimizing cell-free protein expression in CHO: Assessing small molecule mass transfer effects in various reactor configurations.

    Science.gov (United States)

    Peñalber-Johnstone, Chariz; Ge, Xudong; Tran, Kevin; Selock, Nicholas; Sardesai, Neha; Gurramkonda, Chandrasekhar; Pilli, Manohar; Tolosa, Michael; Tolosa, Leah; Kostov, Yordan; Frey, Douglas D; Rao, Govind

    2017-03-07

    Cell-free protein synthesis (CFPS) is an ideal platform for rapid and convenient protein production. However, bioreactor design remains a critical consideration in optimizing protein expression. Using turbo green fluorescent protein (tGFP) as a model, we tracked small molecule components in a Chinese Hamster Ovary (CHO) CFPS system to optimize protein production. Here, three bioreactors in continuous-exchange cell-free (CECF) format were characterized. A GFP optical sensor was built to monitor the product in real-time. Mass transfer of important substrate and by-product components such as nucleoside triphosphates (NTPs), creatine, and inorganic phosphate (Pi) across a 10-kDa MWCO cellulose membrane was calculated. Highest efficiency measured by tGFP yields were found in a microdialysis device configuration; while a negative effect on yield was observed due to limited mass transfer of NTPs in a dialysis cup configuration. In 24-well plate high-throughput CECF format, addition of up to 40 mM creatine phosphate in the system increased yields by up to ∼60% relative to controls. Direct ATP addition, as opposed to creatine phosphate addition, negatively affected the expression. Pi addition of up to 30 mM to the expression significantly reduced yields by over ∼40% relative to controls. Overall, data presented in this report serves as a valuable reference to optimize the CHO CFPS system for next-generation bioprocessing. This article is protected by copyright. All rights reserved.

  7. Absolute first trimester cell-free DNA levels and their associations with adverse pregnancy outcomes

    NARCIS (Netherlands)

    Thurik, Florentine F; Lamain-de Ruiter, Marije; Javadi, Ahmad; Kwee, Anneke; Woortmeijer, Heleen; Page-Christiaens, Godelieve C M L; Franx, Arie; van der Schoot, C Ellen; Koster, Maria P H

    2016-01-01

    OBJECTIVE: To study associations of first trimester cell-free fetal DNA levels (in this paper referred to as cell-free placental DNA (cfpDNA) levels) and preeclampsia (PE), pregnancy-induced hypertension (PIH), gestational diabetes (GDM) and spontaneous preterm birth (sPB). METHOD: A nested case-con

  8. Multidimensional Normalization to Minimize Plate Effects of Suspension Bead Array Data.

    Science.gov (United States)

    Hong, Mun-Gwan; Lee, Woojoo; Nilsson, Peter; Pawitan, Yudi; Schwenk, Jochen M

    2016-10-07

    Enhanced by the growing number of biobanks, biomarker studies can now be performed with reasonable statistical power by using large sets of samples. Antibody-based proteomics by means of suspension bead arrays offers one attractive approach to analyze serum, plasma, or CSF samples for such studies in microtiter plates. To expand measurements beyond single batches, with either 96 or 384 samples per plate, suitable normalization methods are required to minimize the variation between plates. Here we propose two normalization approaches utilizing MA coordinates. The multidimensional MA (multi-MA) and MA-loess both consider all samples of a microtiter plate per suspension bead array assay and thus do not require any external reference samples. We demonstrate the performance of the two MA normalization methods with data obtained from the analysis of 384 samples including both serum and plasma. Samples were randomized across 96-well sample plates, processed, and analyzed in assay plates, respectively. Using principal component analysis (PCA), we could show that plate-wise clusters found in the first two components were eliminated by multi-MA normalization as compared with other normalization methods. Furthermore, we studied the correlation profiles between random pairs of antibodies and found that both MA normalization methods substantially reduced the inflated correlation introduced by plate effects. Normalization approaches using multi-MA and MA-loess minimized batch effects arising from the analysis of several assay plates with antibody suspension bead arrays. In a simulated biomarker study, multi-MA restored associations lost due to plate effects. Our normalization approaches, which are available as R package MDimNormn, could also be useful in studies using other types of high-throughput assay data.

  9. Preparation of a Saccharomyces cerevisiae cell-free extract for in vitro translation.

    Science.gov (United States)

    Wu, Cheng; Sachs, Matthew S

    2014-01-01

    Eukaryotic cell-free in vitro translation systems have been in use since the 1970s. These systems can faithfully synthesize polypeptides when programmed with mRNA, enabling the production of polypeptides for analysis as well as permitting analyses of the cis- and trans-acting factors that regulate translation. Here we describe the preparation and use of cell-free translation systems from the yeast Saccharomyces cerevisiae.

  10. Efficient cell-free expression with the endogenous E. Coli RNA polymerase and sigma factor 70

    Directory of Open Access Journals (Sweden)

    Noireaux Vincent

    2010-06-01

    Full Text Available Abstract Background Escherichia coli cell-free expression systems use bacteriophage RNA polymerases, such as T7, to synthesize large amounts of recombinant proteins. These systems are used for many applications in biotechnology, such as proteomics. Recently, informational processes have been reconstituted in vitro with cell-free systems. These synthetic approaches, however, have been seriously limited by a lack of transcription modularity. The current available cell-free systems have been optimized to work with bacteriophage RNA polymerases, which put significant restrictions to engineer processes related to biological information. The development of efficient cell-free systems with broader transcription capabilities is required to study complex informational processes in vitro. Results In this work, an efficient cell-free expression system that uses the endogenous E. coli RNA polymerase only and sigma factor 70 for transcription was prepared. Approximately 0.75 mg/ml of Firefly luciferase and enhanced green fluorescent protein were produced in batch mode. A plasmid was optimized with different regulatory parts to increase the expression. In addition, a new eGFP was engineered that is more translatable in cell-free systems than the original eGFP. The protein production was characterized with three different adenosine triphosphate (ATP regeneration systems: creatine phosphate (CP, phosphoenolpyruvate (PEP, and 3-phosphoglyceric acid (3-PGA. The maximum protein production was obtained with 3-PGA. Preparation of the crude extract was streamlined to a simple routine procedure that takes 12 hours including cell culture. Conclusions Although it uses the endogenous E. coli transcription machinery, this cell-free system can produce active proteins in quantities comparable to bacteriophage systems. The E. coli transcription provides much more possibilities to engineer informational processes in vitro. Many E. coli promoters/operators specific to sigma

  11. Escherichia coli cell-free protein synthesis and isotope labeling of mammalian proteins.

    Science.gov (United States)

    Terada, Takaho; Yokoyama, Shigeyuki

    2015-01-01

    This chapter describes the cell-free protein synthesis method, using an Escherichia coli cell extract. This is a cost-effective method for milligram-scale protein production and is particularly useful for the production of mammalian proteins, protein complexes, and membrane proteins that are difficult to synthesize by recombinant expression methods, using E. coli and eukaryotic cells. By adjusting the conditions of the cell-free method, zinc-binding proteins, disulfide-bonded proteins, ligand-bound proteins, etc., may also be produced. Stable isotope labeling of proteins can be accomplished by the cell-free method, simply by using stable isotope-labeled amino acid(s) in the cell-free reaction. Moreover, the cell-free protein synthesis method facilitates the avoidance of stable isotope scrambling and dilution over the recombinant expression methods and is therefore advantageous for amino acid-selective stable isotope labeling. Site-specific stable isotope labeling is also possible with a tRNA molecule specific to the UAG codon. By the cell-free protein synthesis method, coupled transcription-translation is performed from a plasmid vector or a PCR-amplified DNA fragment encoding the protein. A milligram quantity of protein can be produced with a milliliter-scale reaction solution in the dialysis mode. More than a thousand solution structures have been determined by NMR spectroscopy for uniformly labeled samples of human and mouse functional domain proteins, produced by the cell-free method. Here, we describe the practical aspects of mammalian protein production by the cell-free method for NMR spectroscopy.

  12. Cell-Free Protein Synthesis: Pros and Cons of Prokaryotic and Eukaryotic Systems.

    Science.gov (United States)

    Zemella, Anne; Thoring, Lena; Hoffmeister, Christian; Kubick, Stefan

    2015-11-01

    From its start as a small-scale in vitro system to study fundamental translation processes, cell-free protein synthesis quickly rose to become a potent platform for the high-yield production of proteins. In contrast to classical in vivo protein expression, cell-free systems do not need time-consuming cloning steps, and the open nature provides easy manipulation of reaction conditions as well as high-throughput potential. Especially for the synthesis of difficult to express proteins, such as toxic and transmembrane proteins, cell-free systems are of enormous interest. The modification of the genetic code to incorporate non-canonical amino acids into the target protein in particular provides enormous potential in biotechnology and pharmaceutical research and is in the focus of many cell-free projects. Many sophisticated cell-free systems for manifold applications have been established. This review describes the recent advances in cell-free protein synthesis and details the expanding applications in this field.

  13. Validation of cell-free culture using scanning electron microscopy (SEM) and gene expression studies.

    Science.gov (United States)

    Yang, R; Elankumaran, Y; Hijjawi, N; Ryan, U

    2015-06-01

    A cell-free culture system for Cryptosporidium parvum was analysed using scanning electron microscopy (SEM) to characterise life cycle stages and compare gene expression in cell-free culture and cell culture using HCT-8 cells. Cryptosporidium parvum samples were harvested at 2 h, 8 h, 14 h, 26 h, 50 h, 74 h, 98 h, 122 h and 170 h, chemically fixed and specimens were observed using a Zeiss 1555 scanning electron microscope. The presence of sporozoites, trophozoites and type I merozoites were identified by SEM. Gene expression in cell culture and cell-free culture was studied using reverse transcriptase quantitative PCR (RT-qPCR) of the sporozoite surface antigen protein (cp15), the glycoprotein 900 (gp900), the Cryptosporidium oocyst wall protein (COWP) and 18S ribosomal RNA (rRNA) genes in both cell free and conventional cell culture. In cell culture, cp15 expression peaked at 74 h, gp900 expression peaked at 74 h and 98 h and COWP expression peaked at 50 h. In cell-free culture, CP15 expression peaked at 98 h, gp900 expression peaked at 74 h and COWP expression peaked at 122 h. The present study is the first to compare gene expression of C. parvum in cell culture and cell-free culture and to characterise life cycle stages of C. parvum in cell-free culture using SEM. Findings from this study showed that gene expression patterns in cell culture and cell-free culture were similar but in cell-free culture, gene expression was delayed for CP15 and COWP in cell free culture compared with the cell culture system and was lower. Although three life cycle stageswere conclusively identified, improvements in SEM methodology should lead to the detection of more life cycle stages.

  14. Plate tectonics

    Digital Repository Service at National Institute of Oceanography (India)

    Chaubey, A.K.

    Content-Type text/plain; charset=UTF-8 209 Plate Tectonics A. K. Chaubey National Institute of Oceanography, Dona Paula, Goa-403 004. chaubey@nio.org Introduction The theory of continental drift, which paved the way for discovery... of plate tectonics, was put forward by Alfred Lother Wegener - a meteorologist from Germany - in 1912. The theory states that continents are not fixed, but have been slowly wandering during the course of Earth’s geological history. Although Wegener...

  15. IRES-mediated translation of membrane proteins and glycoproteins in eukaryotic cell-free systems.

    Directory of Open Access Journals (Sweden)

    Andreas K Brödel

    Full Text Available Internal ribosome entry site (IRES elements found in the 5' untranslated region of mRNAs enable translation initiation in a cap-independent manner, thereby representing an alternative to cap-dependent translation in cell-free protein expression systems. However, IRES function is largely species-dependent so their utility in cell-free systems from different species is rather limited. A promising approach to overcome these limitations would be the use of IRESs that are able to recruit components of the translation initiation apparatus from diverse origins. Here, we present a solution to this technical problem and describe the ability of a number of viral IRESs to direct efficient protein expression in different eukaryotic cell-free expression systems. The IRES from the intergenic region (IGR of the Cricket paralysis virus (CrPV genome was shown to function efficiently in four different cell-free systems based on lysates derived from cultured Sf21, CHO and K562 cells as well as wheat germ. Our results suggest that the CrPV IGR IRES-based expression vector is universally applicable for a broad range of eukaryotic cell lysates. Sf21, CHO and K562 cell-free expression systems are particularly promising platforms for the production of glycoproteins and membrane proteins since they contain endogenous microsomes that facilitate the incorporation of membrane-spanning proteins and the formation of post-translational modifications. We demonstrate the use of the CrPV IGR IRES-based expression vector for the enhanced synthesis of various target proteins including the glycoprotein erythropoietin and the membrane proteins heparin-binding EGF-like growth factor receptor as well as epidermal growth factor receptor in the above mentioned eukaryotic cell-free systems. CrPV IGR IRES-mediated translation will facilitate the development of novel eukaryotic cell-free expression platforms as well as the high-yield synthesis of desired proteins in already established

  16. Preparation of ubiquitin-conjugated proteins using an insect cell-free protein synthesis system.

    Science.gov (United States)

    Suzuki, Takashi; Ezure, Toru; Ando, Eiji; Nishimura, Osamu; Utsumi, Toshihiko; Tsunasawa, Susumu

    2010-01-01

    Ubiquitination is one of the most significant posttranslational modifications (PTMs). To evaluate the ability of an insect cell-free protein synthesis system to carry out ubiquitin (Ub) conjugation to in vitro translated proteins, poly-Ub chain formation was studied in an insect cell-free protein synthesis system. Poly-Ub was generated in the presence of Ub aldehyde (UA), a de-ubiquitinating enzyme inhibitor. In vitro ubiquitination of the p53 tumor suppressor protein was also analyzed, and p53 was poly-ubiquitinated when Ub, UA, and Mdm2, an E3 Ub ligase (E3) for p53, were added to the in vitro reaction mixture. These results suggest that the insect cell-free protein synthesis system contains enzymatic activities capable of carrying out ubiquitination. CBB-detectable ubiquitinated p53 was easily purified from the insect cell-free protein synthesis system, allowing analysis of the Ub-conjugated proteins by mass spectrometry (MS). Lys 305 of p53 was identified as one of the Ub acceptor sites using this strategy. Thus, we conclude that the insect cell-free protein synthesis system is a powerful tool for studying various PTMs of eukaryotic proteins including ubiqutination presented here.

  17. Content of intrinsic disorder influences the outcome of cell-free protein synthesis.

    Science.gov (United States)

    Tokmakov, Alexander A; Kurotani, Atsushi; Ikeda, Mariko; Terazawa, Yumiko; Shirouzu, Mikako; Stefanov, Vasily; Sakurai, Tetsuya; Yokoyama, Shigeyuki

    2015-09-11

    Cell-free protein synthesis is used to produce proteins with various structural traits. Recent bioinformatics analyses indicate that more than half of eukaryotic proteins possess long intrinsically disordered regions. However, no systematic study concerning the connection between intrinsic disorder and expression success of cell-free protein synthesis has been presented until now. To address this issue, we examined correlations of the experimentally observed cell-free protein expression yields with the contents of intrinsic disorder bioinformatically predicted in the expressed sequences. This analysis revealed strong relationships between intrinsic disorder and protein amenability to heterologous cell-free expression. On the one hand, elevated disorder content was associated with the increased ratio of soluble expression. On the other hand, overall propensity for detectable protein expression decreased with disorder content. We further demonstrated that these tendencies are rooted in some distinct features of intrinsically disordered regions, such as low hydrophobicity, elevated surface accessibility and high abundance of sequence motifs for proteolytic degradation, including sites of ubiquitination and PEST sequences. Our findings suggest that identification of intrinsically disordered regions in the expressed amino acid sequences can be of practical use for predicting expression success and optimizing cell-free protein synthesis.

  18. Dynamic imaging of cell-free and cell-associated viral capture in mature dendritic cells.

    Science.gov (United States)

    Izquierdo-Useros, Nuria; Esteban, Olga; Rodriguez-Plata, Maria T; Erkizia, Itziar; Prado, Julia G; Blanco, Julià; García-Parajo, Maria F; Martinez-Picado, Javier

    2011-12-01

    Dendritic cells (DCs) capture human immunodeficiency virus (HIV) through a non-fusogenic mechanism that enables viral transmission to CD4(+) T cells, contributing to in vivo viral dissemination. Although previous studies have provided important clues to cell-free viral capture by mature DCs (mDCs), dynamic and kinetic insight on this process is still missing. Here, we used three-dimensional video microscopy and single-particle tracking approaches to dynamically dissect both cell-free and cell-associated viral capture by living mDCs. We show that cell-free virus capture by mDCs operates through three sequential phases: virus binding through specific determinants expressed in the viral particle, polarized or directional movements toward concrete regions of the cell membrane and virus accumulation in a sac-like structure where trapped viral particles display a hindered diffusive behavior. Moreover, real-time imaging of cell-associated viral transfer to mDCs showed a similar dynamics to that exhibited by cell-free virus endocytosis leading to viral accumulation in compartments. However, cell-associated HIV type 1 transfer to mDCs was the most effective pathway, boosted throughout enhanced cellular contacts with infected CD4(+) T cells. Our results suggest that in lymphoid tissues, mDC viral uptake could occur either by encountering cell-free or cell-associated virus produced by infected cells generating the perfect scenario to promote HIV pathogenesis and impact disease progression.

  19. Atomic force microscopy observation on nuclear reassembly in a cell-free system

    Institute of Scientific and Technical Information of China (English)

    YANG Ning; CHEN Zhongcai; ZHANG Zhaohui; ZHU Xing; ZHAI Zhonghe; TANG Xiaowei

    2003-01-01

    Cell-free system is interesting and useful for studying nuclear assembly in mitosis. Atomic force micro- scopy (AFM), which is a simple way for imaging fixed reassemble nuclei with high resolution, has not been used in the cell-free system. In this paper, we put forward an air-drying sample preparation for AFM. Using AFM, we observed nuclear reassembly process within 100 nm resolution ina cell-free system. As a result, we found that the images were artifact-free, and with higher resolution compared with fluorescent optical microscope images. Furthermore, the morphology of membrane vesicles was obtained clearly, and a dynamic change of morphology during the vesicles' approaching to nuclear envelope was also observed, which is enlightened to understand the mechanism of nuclear envelope assembly.

  20. Improved recovery of bisulphite-treated cell-free DNA in plasma

    DEFF Research Database (Denmark)

    Pedersen, Inge Søkilde; Krarup, H.B.; Thorlacius-Ussing, O.;

    Detection of cell-free methylated DNA in plasma is a promising tool for tumour diagnosis and monitoring. Due to the very low amount of cell-free DNA in plasma, sensitivity of the detection methods are of utmost importance. The vast majority of currently available methods for analysing DNA...... of PCR amplifying methylated and umethylated MEST. This procedure allows low levels of DNA to be easily and reliably analysed, a prerequisite for the clinical usefulness of cell-free methylated DNA detection in plasma........ The analytical sensitivity of the method was analysed by detection of methylated/unmethylated copies of the imprinted (and hemimethylated) gene MEST in a dilution series of plasma DNA. The method is based on an accelerated deamination step and magnetic silica purification of DNA in combination with a first round...

  1. Cell-free DNA for diagnosing myocardial infarction: not ready for prime time.

    Science.gov (United States)

    Lippi, Giuseppe; Sanchis-Gomar, Fabian; Cervellin, Gianfranco

    2015-11-01

    A modest amount of cell-free DNA is constantly present in human blood, originating from programmed cell death, apoptosis and rupture of blood cells or pathogens. Acute or chronic cell injury contributes to enhance the pool of circulating nucleic acids, so that their assessment may be regarded as an appealing perspective for diagnosing myocardial ischemia. We performed a search in Medline, Web of Science and Scopus to identify clinical studies that investigated the concentration of cell-free DNA in patients with myocardial ischemia. Overall, eight case-control studies could be detected and reviewed. Although the concentration of cell-free DNA was found to be higher in the diseased than in the healthy population, the scenario was inconclusive due to the fact that the overall number of subjects studied was modest, the populations were unclearly defined, cases and controls were not adequately matched, the methodology for measuring the reference cardiac biomarkers was inadequately described, and the diagnostic performance of cell-free DNA was not benchmarked against highly sensitive troponin immunoassays. Several biological and technical hurdles were also identified in cell-free DNA testing, including the lack of specificity and unsuitable kinetics for early diagnosis of myocardial ischemia, the long turnaround time and low throughput, the need for specialized instrumentation and dedicated personnel, the lack of standardization or harmonization of analytical techniques, the incremental costs and the high vulnerability to preanalytical variables. Hence it seems reasonable to conclude that the analysis of cell-free DNA is not ready for prime time in diagnostics of myocardial ischemia.

  2. A chimeric vitronectin: IGF-I protein supports feeder-cell-free and serum-free culture of human embryonic stem cells.

    Science.gov (United States)

    Manton, Kerry J; Richards, Sean; Van Lonkhuyzen, Derek; Cormack, Luke; Leavesley, David; Upton, Zee

    2010-09-01

    The therapeutic use of human embryonic stem (hES) cells is severely limited by safety concerns regarding their culture in media containing animal-derived or nondefined factors and on animal-derived feeder cells. Thus, there is a pressing need to develop culture techniques that are xeno-free, fully defined, and synthetic. Our laboratory has discovered that insulin-like growth factor (IGF) and vitronectin (VN) bind to each other resulting in synergistic short-term functional effects in several cell types, including keratinocytes and breast epithelial cells. We have further refined this complex into a single chimeric VN:IGF-I protein that functionally mimics the effects obtained upon binding of IGF-I to VN. The aim of the current study was to determine whether hES cells can be serially propagated in feeder-cell-free and serum-free conditions using medium containing our novel chimeric VN:IGF-I protein. Here we demonstrate that hES cells can be serially propagated and retain their undifferentiated state in vitro for up to 35 passages in our feeder-cell-free, serum-free, chemically defined media. We have utilized real-time polymerase chain reaction (PCR), immunofluorescence, and fluorescence-activated cell sorter (FACS) analysis to show that the hES cells have maintained an undifferentiated phenotype. In vitro differentiation assays demonstrated that the hES cells retain their pluripotent potential and the karyotype of the hES cells remains unchanged. This study demonstrates that the novel, fully defined, synthetic VN:IGF-I chimera-containing medium described herein is a viable alternative to media containing serum, and that in conjunction with laminin-coated plates facilitates feeder-cell-free and serum-free growth of hES.

  3. New bioproduction systems: from molecular circuits to novel reactor concepts in cell-free biotechnology.

    Science.gov (United States)

    Rupp, Steffen

    2013-01-01

    : The last decades witnessed a strong growth in several areas of biotechnology, especially in fields related to health, as well as in industrial biotechnology. Advances in molecular engineering now enable biotechnologists to design more efficient pathways in order to convert a larger spectrum of renewable resources into industrially used biofuels and chemicals as well as into new pharmaceuticals and therapeutic proteins. In addition material sciences advanced significantly making it more and more possible to integrate biology and engineering. One of the key questions currently is how to develop new ways of engineering biological systems to cope with the complexity and limitations given by the cell. The options to integrate biology with classical engineering advanced cell free technologies in the recent years significantly. Cell free protein production using cellular extracts is now a well-established universal technology for production of proteins derived from many organisms even at the milligram scale. Among other applications it has the potential to supply the demand for a multitude of enzymes and enzyme variants facilitating in vitro metabolic engineering. This review will briefly address the recent achievements and limitations of cell free conversions. Especially, the requirements for reactor systems in cell free biotechnology, a currently underdeveloped field, are reviewed and some perspectives are given on how material sciences and biotechnology might be able to advance these new developments in the future.

  4. Cell-free DNA in healthy individuals, noncancerous disease and strong prognostic value in colorectal cancer

    DEFF Research Database (Denmark)

    Spindler, Karen-Lise Garm; Appelt, Ane L; Pallisgaard, Niels;

    2014-01-01

    The purpose was to investigate total cell-free DNA (cfDNA) in colorectal cancer (CRC) patients during treatment with second-line chemotherapy and in healthy controls and patients with different comorbidities. Patient treated with second-line irinotecan for metastatic CRC (n = 100), a cohort of he...

  5. Plasma HER2 amplification in cell-free DNA during neoadjuvant chemotherapy in breast cancer

    DEFF Research Database (Denmark)

    Bechmann, Troels; Andersen, Rikke Fredslund; Pallisgaard, Niels

    2013-01-01

    Measurement of human epidermal growth factor receptor 2 (HER2) gene amplification in cell-free DNA (cfDNA) is an evolving technique in breast cancer, enabling liquid biopsies and treatment monitoring. The present study investigated the dynamics of plasma HER2 gene copy number and amplification in...... in cfDNA during neoadjuvant chemotherapy....

  6. Cell-Free RNA Is a Reliable Fetoplacental Marker in Noninvasive Fetal Sex Determination

    NARCIS (Netherlands)

    Mersy, E.; Faas, B.H.W.; Spierts, S.; Houben, L.M.; Macville, M.V.; Frints, S.G.; Paulussen, A.D.; Veltman, J.A.

    2015-01-01

    BACKGROUND: Noninvasive genetic tests that use cell-free fetal DNA (cffDNA) are used increasingly in prenatal care. A low amount of cffDNA can have detrimental effects on the reliability of these tests. A marker to confirm the presence of fetal nucleic acids is therefore required that is universally

  7. Cell-free plasma microRNA in pancreatic ductal adenocarcinoma and disease controls

    DEFF Research Database (Denmark)

    Carlsen, Anting Liu; Joergensen, Maiken Thyregod; Knudsen, Steen;

    2013-01-01

    There are no tumor-specific biochemical markers for pancreatic ductal adenocarcinoma (PDAC). Tissue-specific gene expression including microRNA (miRNA) profiling, however, identifies specific PDAC signatures. This study evaluates associations between circulating, cell-free plasma-miRNA profiles...

  8. Characterizing and prototyping genetic networks with cell-free transcription-translation reactions.

    Science.gov (United States)

    Takahashi, Melissa K; Hayes, Clarmyra A; Chappell, James; Sun, Zachary Z; Murray, Richard M; Noireaux, Vincent; Lucks, Julius B

    2015-09-15

    A central goal of synthetic biology is to engineer cellular behavior by engineering synthetic gene networks for a variety of biotechnology and medical applications. The process of engineering gene networks often involves an iterative 'design-build-test' cycle, whereby the parts and connections that make up the network are built, characterized and varied until the desired network function is reached. Many advances have been made in the design and build portions of this cycle. However, the slow process of in vivo characterization of network function often limits the timescale of the testing step. Cell-free transcription-translation (TX-TL) systems offer a simple and fast alternative to performing these characterizations in cells. Here we provide an overview of a cell-free TX-TL system that utilizes the native Escherichia coli TX-TL machinery, thereby allowing a large repertoire of parts and networks to be characterized. As a way to demonstrate the utility of cell-free TX-TL, we illustrate the characterization of two genetic networks: an RNA transcriptional cascade and a protein regulated incoherent feed-forward loop. We also provide guidelines for designing TX-TL experiments to characterize new genetic networks. We end with a discussion of current and emerging applications of cell free systems.

  9. Evaluation of prenatal RHD typing strategies on cell-free fetal DNA from maternal plasma

    NARCIS (Netherlands)

    M.G.H.M. Grootkerk-Tax; A.A. Soussan; M. de Haas; P.A. Maaskant-van Wijk; C.E. van der Schoot

    2006-01-01

    BACKGROUND: The discovery of cell-free fetal DNA in maternal plasma led to the development of assays to predict the fetal D status with RHD-specific sequences. Few assays are designed in such a way that the fetus can be typed in RHD psi mothers and that RHD psi fetuses are correctly typed. Owing to

  10. Preparative scale production of functional mouse aquaporin 4 using different cell-free expression modes.

    Directory of Open Access Journals (Sweden)

    Lei Kai

    Full Text Available The continuous progress in the structural and functional characterization of aquaporins increasingly attracts attention to study their roles in certain mammalian diseases. Although several structures of aquaporins have already been solved by crystallization, the challenge of producing sufficient amounts of functional proteins still remains. CF (cell free expression has emerged in recent times as a promising alternative option in order to synthesize large quantities of membrane proteins, and the focus of this report was to evaluate the potential of this technique for the production of eukaryotic aquaporins. We have selected the mouse aquaporin 4 as a representative of mammalian aquaporins. The protein was synthesized in an E. coli extract based cell-free system with two different expression modes, and the efficiencies of two modes were compared. In both, the P-CF (cell-free membrane protein expression as precipitate mode generating initial aquaporin precipitates as well as in the D-CF (cell-free membrane protein expression in presence of detergent mode, generating directly detergent solubilized samples, we were able to obtain mg amounts of protein per ml of cell-free reaction. Purified aquaporin samples solubilized in different detergents were reconstituted into liposomes, and analyzed for the water channel activity. The calculated P(f value of proteoliposome samples isolated from the D-CF mode was 133 µm/s at 10°C, which was 5 times higher as that of the control. A reversible inhibitory effect of mercury chloride was observed, which is consistent with previous observations of in vitro reconstituted aquaporin 4. In this study, a fast and convenient protocol was established for functional expression of aquaporins, which could serve as basis for further applications such as water filtration.

  11. Cell-free fetal DNA in amniotic fluid supernatant for prenatal diagnosis.

    Science.gov (United States)

    Soltani, M; Nemati, M; Maralani, M; Estiar, M A; Andalib, S; Fardiazar, Z; Sakhinia, E

    2016-04-30

    In widespread conviction, amniotic fluid is utilized for prenatal diagnosis. Amniotic fluid supernatant is usually discarded, notwithstanding being a good source of fetal DNA. The aim of the present study was to assess cell-free fetal DNA extracted from amniotic fluid supernatant for application in prenatal diagnosis such as gender determination and early diagnosis of β-thalassemia. Samples of amniotic fluid of 70 pregnant women were collected and went through routine tests along with tests for cell-free fetal DNA from amniotic fluid supernatant. The DNA in the amniotic fluid supernatant was extracted and analyzed for gender determination by PCR and Real-time PCR. ARMS-PCR was applied to test early diagnosis of IVS II-I mutation (common β-thalassemia mutation) and E7V mutation for sickle cell anemia using DNA extracted from the amniotic fluid supernatant. Using the cell-free fetal DNA extracted from the amniotic fluid supernatant, the sensitivity of PCR and Real-time PCR for gender detection was compared with the routine cytogenetic method. The fetus tested for sickle cell anemia and β-thalassemia was observed to be healthy but heterozygous for IVS II-I mutation. The findings indicated that cell-free fetal DNA from amniotic fluid supernatant can be a good source of fetal DNA and be used in early prenatal diagnosis since because of its fast and accurate application. Therefore, it would be suggested that the amniotic fluid supernatant's disposal is prevented because if the tests needs to be repeated, cell-free fetal DNA extracted from the amniotic fluid supernatant can be used as an alternative source for prenatal diagnosis.

  12. Growth Plate Injuries

    Science.gov (United States)

    ... Growth Plate Injuries? Key Words Information Box The Salter-Harris Classification of Growth Plate Injuries What Is ... of Growth Plate Injuries? Since the 1960s, the Salter-Harris classification, which divides most growth plate fractures ...

  13. Admission Cell Free DNA as a Prognostic Factor in Burns: Quantification by Use of a Direct Rapid Fluorometric Technique

    Directory of Open Access Journals (Sweden)

    Yaron Shoham

    2014-01-01

    Full Text Available Background. Despite great advances in the treatment of burn patients, useful prognostic markers are sparse. During the past years there has been increasing interest in circulating plasma cell free DNA as a potential marker for tissue injury. We have developed a rapid direct fluorescent assay for cell free DNA quantification that allows obtaining accurate, fast, and inexpensive measurements. Objective. To use this technique for measuring plasma cell free DNA levels in burn patients and to further explore the use of cell free DNA as a potential marker of patient outcome in burns. Methods. Cell free DNA levels obtained from 14 burn victims within 6 hours of injury and 14 healthy controls were quantified by a direct rapid fluorometric assay. Results. Patient admission cell free DNA levels were significantly elevated compared with that of controls (1797 ± 1523 ng/mL versus 374 ± 245 ng/mL, P=0.004. There are statistically significant correlations between cell free DNA admission levels and burn degree (Spearman’s correlation = 0.78, P=0.001, total body surface area (Spearman’s correlation = 0.61, P=0.02, and total burn volume (Spearman’s correlation = 0.64, P=0.014. Conclusions. Admission cell free DNA levels can serve as a prognostic factor in burns and future routine use can be made possible by use of our direct rapid fluorometric assay.

  14. A cell-free fluorometric high-throughput screen for inhibitors of Rtt109-catalyzed histone acetylation.

    Directory of Open Access Journals (Sweden)

    Jayme L Dahlin

    Full Text Available The lysine acetyltransferase (KAT Rtt109 forms a complex with Vps75 and catalyzes the acetylation of histone H3 lysine 56 (H3K56ac in the Asf1-H3-H4 complex. Rtt109 and H3K56ac are vital for replication-coupled nucleosome assembly and genotoxic resistance in yeast and pathogenic fungal species such as Candida albicans. Remarkably, sequence homologs of Rtt109 are absent in humans. Therefore, inhibitors of Rtt109 are hypothesized as potential and minimally toxic antifungal agents. Herein, we report the development and optimization of a cell-free fluorometric high-throughput screen (HTS for small-molecule inhibitors of Rtt109-catalyzed histone acetylation. The KAT component of the assay consists of the yeast Rtt109-Vps75 complex, while the histone substrate complex consists of full-length Drosophila histone H3-H4 bound to yeast Asf1. Duplicated assay runs of the LOPAC demonstrated day-to-day and plate-to-plate reproducibility. Approximately 225,000 compounds were assayed in a 384-well plate format with an average Z' factor of 0.71. Based on a 3σ cut-off criterion, 1,587 actives (0.7% were identified in the primary screen. The assay method is capable of identifying previously reported KAT inhibitors such as garcinol. We also observed several prominent active classes of pan-assay interference compounds such as Mannich bases, catechols and p-hydroxyarylsulfonamides. The majority of the primary active compounds showed assay signal interference, though most assay artifacts can be efficiently removed by a series of straightforward counter-screens and orthogonal assays. Post-HTS triage demonstrated a comparatively small number of confirmed actives with IC50 values in the low micromolar range. This assay, which utilizes five label-free proteins involved in H3K56 acetylation in vivo, can in principle identify compounds that inhibit Rtt109-catalyzed H3K56 acetylation via different mechanisms. Compounds discovered via this assay or adaptations thereof could

  15. Synthesis and cell-free cloning of DNA libraries using programmable microfluidics.

    Science.gov (United States)

    Ben Yehezkel, Tuval; Rival, Arnaud; Raz, Ofir; Cohen, Rafael; Marx, Zipora; Camara, Miguel; Dubern, Jean-Frédéric; Koch, Birgit; Heeb, Stephan; Krasnogor, Natalio; Delattre, Cyril; Shapiro, Ehud

    2016-02-29

    Microfluidics may revolutionize our ability to write synthetic DNA by addressing several fundamental limitations associated with generating novel genetic constructs. Here we report the first de novo synthesis and cell-free cloning of custom DNA libraries in sub-microliter reaction droplets using programmable digital microfluidics. Specifically, we developed Programmable Order Polymerization (POP), Microfluidic Combinatorial Assembly of DNA (M-CAD) and Microfluidic In-vitro Cloning (MIC) and applied them to de novo synthesis, combinatorial assembly and cell-free cloning of genes, respectively. Proof-of-concept for these methods was demonstrated by programming an autonomous microfluidic system to construct and clone libraries of yeast ribosome binding sites and bacterial Azurine, which were then retrieved in individual droplets and validated. The ability to rapidly and robustly generate designer DNA molecules in an autonomous manner should have wide application in biological research and development.

  16. Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry.

    Science.gov (United States)

    Harris, D Calvin; Jewett, Michael C

    2012-10-01

    Just as synthetic organic chemistry once revolutionized the ability of chemists to build molecules (including those that did not exist in nature) following a basic set of design rules, cell-free synthetic biology is beginning to provide an improved toolbox and faster process for not only harnessing but also expanding the chemistry of life. At the interface between chemistry and biology, research in cell-free synthetic systems is proceeding in two different directions: using synthetic biology for synthetic chemistry and using synthetic chemistry to reprogram or mimic biology. In the coming years, the impact of advances inspired by these approaches will make possible the synthesis of nonbiological polymers having new backbone compositions, new chemical properties, new structures, and new functions.

  17. Synthetic biology outside the cell: linking computational tools to cell-free systems.

    Science.gov (United States)

    Lewis, Daniel D; Villarreal, Fernando D; Wu, Fan; Tan, Cheemeng

    2014-01-01

    As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.

  18. Elevated levels of cell-free circulating DNA in patients with acute dengue virus infection.

    Directory of Open Access Journals (Sweden)

    Tran Thi Ngoc Ha

    Full Text Available BACKGROUND: Apoptosis is thought to play a role in the pathogenesis of severe dengue and the release of cell-free DNA into the circulatory system in several medical conditions. Therefore, we investigated circulating DNA as a potential biomarker for severe dengue. METHODS AND FINDINGS: A direct fluorometric degradation assay using PicoGreen was performed to quantify cell-free DNA from patient plasma. Circulating DNA levels were significantly higher in patients with dengue virus infection than with other febrile illnesses and healthy controls. Remarkably, the increase of DNA levels correlated with the severity of dengue. Additionally, multivariate logistic regression analysis showed that circulating DNA levels independently correlated with dengue shock syndrome. CONCLUSIONS: Circulating DNA levels were increased in dengue patients and correlated with dengue severity. Additional studies are required to show the benefits of this biomarker in early dengue diagnosis and for the prognosis of shock complication.

  19. Efficient cell-free production of olfactory receptors: detergent optimization, structure, and ligand binding analyses.

    Science.gov (United States)

    Kaiser, Liselotte; Graveland-Bikker, Johanna; Steuerwald, Dirk; Vanberghem, Mélanie; Herlihy, Kara; Zhang, Shuguang

    2008-10-14

    High-level production of membrane proteins, particularly of G protein-coupled receptors (GPCRs) in heterologous cell systems encounters a number of difficulties from their inherent hydrophobicity in their transmembrane domains, which frequently cause protein aggregation and cytotoxicity and thus reduce the protein yield. Recent advances in cell-free protein synthesis circumvent those problems to produce membrane proteins with a yield sometimes exceeding the cell-based approach. Here, we report cell-free production of a human olfactory receptor 17-4 (hOR17-4) using the wheat germ extract. Using the simple method, we also successful produced two additional olfactory receptors. To obtain soluble olfactory receptors and to increase yield, we directly added different detergents in varying concentrations to the cell-free reaction. To identify a purification buffer system that maintained the receptor in a nonaggregated form, we developed a method that uses small-volume size-exclusion column chromatography combined with rapid and sensitive dot-blot detection. Different buffer components including salt concentration, various detergents and detergent concentration, and reducing agent and its concentrations were evaluated for their ability to maintain the cell-free produced protein stable and nonaggregated. The purified olfactory receptor displays a typical a alpha-helical CD spectrum. Surface plasmon resonance measurements were used to show binding of a known ligand undecanal to hOR17-4. Our approach to produce a high yield of purified olfactory receptor is a milestone toward obtaining a large quantity of olfactory receptors for designing bionic sensors. Furthermore, this simple approach may be broadly useful not only for other classes of GPCRs but also for other membrane proteins.

  20. Cell-free synthesis of functional thermostable direct hemolysins of Vibrio parahaemolyticus.

    Science.gov (United States)

    Bechlars, Silke; Wüstenhagen, Doreen A; Drägert, Katja; Dieckmann, Ralf; Strauch, Eckhard; Kubick, Stefan

    2013-12-15

    Vibrio parahaemolyticus is a recognized enteropathogen causing diarrhea in humans and is one of the major causes of seafoodborne gastroenteritis. An important virulence factor is thermostable direct hemolysin (TDH), a pore-forming toxin, which is able to lyse eukaryotic cells. The active toxin is a tetramer of four identical protein subunits, which is secreted by the pathogen after cleavage of a signal peptide. To establish diagnostic detection systems for TDH we expressed the hemolysin with and without the signal peptide in a prokaryotic cell-free system to obtain pure toxin. In order to purify and to facilitate the isolation from cell lysates we synthesized TDH variants with different tags. Important regulatory sequences for cell-free protein synthesis as well as sequences for N-terminal Strep-tag and C-terminal 6xHis-tag were added by a two-step PCR. For the expression in the cell-free system these linear tdh templates were subjected directly to prokaryotic cell extracts. Protein yields were in the range of 500-600 μg/ml for the preproteins and approx. 300-400 μg/ml for the mature proteins. The identities of expressed proteins were further confirmed by SDS-PAGE, immunological and MALDI-TOF mass spectrometric analyses. The functionality of newly synthesized toxin variants was tested by performing qualitative and semiquantitative hemolysis assays. Cell-free produced mature TDH and its variants were active while the preprotein and its derivatives lacked hemolytic activity. A C-terminal 6xHis-tag showed less influence on functionality compared to the N-terminal Strep-tag.

  1. Conformational Antibody Binding to a Native, Cell-Free Expressed GPCR in Block Copolymer Membranes

    OpenAIRE

    de Hoog, Hans-Peter M.; Esther M Lin JieRong; Sourabh Banerjee; Décaillot, Fabien M.; Madhavan Nallani

    2014-01-01

    G-protein coupled receptors (GPCRs) play a key role in physiological processes and are attractive drug targets. Their biophysical characterization is, however, highly challenging because of their innate instability outside a stabilizing membrane and the difficulty of finding a suitable expression system. We here show the cell-free expression of a GPCR, CXCR4, and its direct embedding in diblock copolymer membranes. The polymer-stabilized CXCR4 is readily immobilized onto biosensor chips for l...

  2. A cell-free expression and purification process for rapid production of protein biologics.

    Science.gov (United States)

    Sullivan, Challise J; Pendleton, Erik D; Sasmor, Henri H; Hicks, William L; Farnum, John B; Muto, Machiko; Amendt, Eric M; Schoborg, Jennifer A; Martin, Rey W; Clark, Lauren G; Anderson, Mark J; Choudhury, Alaksh; Fior, Raffaella; Lo, Yu-Hwa; Griffey, Richard H; Chappell, Stephen A; Jewett, Michael C; Mauro, Vincent P; Dresios, John

    2016-02-01

    Cell-free protein synthesis has emerged as a powerful technology for rapid and efficient protein production. Cell-free methods are also amenable to automation and such systems have been extensively used for high-throughput protein production and screening; however, current fluidic systems are not adequate for manufacturing protein biopharmaceuticals. In this work, we report on the initial development of a fluidic process for rapid end-to-end production of recombinant protein biologics. This process incorporates a bioreactor module that can be used with eukaryotic or prokaryotic lysates that are programmed for combined transcription/translation of an engineered DNA template encoding for specific protein targets. Purification of the cell-free expressed product occurs through a series of protein separation modules that are configurable for process-specific isolation of different proteins. Using this approach, we demonstrate production of two bioactive human protein therapeutics, erythropoietin and granulocyte-macrophage colony-stimulating factor, in yeast and bacterial extracts, respectively, each within 24 hours. This process is flexible, scalable and amenable to automation for rapid production at the point-of-need of proteins with significant pharmaceutical, medical, or biotechnological value.

  3. In vitro Fab display: a cell-free system for IgG discovery.

    Science.gov (United States)

    Stafford, Ryan L; Matsumoto, Marissa L; Yin, Gang; Cai, Qi; Fung, Juan Jose; Stephenson, Heather; Gill, Avinash; You, Monica; Lin, Shwu-Hwa; Wang, Willie D; Masikat, Mary Rose; Li, Xiaofan; Penta, Kalyani; Steiner, Alex R; Baliga, Ramesh; Murray, Christopher J; Thanos, Christopher D; Hallam, Trevor J; Sato, Aaron K

    2014-04-01

    Selection technologies such as ribosome display enable the rapid discovery of novel antibody fragments entirely in vitro. It has been assumed that the open nature of the cell-free reactions used in these technologies limits selections to single-chain protein fragments. We present a simple approach for the selection of multi-chain proteins, such as antibody Fab fragments, using ribosome display. Specifically, we show that a two-chain trastuzumab (Herceptin) Fab domain can be displayed in a format which tethers either the heavy or light chain to the ribosome while retaining functional antigen binding. Then, we constructed synthetic Fab HC and LC libraries and performed test selections against carcinoembryonic antigen (CEA) and vascular endothelial growth factor (VEGF). The Fab selection output was reformatted into full-length immunoglobulin Gs (IgGs) and directly expressed at high levels in an optimized cell-free system for immediate screening, purification and characterization. Several novel IgGs were identified using this cell-free platform that bind to purified CEA, CEA positive cells and VEGF.

  4. Monitoring of organ transplants through genomic analyses of circulating cell-free DNA

    Science.gov (United States)

    de Vlaminck, Iwijn

    Solid-organ transplantation is the preferred treatment for patients with end-stage organ diseases, but complications due to infection and acute rejection undermine its long-term benefits. While clinicians strive to carefully monitor transplant patients, diagnostic options are currently limited. My colleagues and I in the lab of Stephen Quake have found that a combination of next-generation sequencing with a phenomenon called circulating cell-free DNA enables non-invasive diagnosis of both infection and rejection in transplantation. A substantial amount of small fragments of cell-free DNA circulate in blood that are the debris of dead cells. We discovered that donor specific DNA is released in circulation during injury to the transplant organ and we show that the proportion of donor DNA in plasma is predictive of acute rejection in heart and lung transplantation. We profiled viral and bacterial DNA sequences in plasma of transplant patients and discovered that the relative representation of different viruses and bacteria is informative of immunosuppression. This discovery suggested a novel biological measure of a person's immune strength, a finding that we have more recently confirmed via B-cell repertoire sequencing. Lastly, our studies highlight applications of shotgun sequencing of cell-free DNA in the broad, hypothesis free diagnosis of infection.

  5. 'Break-point Checkerboard Plate' for screening of appropriate antibiotic combinations against multidrug-resistant Pseudomonas aeruginosa.

    Science.gov (United States)

    Tateda, Kazuhiro; Ishii, Yoshikazu; Matsumoto, Tetsuya; Yamaguchi, Keizo

    2006-01-01

    Increase of multiple drug resistant Pseudomonas aeruginosa (MDRP) is becoming a serious problem in the clinical setting. Although the checkerboard method to determine FIC index and synergistic effects of antibiotic combinations is useful, it is not well adapted to a routine test, mainly because of its time-consuming and labor-intensive nature. Here we report 'Break-point Checkerboard Plate', in which breakpoint concentrations, such as 'S' (sensitive) and 'I' (intermediate), were combined in a microtiter plate with 8 antibiotics, including carbapenem, aminoglycoside and fluoroquinolone. The results obtained from 12 strains of MDRP demonstrated a strong synergistic effect of some antibiotic combinations at clinically relevant concentrations. Our data suggest a usefulness of 'Break-point Checkerboard Plate' to screen appropriate antibiotic combinations against drug resistant organisms, including MDRP.

  6. Construction of a Sequencing Library from Circulating Cell-Free DNA.

    Science.gov (United States)

    Fang, Nan; Löffert, Dirk; Akinci-Tolun, Rumeysa; Heitz, Katja; Wolf, Alexander

    2016-04-01

    Circulating DNA is cell-free DNA (cfDNA) in serum or plasma that can be used for non-invasive prenatal testing, as well as cancer diagnosis, prognosis, and stratification. High-throughput sequence analysis of the cfDNA with next-generation sequencing technologies has proven to be a highly sensitive and specific method in detecting and characterizing mutations in cancer and other diseases, as well as aneuploidy during pregnancy. This unit describes detailed procedures to extract circulating cfDNA from human serum and plasma and generate sequencing libraries from a wide concentration range of circulating DNA.

  7. Circulating Cell-Free Tumour DNA in the Management of Cancer

    Directory of Open Access Journals (Sweden)

    Glenn Francis

    2015-06-01

    Full Text Available With the development of new sensitive molecular techniques, circulating cell-free tumour DNA containing mutations can be identified in the plasma of cancer patients. The applications of this technology may result in significant changes to the care and management of cancer patients. Whilst, currently, these “liquid biopsies” are used to supplement the histological diagnosis of cancer and metastatic disease, in the future these assays may replace the need for invasive procedures. Applications include the monitoring of tumour burden, the monitoring of minimal residual disease, monitoring of tumour heterogeneity, monitoring of molecular resistance and early diagnosis of tumours and metastatic disease.

  8. Conformational antibody binding to a native, cell-free expressed GPCR in block copolymer membranes.

    Science.gov (United States)

    de Hoog, Hans-Peter M; Lin JieRong, Esther M; Banerjee, Sourabh; Décaillot, Fabien M; Nallani, Madhavan

    2014-01-01

    G-protein coupled receptors (GPCRs) play a key role in physiological processes and are attractive drug targets. Their biophysical characterization is, however, highly challenging because of their innate instability outside a stabilizing membrane and the difficulty of finding a suitable expression system. We here show the cell-free expression of a GPCR, CXCR4, and its direct embedding in diblock copolymer membranes. The polymer-stabilized CXCR4 is readily immobilized onto biosensor chips for label-free binding analysis. Kinetic characterization using a conformationally sensitive antibody shows the receptor to exist in the correctly folded conformation, showing binding behaviour that is commensurate with heterologously expressed CXCR4.

  9. Conformational antibody binding to a native, cell-free expressed GPCR in block copolymer membranes.

    Directory of Open Access Journals (Sweden)

    Hans-Peter M de Hoog

    Full Text Available G-protein coupled receptors (GPCRs play a key role in physiological processes and are attractive drug targets. Their biophysical characterization is, however, highly challenging because of their innate instability outside a stabilizing membrane and the difficulty of finding a suitable expression system. We here show the cell-free expression of a GPCR, CXCR4, and its direct embedding in diblock copolymer membranes. The polymer-stabilized CXCR4 is readily immobilized onto biosensor chips for label-free binding analysis. Kinetic characterization using a conformationally sensitive antibody shows the receptor to exist in the correctly folded conformation, showing binding behaviour that is commensurate with heterologously expressed CXCR4.

  10. Cell-free supernatants obtained from fermentation of cheese whey hydrolyzates and phenylpyruvic acid by Lactobacillus plantarum as a source of antimicrobial compounds, bacteriocins, and natural aromas.

    Science.gov (United States)

    Rodríguez-Pazo, Noelia; Vázquez-Araújo, Laura; Pérez-Rodríguez, Noelia; Cortés-Diéguez, Sandra; Domínguez, José Manuel

    2013-10-01

    Cheese whey hydrolyzates supplemented with phenylpyruvic acid (PPA) and commercial nutrients can be efficiently metabolized by Lactobacillus plantarum CECT-221 to biosynthesize some compounds with attractive applications in the food market. The main metabolites of cell-free extracts were antimicrobial compounds such as phenyllactic acid (PLA) and lactic acid (LA). The production of PLA by L. plantarum CECT-221 was evaluated in the Man-Rogosa-Sharpe broth supplemented with two biosynthetic precursors: phenylalanine or PPA. Using 30.5 mM PPA, the microorganism increased sevenfold the concentration of PLA producing 16.4 mM PLA in 46 h. A concentration of 40 mM PPA was a threshold to avoid substrate inhibition. The biosynthesis of whey hydrolyzates as a carbon source was enhanced by fed-batch fermentation of PPA; the average productivity of PLA increased up to 45.4 ± 3.02 mM after 120 h with a product yield of 0.244 mM mM(-1); meanwhile, LA reached 26.1 ± 1.3 g L(-1) with a product yield of 0.72 g g(-1). Cell-free fed-batch extracts charged in wells showed bacteriocin activity with halos of 7.49 ± 1.44 mm in plates inoculated with Carnobacterium piscicola and antimicrobial activity against Staphylococcus aureus (11.54 ± 1.14 mm), Pseudomonas aeruginosa (10.17 ± 2.46 mm), Listeria monocytogenes (7.75 ± 1.31 mm), and Salmonella enterica (3.60 ± 1.52 mm). Additionally, the analysis of the volatile composition of the headspace of this cell-free extract revealed that L. plantarum is a potential producer for natural aromas, such as acetophenone, with high price in the market. This is the first report of PLA production from cheese whey and PPA. The extracts showed bacteriocin activity and potential to be applied as an antimicrobial in the elaboration of safer foods.

  11. A Simple and Rapid Method for Preparing a Cell-Free Bacterial Lysate for Protein Synthesis

    Science.gov (United States)

    Kaduri, Maya; Shainsky-Roitman, Janna; Goldfeder, Mor; Ivanir, Eran; Benhar, Itai; Shoham, Yuval; Schroeder, Avi

    2016-01-01

    Cell-free protein synthesis (CFPS) systems are important laboratory tools that are used for various synthetic biology applications. Here, we present a simple and inexpensive laboratory-scale method for preparing a CFPS system from E. coli. The procedure uses basic lab equipment, a minimal set of reagents, and requires less than one hour to process the bacterial cell mass into a functional S30-T7 extract. BL21(DE3) and MRE600 E. coli strains were used to prepare the S30-T7 extract. The CFPS system was used to produce a set of fluorescent and therapeutic proteins of different molecular weights (up to 66 kDa). This system was able to produce 40–150 μg-protein/ml, with variations depending on the plasmid type, expressed protein and E. coli strain. Interestingly, the BL21-based CFPS exhibited stability and increased activity at 40 and 45°C. To the best of our knowledge, this is the most rapid and affordable lab-scale protocol for preparing a cell-free protein synthesis system, with high thermal stability and efficacy in producing therapeutic proteins. PMID:27768741

  12. Non-invasive prenatal testing using cell-free fetal DNA in maternal circulation.

    Science.gov (United States)

    Liao, Gary J W; Gronowski, Ann M; Zhao, Zhen

    2014-01-20

    The identification of cell-free fetal DNA (cffDNA) in maternal circulation has made non-invasive prenatal testing (NIPT) possible. Maternal plasma cell free DNA is a mixture of maternal and fetal DNA, of which, fetal DNA represents a minor population in maternal plasma. Therefore, methods with high sensitivity and precision are required to detect and differentiate fetal DNA from the large background of maternal DNA. In recent years, technical advances in the molecular analysis of fetal DNA (e.g., digital PCR and massively parallel sequencing (MPS)) has enabled the successful implementation of noninvasive testing into clinical practice, such as fetal sex assessment, RhD genotyping, and fetal chromosomal aneuploidy detection.With the ability to decipher the entire fetal genome from maternal plasma DNA, we foresee that an increased number of non-invasive prenatal tests will be available for detecting many single-gene disorders in the near future. This review briefly summarizes the technical aspects of the NIPT and application of NIPT in clinical practice.

  13. False Negative Cell-Free DNA Screening Result in a Newborn with Trisomy 13

    Directory of Open Access Journals (Sweden)

    Yang Cao

    2016-01-01

    Full Text Available Background. Noninvasive prenatal screening (NIPS is revolutionizing prenatal screening as a result of its increased sensitivity, specificity. NIPS analyzes cell-free fetal DNA (cffDNA circulating in maternal plasma to detect fetal chromosome abnormalities. However, cffDNA originates from apoptotic placental trophoblast; therefore cffDNA is not always representative of the fetus. Although the published data for NIPS testing states that the current technique ensures high sensitivity and specificity for aneuploidy detection, false positives are possible due to isolated placental mosaicism, vanishing twin or cotwin demise, and maternal chromosome abnormalities or malignancy. Results. We report a case of false negative cell-free DNA (cfDNA screening due to fetoplacental mosaicism. An infant male with negative cfDNA screening result was born with multiple congenital abnormalities. Postnatal chromosome and FISH studies on a blood specimen revealed trisomy 13 in 20/20 metaphases and 100% interphase nuclei, respectively. FISH analysis on tissues collected after delivery revealed extraembryonic mosaicism. Conclusions. Extraembryonic tissue mosaicism is likely responsible for the false negative cfDNA screening result. This case illustrates that a negative result does not rule out the possibility of a fetus affected with a trisomy, as cffDNA is derived from the placenta and therefore may not accurately represent the fetal genetic information.

  14. Cell-Free Expression of Protein Kinase A for Rapid Activity Assays

    Directory of Open Access Journals (Sweden)

    Donna M. Leippe

    2010-05-01

    Full Text Available Functional protein analysis often calls for lengthy, laborious in vivo protein expression and purification, and can be complicated by the lack of stability of the purified protein. In this study, we demonstrate the feasibility of a simplified procedure for functional protein analysis on magnetic particles using cell-free protein synthesis of the catalytic subunit of human cAMP-dependent protein kinase as a HaloTag® fusion protein. The cell-free protein synthesis systems provide quick access to the protein of interest, while the HaloTag technology provides efficient, covalent protein immobilization of the fusion protein, eliminating the need for further protein purification and minimizing storage-related stability issues. The immobilized cPKA fusion protein is assayed directly on magnetic beads and can be used in inhibitor analyses. The combination of rapid protein synthesis and capture technologies can greatly facilitate the process of protein expression and activity screening, and therefore, can become a valuable tool for functional proteomics studies.

  15. Cell-free layer and wall shear stress variation in microvessels.

    Science.gov (United States)

    Yin, Xuewen; Zhang, Junfeng

    2012-01-01

    In this study, we simulated multiple red blood cells flowing through straight microvessels with the immersed-boundary lattice-Boltzmann model to examine the shear stress variation on the microvessel surface and its relation to the properties of cell-free layer. Significant variation in shear stress has been observed due to the irregular configuration of blood cells flowing near the microvessel wall. A low shear stress is typically found at locations where there is a cell flowing close to the wall, and a large shear stress at locations with a relatively wide gap between cell and wall. This relationship between the shear stress magnitude and the distance between cell and wall has been attributed to the reverse pressure difference developed between the front and rear sides of a cell flowing near the vessel wall. We further studied the effects of several hemodynamic factors on the variation of shear stress, including the cell deformability, the flow rate, and the aggregation among red blood cells. These simulations show that the shear stress variation is less profound in situations with wider cell-free layers, since the reverse pressure difference around the edge cells is less evident, and the influence of this pressure difference on wall shear stress becomes weaker. This study also demonstrates the complexity of the flow field in the gap between cell and wall. More precise experimental techniques are required accurately measure such shear stress variation in microcirculation.

  16. Preliminary study on preparation of E.coli cell-free system for protein expression

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    In the new era of "Omics",the traditional techniques of protein expression in vivo can not come up with the exponential increase of genetic information.The cellfree protein synthesis system provides a new strategy of protein expression with advantages of rapid,convenient and high-throughput expression.The preparation of cell extracts,the optimization of substrate concentrations and the energy regeneration system are the key factors for the successful construction of cell-free protein expression system.In this work,the cell extract was prepared from RNase I- defective strain E.coli A19.The cell growth phase,the pressure for cell disruption and the storage condition of cell extracts were optimized.Meanwhile,the optimal substrate concentrations and the energy regeneration system were selected.Under the optimized conditions,the green fluorescent protein (GFP) reporter gene was expressed in the E.coli cell-free system with high expression level (Ca.154 μg/mL) which was 29 times higher than the expression level before optimization.

  17. Optimized extract preparation methods and reaction conditions for improved yeast cell-free protein synthesis.

    Science.gov (United States)

    Hodgman, C Eric; Jewett, Michael C

    2013-10-01

    Cell-free protein synthesis (CFPS) has emerged as a powerful platform technology to help satisfy the growing demand for simple, affordable, and efficient protein production. In this article, we describe a novel CFPS platform derived from the popular bio-manufacturing organism Saccharomyces cerevisiae. By developing a streamlined crude extract preparation protocol and optimizing the CFPS reaction conditions we were able to achieve active firefly luciferase synthesis yields of 7.7 ± 0.5 µg mL(-1) with batch reactions lasting up to 2 h. This duration of synthesis is the longest ever reported for a yeast CFPS batch reaction. Furthermore, by removing extraneous processing steps and eliminating expensive reagents from the cell-free reaction, we have increased relative product yield (µg protein synthesized per $ reagent cost) over an alternative commonly used method up to 2000-fold from ∼2 × 10(-4) to ∼4 × 10(-1)  µg $(-1) , which now puts the yeast CPFS platform on par with other eukaryotic CFPS platforms commercially available. Our results set the stage for developing a yeast CFPS platform that provides for high-yielding and cost-effective expression of a variety of protein therapeutics and protein libraries.

  18. Processless offset printing plates

    Directory of Open Access Journals (Sweden)

    Sanja Mahović Poljaček

    2015-06-01

    Full Text Available With the implementation of platesetters in the offset printing plate making process, imaging of the printing plate became more stable and ensured increase of the printing plate quality. But as the chemical processing of the printing plates still highly influences the plate making process and the graphic reproduction workflow, development of printing plates that do not require chemical processing for offset printing technique has been one of the top interests in graphic technology in the last few years. The main reason for that came from the user experience, where majority of the problems with plate making process could be connected with the chemical processing of the printing plate. Furthermore, increased environmental standards lead to reducing of the chemicals used in the industrial processes. Considering these facts, different types of offset printing plates have been introduced to the market today. This paper presents some of the processless printing plates.

  19. Applications of cell-free protein synthesis in synthetic biology: Interfacing bio-machinery with synthetic environments.

    Science.gov (United States)

    Lee, Kyung-Ho; Kim, Dong-Myung

    2013-11-01

    Synthetic biology is built on the synthesis, engineering, and assembly of biological parts. Proteins are the first components considered for the construction of systems with designed biological functions because proteins carry out most of the biological functions and chemical reactions inside cells. Protein synthesis is considered to comprise the most basic levels of the hierarchical structure of synthetic biology. Cell-free protein synthesis has emerged as a powerful technology that can potentially transform the concept of bioprocesses. With the ability to harness the synthetic power of biology without many of the constraints of cell-based systems, cell-free protein synthesis enables the rapid creation of protein molecules from diverse sources of genetic information. Cell-free protein synthesis is virtually free from the intrinsic constraints of cell-based methods and offers greater flexibility in system design and manipulability of biological synthetic machinery. Among its potential applications, cell-free protein synthesis can be combined with various man-made devices for rapid functional analysis of genomic sequences. This review covers recent efforts to integrate cell-free protein synthesis with various reaction devices and analytical platforms.

  20. In Vitro Evolution of Bovine Foamy Virus Variants with Enhanced Cell-Free Virus Titers and Transmission.

    Science.gov (United States)

    Bao, Qiuying; Hipp, Michaela; Hugo, Annette; Lei, Janet; Liu, Yang; Kehl, Timo; Hechler, Torsten; Löchelt, Martin

    2015-11-11

    Virus transmission is essential for spreading viral infections and is a highly coordinated process which occurs by cell-free transmission or cell-cell contact. The transmission of Bovine Foamy Virus (BFV) is highly cell-associated, with undetectable cell-free transmission. However, BFV particle budding can be induced by overexpression of wild-type (wt) BFV Gag and Env or artificial retargeting of Gag to the plasma membrane via myristoylation membrane targeting signals, closely resembling observations in other foamy viruses. Thus, the particle release machinery of wt BFV appears to be an excellent model system to study viral adaption to cell-free transmission by in vitro selection and evolution. Using selection for BFV variants with high cell-free infectivity in bovine and non-bovine cells, infectivity dramatically increased from almost no infectious units to about 105-106 FFU (fluorescent focus forming units)/mL in both cell types. Importantly, the selected BFV variants with high titer (HT) cell-free infectivity could still transmit via cell-cell contacts and were neutralized by serum from naturally infected cows. These selected HT-BFV variants will shed light into virus transmission and potential routes of intervention in the spread of viral infections. It will also allow the improvement or development of new promising approaches for antiretroviral therapies.

  1. More Than Tiny Sacks: Stem Cell Exosomes as Cell-Free Modality for Cardiac Repair.

    Science.gov (United States)

    Kishore, Raj; Khan, Mohsin

    2016-01-22

    Stem cell therapy provides immense hope for regenerating the pathological heart, yet has been marred by issues surrounding the effectiveness, unclear mechanisms, and survival of the donated cell population in the ischemic myocardial milieu. Poor survival and engraftment coupled to inadequate cardiac commitment of the adoptively transferred stem cells compromises the improvement in cardiac function. Various alternative approaches to enhance the efficacy of stem cell therapies and to overcome issues with cell therapy have been used with varied success. Cell-free components, such as exosomes enriched in proteins, messenger RNAs, and miRs characteristic of parental stem cells, represent a potential approach for treating cardiovascular diseases. Recently, exosomes from different kinds of stem cells have been effectively used to promote cardiac function in the pathological heart. The aim of this review is to summarize current research efforts on stem cell exosomes, including their potential benefits and limitations to develop a potentially viable therapy for cardiovascular problems.

  2. Non-standard amino acid incorporation into proteins using Escherichia coli cell-free protein synthesis

    Directory of Open Access Journals (Sweden)

    Seok Hoon eHong

    2014-06-01

    Full Text Available Incorporating non-standard amino acids (NSAAs into proteins enables new chemical properties, new structures, and new functions. In recent years, improvements in cell-free protein synthesis (CFPS systems have opened the way to accurate and efficient incorporation of NSAAs into proteins. The driving force behind this development has been three-fold. First, a technical renaissance has enabled high-yielding (>1 g/L and long-lasting (>10 h in batch operation CFPS in systems derived from Escherichia coli. Second, the efficiency of orthogonal translation systems has improved. Third, the open nature of the CFPS platform has brought about an unprecedented level of control and freedom of design. Here, we review recent developments in CFPS platforms designed to precisely incorporate NSAAs. In the coming years, we anticipate that CFPS systems will impact efforts to elucidate structure/function relationships of proteins and to make biomaterials and sequence-defined biopolymers for medical and industrial applications.

  3. Kinetics of Circulating Plasma Cell-Free DNA in Paediatric Classical Hodgkin Lymphoma

    Science.gov (United States)

    Primerano, Simona; Burnelli, Roberta; Carraro, Elisa; Pillon, Marta; Elia, Caterina; Farruggia, Piero; Sala, Alessandra; Vinti, Luciana; Buffardi, Salvatore; Basso, Giuseppe; Mascarin, Maurizio; Mussolin, Lara

    2016-01-01

    Levels of plasma cell-free DNA (cfDNA) of a large series of children with classical Hodgkin lymphoma (cHL) were evaluated and analyzed at diagnosis and during chemotherapy treatment in relation with clinical characteristics. CfDNA levels in cHL patients were significantly higher compared with controls (p=0.002). CfDNA at diagnosis was correlated with presence of B symptoms (p=0.027) and high erythrocyte sedimentation rate (p=0.049). We found that the increasing of plasma cfDNA after first chemotherapy cycle seems to be associated with a worse prognosis (p=0.049). Levels of plasma cfDNA might constitute an interesting non-invasive tool in cHL patients' management. PMID:26918050

  4. Quantification of cell-free layer thickness and cell distribution of blood by optical coherence tomography

    Science.gov (United States)

    Lauri, Janne; Bykov, Alexander; Fabritius, Tapio

    2016-04-01

    A high-speed optical coherence tomography (OCT) with 1-μm axial resolution was applied to assess the thickness of a cell-free layer (CFL) and a spatial distribution of red blood cells (RBC) next to the microchannel wall. The experiments were performed in vitro in a plain glass microchannel with a width of 2 mm and height of 0.2 mm. RBCs were suspended in phosphate buffered saline solution at the hematocrit level of 45%. Flow rates of 0.1 to 0.5 ml/h were used to compensate gravity induced CFL. The results indicate that OCT can be efficiently used for the quantification of CFL thickness and spatial distribution of RBCs in microcirculatory blood flow.

  5. Dissecting functions of the conserved oligomeric Golgi tethering complex using a cell-free assay.

    Science.gov (United States)

    Cottam, Nathanael P; Wilson, Katherine M; Ng, Bobby G; Körner, Christian; Freeze, Hudson H; Ungar, Daniel

    2014-01-01

    Vesicle transport sorts proteins between compartments and is thereby responsible for generating the non-uniform protein distribution along the eukaryotic secretory and endocytic pathways. The mechanistic details of specific vesicle targeting are not yet well characterized at the molecular level. We have developed a cell-free assay that reconstitutes vesicle targeting utilizing the recycling of resident enzymes within the Golgi apparatus. The assay has physiological properties, and could be used to show that the two lobes of the conserved oligomeric Golgi tethering complex play antagonistic roles in trans-Golgi vesicle targeting. Moreover, we can show that the assay is sensitive to several different congenital defects that disrupt Golgi function and therefore cause glycosylation disorders. Consequently, this assay will allow mechanistic insight into the targeting step of vesicle transport at the Golgi, and could also be useful for characterizing some novel cases of congenital glycosylation disorders.

  6. In-Situ Observation of Membrane Protein Folding during Cell-Free Expression.

    Directory of Open Access Journals (Sweden)

    Axel Baumann

    Full Text Available Proper insertion, folding and assembly of functional proteins in biological membranes are key processes to warrant activity of a living cell. Here, we present a novel approach to trace folding and insertion of a nascent membrane protein leaving the ribosome and penetrating the bilayer. Surface Enhanced IR Absorption Spectroscopy selectively monitored insertion and folding of membrane proteins during cell-free expression in a label-free and non-invasive manner. Protein synthesis was performed in an optical cell containing a prism covered with a thin gold film with nanodiscs on top, providing an artificial lipid bilayer for folding. In a pilot experiment, the folding pathway of bacteriorhodopsin via various secondary and tertiary structures was visualized. Thus, a methodology is established with which the folding reaction of other more complex membrane proteins can be observed during protein biosynthesis (in situ and in operando at molecular resolution.

  7. Cell-free circulating tumour DNA as a liquid biopsy in breast cancer.

    Science.gov (United States)

    De Mattos-Arruda, Leticia; Caldas, Carlos

    2016-03-01

    Recent developments in massively parallel sequencing and digital genomic techniques support the clinical validity of cell-free circulating tumour DNA (ctDNA) as a 'liquid biopsy' in human cancer. In breast cancer, ctDNA detected in plasma can be used to non-invasively scan tumour genomes and quantify tumour burden. The applications for ctDNA in plasma include identifying actionable genomic alterations, monitoring treatment responses, unravelling therapeutic resistance, and potentially detecting disease progression before clinical and radiological confirmation. ctDNA may be used to characterise tumour heterogeneity and metastasis-specific mutations providing information to adapt the therapeutic management of patients. In this article, we review the current status of ctDNA as a 'liquid biopsy' in breast cancer.

  8. Production of meganucleases by cell-free protein synthesis for functional and structural studies.

    Science.gov (United States)

    Villate, Maider; Merino, Nekane; Blanco, Francisco J

    2012-10-01

    Meganucleases are highly specific endonucleases that recognize and cleave long DNA sequences, making them powerful tools for gene targeting. We describe the production of active recombinant meganucleases suitable for functional and structural studies using a batch-based cell-free protein synthesis method. Isotopic labeling of the I-CreI meganuclease is demonstrated opening the way for structural and ligand binding studies in solution by nuclear magnetic resonance (NMR)(2) which was previously hampered by the problems associated with the toxicity of the enzyme for Escherichia coli limiting its growth. The method can be adapted for the synthesis of soluble engineered variants that are produced as inclusion bodies in bacterial cells, thus facilitating their purification as soluble proteins instead of using denaturing-refolding protocols.

  9. In vitro translation of cardiovirus ribonucleic acid by mammalian cell-free extracts.

    Science.gov (United States)

    Eggen, K L; Shatkin, A J

    1972-04-01

    Cell-free extracts prepared from Ehrlich ascites and mouse L cells synthesize viral proteins in response to encephalomyocarditis virus, mouse Elberfeld virus, and mengovirus ribonucleic acid. Although HeLa cell extracts are inactive, their ribosomes are functional in the presence of heterologous supernatant fractions. Synthesis depends upon the addition of adenosine triphosphate, guanosine triphosphate, an energy-generating system, and 4 mm Mg(2+). Initiation is completed during the first 10 to 20 min of incubation, but chain elongation continues for 1 hr or more. The products are of higher molecular weight than virion structural proteins and resemble polypeptides formed in virus-infected cells during a short pulse. Tryptic peptides of virion proteins and in vitro products are similar for all three cardioviruses.

  10. Cell-free synthesis of membrane proteins: tailored cell models out of microsomes.

    Science.gov (United States)

    Fenz, Susanne F; Sachse, Rita; Schmidt, Thomas; Kubick, Stefan

    2014-05-01

    Incorporation of proteins in biomimetic giant unilamellar vesicles (GUVs) is one of the hallmarks towards cell models in which we strive to obtain a better mechanistic understanding of the manifold cellular processes. The reconstruction of transmembrane proteins, like receptors or channels, into GUVs is a special challenge. This procedure is essential to make these proteins accessible to further functional investigation. Here we describe a strategy combining two approaches: cell-free eukaryotic protein expression for protein integration and GUV formation to prepare biomimetic cell models. The cell-free protein expression system in this study is based on insect lysates, which provide endoplasmic reticulum derived vesicles named microsomes. It enables signal-induced translocation and posttranslational modification of de novo synthesized membrane proteins. Combining these microsomes with synthetic lipids within the electroswelling process allowed for the rapid generation of giant proteo-liposomes of up to 50 μm in diameter. We incorporated various fluorescent protein-labeled membrane proteins into GUVs (the prenylated membrane anchor CAAX, the heparin-binding epithelial growth factor like factor Hb-EGF, the endothelin receptor ETB, the chemokine receptor CXCR4) and thus presented insect microsomes as functional modules for proteo-GUV formation. Single-molecule fluorescence microscopy was applied to detect and further characterize the proteins in the GUV membrane. To extend the options in the tailoring cell models toolbox, we synthesized two different membrane proteins sequentially in the same microsome. Additionally, we introduced biotinylated lipids to specifically immobilize proteo-GUVs on streptavidin-coated surfaces. We envision this achievement as an important first step toward systematic protein studies on technical surfaces.

  11. Acrolein and chloroacetaldehyde: an examination of the cell and cell-free biomarkers of toxicity.

    Science.gov (United States)

    MacAllister, Stephanie L; Martin-Brisac, Nicolas; Lau, Vincent; Yang, Kai; O'Brien, Peter J

    2013-02-25

    Cyclophosphamide and ifosfamide are two commonly used DNA-alkylating agents in cancer chemotherapy that undergo biotransformation to several toxic and non-toxic metabolites, including acrolein and chloroacetaldehyde (CAA). Acrolein and CAA toxicities occur by several different mechanisms, including ROS formation and protein damage (oxidation), however, these pathways of toxicity and protecting agents used to prevent them have yet to be compared and ranked in a single study. This research focused on the molecular targets of acrolein and CAA toxicities and strategies to decrease toxicities. Hepatocyte viability (cytotoxicity) was assessed using Trypan blue uptake; formation of reactive oxygen species (ROS) and endogenous H2O2 were also assessed in the hepatocyte model. In cell-free models (bovine serum albumin and hepatic microsomes), protein carbonylation was the measurement of toxicity. The present study demonstrated that acrolein was a more potent toxin than CAA for freshly isolated rat hepatocytes, bovine serum albumin and rat hepatic microsomes. Acrolein protein carbonylation was dependent on its concentration; as acrolein concentration increased, protein carbonylation increased in a linear trend, whereas, CAA deviated from the trend and did not cause protein carbonylation at lower concentrations (acrolein-treated hepatocytes. The overall effectiveness of protecting agents to prevent or suppress acrolein or CAA toxicities in cell and cell-free models were ranked in order of most effective to least effective: reducing agents (sodium borohydride, sodium bisulfite)>thiol-containing compounds (N-acetylcysteine, cysteine, glutathione, 2-mercaptoethane sulfonate [MESNA], penicillamine)>carbonyl scavengers/amines (aminoguanidine, hydralazine, hydroxylamine)>antioxidants/ROS scavengers (ascorbic acid, Trolox; only utilized in hepatocyte system). An understanding of acrolein and CAA toxicities and the ability of protecting agents to protect against toxicities may help to

  12. An Advanced Model to Precisely Estimate the Cell-Free Fetal DNA Concentration in Maternal Plasma

    Science.gov (United States)

    Xu, Huixin; Jiang, Haojun; Xie, Weiwei; Chen, Fang; Zeng, Peng; Li, Xuchao; Xie, Yifan; Liu, Hongtai; Huang, Guodong; Chen, Dayang; Liu, Ping; Jiang, Hui; Zhang, Xiuqing

    2016-01-01

    Background With the speedy development of sequencing technologies, noninvasive prenatal testing (NIPT) has been widely applied in clinical practice for testing for fetal aneuploidy. The cell-free fetal DNA (cffDNA) concentration in maternal plasma is the most critical parameter for this technology because it affects the accuracy of NIPT-based sequencing for fetal trisomies 21, 18 and 13. Several approaches have been developed to calculate the cffDNA fraction of the total cell-free DNA in the maternal plasma. However, most approaches depend on specific single nucleotide polymorphism (SNP) allele information or are restricted to male fetuses. Methods In this study, we present an innovative method to accurately deduce the concentration of the cffDNA fraction using only maternal plasma DNA. SNPs were classified into four maternal-fetal genotype combinations and three boundaries were added to capture effective SNP loci in which the mother was homozygous and the fetus was heterozygous. The median value of the concentration of the fetal DNA fraction was estimated using the effective SNPs. A depth-bias correction was performed using simulated data and corresponding regression equations for adjustments when the depth of the sequencing data was below 100-fold or the cffDNA fraction is less than 10%. Results Using our approach, the median of the relative bias was 0.4% in 18 maternal plasma samples with a median sequencing depth of 125-fold. There was a significant association (r = 0.935) between our estimations and the estimations inferred from the Y chromosome. Furthermore, this approach could precisely estimate a cffDNA fraction as low as 3%, using only maternal plasma DNA at the targeted region with a sequencing depth of 65-fold. We also used PCR instead of parallel sequencing to calculate the cffDNA fraction. There was a significant association (r = 98.2%) between our estimations and those inferred from the Y chromosome. PMID:27662469

  13. Biological activity assays of cell-free reassembled nuclei——Injecting cell-free reassembled nuclei into unfertilized eggs can induce the eggs to cleave and reconstitute asters,and the injected nuclei undergo cell cycle changes

    Institute of Scientific and Technical Information of China (English)

    张传茂; 曲健; 梁金华; 翟中和

    1995-01-01

    Nucleus may reassemble spontaneously in cell-free mixture of HeLa metaphase chromosomes,Xenopus egg extracts and ATP-regenerating system,and the nucleus shows some biological activities.It isfound that,after being injected into unfertilized mature eggs,the cell-free reassembled nuclei can cause theeggs to cleave and reconstitute asters in their cytoplasm,and the injected nuclei undergo changes in response tocell cycle regulators stored in the eggs,and that reinjecting cytostatic factors(CSF)into the eggs can stabilizethe eggs in mitotic phase,cause the nuclei disassembly and chromatin condensation to chromosomes.

  14. Cell-free synthesis of the H-cluster: a model for the in vitro assembly of metalloprotein metal centers.

    Science.gov (United States)

    Kuchenreuther, Jon M; Shiigi, Stacey A; Swartz, James R

    2014-01-01

    Many organometallic cofactors are highly complex and require multiple accessory proteins for both their assembly and transfer to a target protein. A cell-free system in which the biosynthetic pathway for a prosthetic group has been fully or even partially reconstructed enables investigations of the reaction sequence as well as the cofactor itself. As a model for the in vitro assembly of protein-bound metal centers, we describe a procedure for the cell-free synthesis of the H-cluster in the context of producing purified and active [FeFe] hydrogenase samples for spectroscopic studies. In general terms, this in vitro system is a combination of non-purified accessory proteins, exogenous substrates, and purified hydrogenase apoprotein. We also describe methods for making the required components used in the cell-free system. Specifically, these procedures include anaerobic expression of heterologous metalloproteins in Escherichia coli, anaerobic cell lysate production, and anaerobic metalloprotein purification using Strep-Tactin(®) chromatography.

  15. Protein Degradation in a TX-TL Cell-free Expression System Using ClpXP Protease

    Science.gov (United States)

    2014-07-14

    1! Protein degradation in a TX-TL cell-free expression system using ClpXP protease AUTHORS: Zachary Z. Sun1, Jongmin Kim1, Vipul Singhal2...COVERED 00-00-2014 to 00-00-2014 4. TITLE AND SUBTITLE Protein Degradation in a TX-TL Cell-free Expression System Using ClpXP Protease 5a...equipment and expertise or demand lower reaction throughput. We explored the possibility of supplementing TX-TL with ClpXP, an AAA+ protease

  16. Growth Plate Fractures

    Science.gov (United States)

    ... the most widely used by doctors is the Salter-Harris system, described below. Type I Fractures These ... incidence of growth plate fractures peaks in adolescence. Salter-Harris classification of growth plate fractures. AAOS does ...

  17. Create Your Plate

    Medline Plus

    Full Text Available ... Planning Meals Diabetes Meal Plans Create Your Plate Gluten Free Diets Meal Planning for Vegetarian Diets Cook ... Create Your Plate Meal Planning for Vegetarian Diets Gluten Free Diets Holiday Meal Planning Cook with Heart- ...

  18. Create Your Plate

    Medline Plus

    Full Text Available ... steps to get started: Using your dinner plate, put a line down the middle of the plate. ... vegetables . Now in one of the small sections, put grains and starchy foods. See this list of ...

  19. Accelerated plate tectonics.

    Science.gov (United States)

    Anderson, D L

    1975-03-21

    The concept of a stressed elastic lithospheric plate riding on a viscous asthenosphere is used to calculate the recurrence interval of great earthquakes at convergent plate boundaries, the separation of decoupling and lithospheric earthquakes, and the migration pattern of large earthquakes along an arc. It is proposed that plate motions accelerate after great decoupling earthquakes and that most of the observed plate motions occur during short periods of time, separated by periods of relative quiescence.

  20. The effect of NaCl substitution with KCl on proteinase activities of cell-free extract and cell-free supernatant at different pH levels and salt concentrations: Lactobacillus acidophilus and Lactobacillus casei.

    Science.gov (United States)

    Ayyash, M M; Sherkat, F; Shah, N P

    2013-01-01

    The aim of this study was to investigate the effect of substitution of NaCl with KCl at different pH levels and salt concentrations on proteinase activity of cell-free extract and cell-free supernatant of the probiotics Lactobacillus acidophilus and Lactobacillus casei. de Man, Rogosa, and Sharpe broth aliquots were mixed with 2 pure salts (NaCl and KCl) and 2 salt concentrations at 2 concentration levels (5 and 10%), inoculated with Lactobacillus acidophilus or Lactobacillus casei, and incubated aerobically at 37°C for 22 h. The cultures were then centrifuged at 4,000×g for 30 min, and the collected cell pellets were used to prepare cell-wall proteinases and the supernatants used as a source of supernatant (extracellular) proteinases. The proteolytic activity and protein content of both portions were determined. After incubation of both portions with 3 milk caseins (α-, β-, κ-casein), the supernatants were individually subjected to analysis of angiotensin-converting enzyme (ACE)-inhibitory activity and proteolytic activity using the o-phthalaldehyde method. Significant differences were observed in ACE-inhibitory and proteolytic activities between salt substitution treatments of cell-free extract and cell-free supernatant from both probiotic strains at the same salt concentration and pH level.

  1. Anti-adherence potential of Enterococcus durans cells and its cell-free supernatant on plastic and stainless steel against foodborne pathogens.

    Science.gov (United States)

    Amel, Ait Meddour; Farida, Bendali; Djamila, Sadoun

    2015-07-01

    It is demonstrated that numerous bacteria are able to attach to surfaces of equipment used for food handling or processing. In this study, a strain of Enterococcus durans, originally isolated from a milking machine surface, was firstly studied for its biofilm formation potential on plastic and stainless steel supports. The strain was found to be a biofilm producer either at 25, 30 or 37 °C on polystyrene microtitre plates, with a best adherence level observed at 25 °C. En. durans showed a strong adhesion to stainless steel AISI-304. Antibacterial and anti-adherence activities of En. durans were tested against four foodborne pathogens (Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 25923, Pseudomonas aeruginosa ATCC 27853 and Listeria innocua CLIP 74915) which were shown as biofilm producers on both plastic and stainless steel. En. durans cells and cell-free culture supernatant showed a significant (P < 0.05) inhibition potential of the pathogens either on solid media or in broth co-cultures. Characterization of the antibacterial substances indicated their proteinaceous nature which assigned them most probably to bacteriocins group.

  2. Obliquity along plate boundaries

    Science.gov (United States)

    Philippon, Mélody; Corti, Giacomo

    2016-12-01

    Most of the plate boundaries are activated obliquely with respect to the direction of far field stresses, as roughly only 8% of the plate boundaries total length shows a very low obliquity (ranging from 0 to 10°, sub-orthogonal to the plate displacement). The obliquity along plate boundaries is controlled by (i) lateral rheological variations within the lithosphere and (ii) consistency with the global plate circuit. Indeed, plate tectonics and magmatism drive rheological changes within the lithosphere and consequently influence strain localization. Geodynamical evolution controls large-scale mantle convection and plate formation, consumption, and re-organization, thus triggering plate kinematics variations, and the adjustment and re-orientation of far field stresses. These geological processes may thus result in plate boundaries that are not perpendicular but oblique to the direction of far field stresses. This paper reviews the global patterns of obliquity along plate boundaries. Using GPlate, we provide a statistical analysis of present-day obliquity along plate boundaries. Within this framework, by comparing natural examples and geological models, we discuss deformation patterns and kinematics recorded along oblique plate boundaries.

  3. Significance of Cell-Free Epstein-Barr Virus DNA in Monitoring Prognosis of Nasopharyngeal Carcinoma

    Institute of Scientific and Technical Information of China (English)

    SurmeiCao; HuaqingMin; JinsongGao; MinghuongHong; XibinXiao; ChangqingZhong; XiaodongLiu; AilonZhong; XiangGuo

    2004-01-01

    OBJECTIVE It has been reported that cell-free Epstein-Barr virus (EBVDNA) in plasma was useful in diagnosing and monitoring nasopharyngeal carcinoma (NPC). The current study was designed to evaluate the significance of EBV-DNA in monitoring the prognosis of nasopharyngeal carcinoma and comparing its significance with that of plasma VCA/IgA and EA/IgA levels. METHODS EBV-DNA, VCA/IgA, and EA/IgA levels in plasma were determined in NPC patients with different prognosis after radiotherapy, including 30 distant metastatic patients, 22 local recurrence patients and 24 individuals with remission who had been followed-up for more than 2 years after treatment. EBV-DNA was determined using a real-time quantitative PCR system, and levels of VCA/IgA and EA/IgA were measured using standard immunofluorescence. In a cohort study, the indexes were determined after different radiation periods for the 20 new cases of nasopharyngeal carcinoma. RESULTS The median plasma EBV-DNA concentration was 135,100 copies/ml (interquartile range: 5,525-1,003 750)in metastatic group, 20,500 copies/ml (interquartile range: 0-58,500) in the local recurrence group and 0 copies/ml (interquartile range: 0-0) in the continuous remission group (P<0.05). The levels of VCA/IgA and EA/IgA showed no significant differences among the different groups. The high level of EBV-DNA concentration in the metastatic group was more than that in the local recurrence group. A level of 1,000,000 copies/ml of EBV DNA was an indication of distant metastasis of the NPC patients with a sensitivity of 27.3%. However, the sensitivity was 0 in the local recurrence group. For the 20 new patients, EBV-DNA concentration gradually decreased during the radiation period. Before radiation there were 32,050 copies/ml (interquartile range: 3,880-317,750), 0 copies/ml (interquartile range: 0-14 375) after a 40 Gy radiation dose and 0 copies/ml (interquartile range: 0-2940)after the radiation was finished (P<0.05). However, the levels of

  4. Optimizing Immobilized Enzyme Performance in Cell-Free Environments to Produce Liquid Fuels

    Energy Technology Data Exchange (ETDEWEB)

    Belfort, Georges [Rensselaer Polytechnic Inst., Troy, NY (United States). Dept. of Chemical and Biological Engineering; Grimaldi, Joseph J. [Rensselaer Polytechnic Inst., Troy, NY (United States). Dept. of Chemical and Biological Engineering

    2015-01-27

    Limitations on biofuel production using cell culture (Escherichia coli, Clostridium, Saccharomyces cerevisiae, brown microalgae, blue-green algae and others) include low product (alcohol) concentrations (≤0.2 vol%) due to feedback inhibition, instability of cells, and lack of economical product recovery processes. To overcome these challenges, an alternate simplified biofuel production scheme was tested based on a cell-free immobilized enzyme system. Using this cell free system, we were able to obtain about 2.6 times higher concentrations of iso-butanol using our non-optimized system as compared with live cell systems. This process involved two steps: (i) converts acid to aldehyde using keto-acid decarboxylase (KdcA), and (ii) produces alcohol from aldehyde using alcohol dehydrogenase (ADH) with a cofactor (NADH) conversion from inexpensive formate using a third enzyme, formate dehydrogenase (FDH). To increase stability and conversion efficiency with easy separations, the first two enzymes were immobilized onto methacrylate resin. Fusion proteins of labile KdcA (fKdcA) were expressed to stabilize the covalently immobilized KdcA. Covalently immobilized ADH exhibited long-term stability and efficient conversion of aldehyde to alcohol over multiple batch cycles without fusions. High conversion rates and low protein leaching were achieved by covalent immobilization of enzymes on methacrylate resin. The complete reaction scheme was demonstrated by immobilizing both ADH and fKdcA and using FDH free in solution. The new system without in situ removal of isobutanol achieved a 55% conversion of ketoisovaleric acid to isobutanol at a concentration of 0.5 % (v/v). Further increases in titer will require continuous removal of the isobutanol using our novel brush membrane system that exhibits a 1.5 fold increase in the separation factor of isobutanol from water versus that obtained for commercial silicone rubber membranes. These bio-inspired brush membranes are based on the

  5. Circulating Cell-Free DNA from Colorectal Cancer Patients May Reveal High KRAS or BRAF Mutation Load

    NARCIS (Netherlands)

    Mouliere, F.; Messaoudi, S. El; Gongora, C.; Guedj, A.S.; Robert, B.; Rio, M. del; Molina, F.; Lamy, P.J.; Lopez-Crapez, E.; Mathonnet, M.; Ychou, M.; Pezet, D.; Thierry, A.R.

    2013-01-01

    We used a novel method based on allele-specific quantitative polymerase chain reaction (Intplex) for the analysis of circulating cell.free DNA (ccfDNA) to compare total ccfDNA and KRAS- or BRAF-mutated ccfDNA concentrations in blood samples from mice xenografted with the human SW620 colorectal cance

  6. Conversion of dechlorodauricumine into miharumine by a cell-free preparation from cultured roots of Menispermum dauricum.

    Science.gov (United States)

    Hori, Rieko; Sugimoto, Gen; Matsui, Miharu; Yamauchi, Yasuo; Takikawa, Hirosato; Sugimoto, Yukihiro

    2009-02-01

    Dechlorodauricumine (5) and dechloroacutumine (6) were converted to miharumine (7) and dechloroacutumidine (8), respectively, by a cell-free preparation from cultured roots of Menispermum dauricum in the presence of FAD. The structures of 7 and 8 were elucidated on the basis of spectroscopic analyses and chemical conversion.

  7. Sodium nitrite induces acute central nervous system toxicity in guinea pigs exposed to systemic cell-free hemoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Buehler, Paul W.; Butt, Omer I. [Laboratory of Biochemistry and Vascular Biology, Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD (United States); D' Agnillo, Felice, E-mail: felice.dagnillo@fda.hhs.gov [Laboratory of Biochemistry and Vascular Biology, Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD (United States)

    2011-06-10

    Highlights: {yields} Toxicological implications associated with the use of NaNO{sub 2} therapy to treat systemic cell-free Hb exposure are not well-defined. {yields} Systemic Hb exposure followed by NaNO{sub 2} infusion induces acute CNS toxicities in guinea pigs. {yields} These CNS effects were not reproduced by the infusion of cell-free Hb or NaNO{sub 2} alone. {yields} NaNO{sub 2}-mediated oxidation of cell-free Hb may play a causative role in the observed CNS changes. -- Abstract: Systemic cell-free hemoglobin (Hb) released via hemolysis disrupts vascular homeostasis, in part, through the scavenging of nitric oxide (NO). Sodium nitrite (NaNO{sub 2}) therapy can attenuate the hypertensive effects of Hb. However, the chemical reactivity of NaNO{sub 2} with Hb may enhance heme- or iron-mediated toxicities. Here, we investigate the effect of NaNO{sub 2} on the central nervous system (CNS) in guinea pigs exposed to systemic cell-free Hb. Intravascular infusion of NaNO{sub 2}, at doses sufficient to alleviate Hb-mediated blood pressure changes, reduced the expression of occludin, but not zona occludens-1 (ZO-1) or claudin-5, in cerebral tight junctions 4 h after Hb infusion. This was accompanied by increased perivascular heme oxygenase-1 expression, neuronal iron deposition, increased astrocyte and microglial activation, and reduced expression of neuron-specific nuclear protein (NeuN). These CNS changes were not observed in animals treated with Hb or NaNO{sub 2} alone. Taken together, these findings suggest that the use of nitrite salts to treat systemic Hb exposure may promote acute CNS toxicity.

  8. Textile cell-free scaffolds for in situ tissue engineering applications.

    Science.gov (United States)

    Aibibu, Dilbar; Hild, Martin; Wöltje, Michael; Cherif, Chokri

    2016-03-01

    In this article, the benefits offered by micro-fibrous scaffold architectures fabricated by textile manufacturing techniques are discussed: How can established and novel fiber-processing techniques be exploited in order to generate templates matching the demands of the target cell niche? The problems related to the development of biomaterial fibers (especially from nature-derived materials) ready for textile manufacturing are addressed. Attention is also paid on how biological cues may be incorporated into micro-fibrous scaffold architectures by hybrid manufacturing approaches (e.g. nanofiber or hydrogel functionalization). After a critical review of exemplary recent research works on cell-free fiber based scaffolds for in situ TE, including clinical studies, we conclude that in order to make use of the whole range of favors which may be provided by engineered fibrous scaffold systems, there are four main issues which need to be addressed: (1) Logical combination of manufacturing techniques and materials. (2) Biomaterial fiber development. (3) Adaption of textile manufacturing techniques to the demands of scaffolds for regenerative medicine. (4) Incorporation of biological cues (e.g. stem cell homing factors).

  9. Effects of polymorphisms in ovine and caprine prion protein alleles on cell-free conversion

    Directory of Open Access Journals (Sweden)

    Eiden Martin

    2011-02-01

    Full Text Available Abstract In sheep polymorphisms of the prion gene (PRNP at the codons 136, 154 and 171 strongly influence the susceptibility to scrapie and bovine spongiform encephalopathy (BSE infections. In goats a number of other gene polymorphisms were found which are suspected to trigger similar effects. However, no strong correlation between polymorphisms and TSE susceptibility in goats has yet been obtained from epidemiological studies and only a low number of experimental challenge data are available at present. We have therefore studied the potential impact of these polymorphisms in vitro by cell-free conversion assays using mouse scrapie strain Me7. Mouse scrapie brain derived PrPSc served as seeds and eleven recombinant single mutation variants of sheep and goat PrPC as conversion targets. With this approach it was possible to assign reduced conversion efficiencies to specific polymorphisms, which are associated to low frequency in scrapie-affected goats or found only in healthy animals. Moreover, we could demonstrate a dominant-negative inhibition of prion polymorphisms associated with high susceptibility by alleles linked to low susceptibility in vitro.

  10. Intralaboratory validation of cell-free translation assay for detecting ricin toxin biological activity.

    Science.gov (United States)

    Lindsey, Changhong Y; Richardson, Jenny D; Brown, J Edward; Hale, Martha L

    2007-01-01

    A cell-free translation (CFT) assay for determining ricin biological activity was validated. The statistical data from the validation study showed a high level of precision within and between runs of the assay. The assay was specific for determining ricin biological activity in food-based matrixes and discriminated ricin from other ribosome-inactivating proteins. The mean bias (relative error) between measured ricin concentrations of 3 validation samples and their nominal concentrations was 1.1, 6.6, and 20.3%, while the coefficient of variation (CV) was 14.1, 7.7, and 13.5%, respectively, demonstrating good precision, accuracy, and linearity. The CVs of ricin concentrations in 2 ricin-containing samples calculated from a dilution series were <5 and <12%, respectively, demonstrating very good parallelism. The analyte stability of ricin-containing samples stored for 1 month either at 4 or -20 degrees C, the stability of ricin stock solutions, and the results of assays executed by different analysts and using different luminometers were evaluated. The statistical validation data confirmed that the 4-parameter logistic equation, y = (a - d)/[1 + (x/c)b] + d, provided an accurate representation of a sigmoidal relationship between the measured response and the observed ricin concentration for the CFT assay.

  11. Cell-free nucleic acids as noninvasive biomarkers for colorectal cancer detection

    KAUST Repository

    Mansour, Hicham

    2014-08-27

    Cell-free nucleic acids (CFNA) have been reported by several authors in blood, stool, and urine of patients with colorectal cancer (CRC). These genetic biomarkers can be an indication of neoplastic colorectal epithelial cells, and can thus potentially be used as noninvasive tests for the detection of the disease in CRC patients and monitor their staging, without the need to use heavier and invasive tools. In a number of test-trials, these genetic tests have shown the advantage of non-invasiveness, making them well accepted by most of the patients, without major side effects. They have also shown a promising sensitivity and specificity in the detection of malignant and premalignant neoplasms. Moreover, costs for performing such tests are very low. Several studies reported and confirmed the proof of the principle for these genetic tests for screening, diagnosis, and prognosis; the main challenge of translating this approach from research to clinical laboratory is the validation from large and long-term randomized trials to prove sustainable high sensitivity and specificity. In this paper, we present a review on the noninvasive genetics biomarkers for CRC detection described in the literature and the challenges that can be encountered for validation processes.

  12. Circulating cell-free mitochondrial DNA as a novel cancer biomarker: opportunities and challenges.

    Science.gov (United States)

    Yu, Man

    2012-10-01

    The unique characteristics of the mitochondrial genome, such as short length, simple molecular structure, and high copy number, have made monitoring aberrant changes of mitochondrial DNA (mtDNA) quantity an interesting molecular tool for early tumor detection with many advantages over the nuclear genome-based methods. Recently, circulating cell-free (ccf) mtDNA in blood has emerged on the platform as a non-invasive diagnostic and prognostic biomarker for many forms of solid tumors. Accumulating evidence demonstrate that plasma or serum ccf mtDNA levels are significantly different between cancer patients and healthy individuals. Furthermore, quantification of ccf mtDNA levels in circulation may assist in identifying patients from cancer-free healthy population. This minireview attempts to summarize our recent findings in this very promising field of cancer research. The potential technical challenges that we have encountered during the quantitative analysis of ccf mtDNA and mtDNA in general are also briefly discussed. Prospective studies with a larger cohort of patients in various cancer entities are beneficial to precisely define the clinical importance of assessing the ccf mtDNA amount for diagnosing and tracking malignant diseases and their progression.

  13. Mesenchymal Stem Cell-Derived Exosomes: New Opportunity in Cell-Free Therapy

    Science.gov (United States)

    Pashoutan Sarvar, Davod; Shamsasenjan, Karim; Akbarzadehlaleh, Parvin

    2016-01-01

    Mesenchymal stromal/stem cells (MSCs) are involved in tissue homeostasis through direct cell-to-cell interaction, as well as secretion of soluble factors. Exosomes are the sort of soluble biological mediators that obtained from MSCs cultured media in vitro. MSC-derived exosomes (MSC-DEs) which produced under physiological or pathological conditions are central mediators of intercellular communications by conveying proteins, lipids, mRNAs, siRNA, ribosomal RNAs and miRNAs to the neighbor or distant cells. MSC-DEs have been tested in various disease models, and the results have revealed that their functions are similar to those of MSCs. They have the supportive functions in organisms such as repairing tissue damages, suppressing inflammatory responses, and modulating the immune system. MSC-DEs are of great interest in the scope of regenerative medicine because of their unique capacity to the regeneration of the damaged tissues, and the present paper aims to introduce MSC-DEs as a novel hope in cell-free therapy.

  14. Cholesterol: A modulator of the phagocyte NADPH oxidase activity - A cell-free study

    Directory of Open Access Journals (Sweden)

    Rawand Masoud

    2014-01-01

    Full Text Available The NADPH oxidase Nox2, a multi-subunit enzyme complex comprising membrane and cytosolic proteins, catalyzes a very intense production of superoxide ions O2•−, which are transformed into other reactive oxygen species (ROS. In vitro, it has to be activated by addition of amphiphiles like arachidonic acid (AA. It has been shown that the membrane part of phagocyte NADPH oxidase is present in lipid rafts rich in cholesterol. Cholesterol plays a significant role in the development of cardio-vascular diseases that are always accompanied by oxidative stress. Our aim was to investigate the influence of cholesterol on the activation process of NADPH oxidase. Our results clearly show that, in a cell-free system, cholesterol is not an efficient activator of NADPH oxidase like arachidonic acid (AA, however it triggers a basal low superoxide production at concentrations similar to what found in neutrophile. A higher concentration, if present during the assembly process of the enzyme, has an inhibitory role on the production of O2•−. Added cholesterol acts on both cytosolic and membrane components, leading to imperfect assembly and decreasing the affinity of cytosolic subunits to the membrane ones. Added to the cytosolic proteins, it retains their conformations but still allows some conformational change induced by AA addition, indispensable to activation of NADPH oxidase.

  15. Characterization of a cell-free protein synthesizing system isolated from rat brain

    Energy Technology Data Exchange (ETDEWEB)

    Rajagopalan, L.E.; Harper, A.E.

    1987-05-01

    The authors have characterized a cell-free preparation from rat brain that can initiate translation of endogenous mRNAs in vitro and maintain protein synthesis for at least 90 minutes at an optimum temperature of 37C. The essential component of this system is a postmitochondrial supernate (PMS) obtained by centrifuging a whole brain homogenate at 10,000 x g for 10 minutes at 4C. In the presence of phosphocreatine (PC), ATP and GTP there is active incorporation of (TVS)methionine into trichloroacetic acid precipitable protein. Incorporation is sensitive to the concentrations of PC, magnesium and potassium ions and spermidine and is inhibited 50-60% in the presence of 7-methylguanosine 5'-monophosphate, a specific inhibitor of polypeptide chain initiation. The proteolysis of brain protein that occurs when the system is incubated for more than 60 min. can be minimized by adding bovine serum albumin. The addition of 3.0 mM 5'-guanylimidodiphosphate a non-hydrolyzable analog of GTP, blocks incorporation entirely. The phosphocreatine requirement for maintaining an optimum endogenous concentration of GTP is lowered from 10.0 mM to 5.0 mM in the presence of 2.0 mM NADPH. The system that initiates protein synthesis in vitro can be used to study changes in brain protein synthesis as a result of various treatments, and the mechanisms underlying such changes.

  16. Cell free fetal DNA testing in maternal blood of Romanian pregnant women

    Directory of Open Access Journals (Sweden)

    Viorica E Radoi

    2015-10-01

    Full Text Available Background: The discovery of circulating fetal DNA in maternal blood led to the discovery of new strategies to perform noninvasive testing for prenatal diagnosis. Objective: The purpose of the study was to detect fetal aneuploidy at chromosomes 13, 18, 21, X, and Y by analysis of fetal cell-free DNA from maternal blood, without endangering pregnancy. Materials and Methods: This retrospective study has been performed in Bucharest at Medlife Maternal and Fetal Medicine Department between 2013-2014. In total 201 women were offered noninvasive prenatal test. Maternal plasma samples were collected from women at greater than 9 weeks of gestation after informed consent and genetics counseling. Results: From 201 patients; 28 (13.93% had screening test with high risk for trisomy 21, 116 (57.71% had advanced maternal age, 1 (0.49% had second trimester ultrasound markers and the remaining 56 patients (27.86% performed the test on request. Of those patients, 189 (94.02% had a “low risk” result (99% risk all for trisomy 21 (T21. T21 was confirmed by amniocentesis in 1 patient and the other 4 patients declined confirmation. The 7 remaining patients (3.48% had a low fetal fraction of DNA. Conclusion: It is probably that prenatal diagnosis using fetal DNA in maternal blood would play an increasingly role in the future practice of prenatal testing because of high accuracy.

  17. The crosstalk of telomere dysfunction and inflammation through cell-free TERRA containing exosomes.

    Science.gov (United States)

    Wang, Zhuo; Lieberman, Paul M

    2016-08-01

    Telomeric repeats-containing RNA (TERRA) are telomere-derived non-coding RNAs that contribute to telomere function in protecting chromosome ends. We recently identified a cell-free form of TERRA (cfTERRA) enriched in extracellular exosomes. These cfTERRA-containing exosomes stimulate inflammatory cytokines when incubated with immune responsive cells. Here, we report that cfTERRA levels were increased in exosomes during telomere dysfunction induced by the expression of the dominant negative TRF2. The exosomes from these damaged cells also enriched with DNA damage marker γH2AX and fragmented telomere repeat DNA. Purified cfTERRA stimulated inflammatory cytokines, but the intact membrane-associated nucleoprotein complexes produced a more robust cytokine activation. Therefore, we propose cfTERRA-containing exosomes transport a telomere-associated molecular pattern (TAMP) and telomere-specific alarmin from dysfunctional telomeres to the extracellular environment to elicit an inflammatory response. Since cfTERRA can be readily detected in human serum it may provide a useful biomarker for the detection of telomere dysfunction in the early stage of cancers and aging-associated inflammatory disease.

  18. Equine fetal sex determination using circulating cell-free fetal DNA (ccffDNA).

    Science.gov (United States)

    de Leon, Priscila Marques Moura; Campos, Vinicius Farias; Dellagostin, Odir Antônio; Deschamps, João Carlos; Seixas, Fabiana Kömmling; Collares, Tiago

    2012-02-01

    In this study, polymerase chain reaction (PCR) reamplification of the first PCR product (2nd-PCR) and a qPCR assay were used to detect the sex determining region Y (SRY) gene from circulating cell-free fetal DNA (ccffDNA) in blood plasma of pregnant mares to determine fetal sex. The ccffDNA was isolated from plasma of 20 Thoroughbred mares (5-13 y old) in the final 3 mo of pregnancy (fetal sex was verified after foaling). For controls, plasma from two non-pregnant mares and two virgin mares were used, in addition to the non-template control. The 182 bp nucleotide sequence corresponding to the SRY-PCR product was confirmed by DNA sequencing. Based on SRY/PCR, 8 of 11 male and 9 of 9 female fetuses were correctly identified, resulting in a sensitivity of 72.7% (for male fetuses) and an overall accuracy of 85%. Furthermore, using SRY/2nd-PCR and qPCR techniques, sensitivity and accuracy were 90.9 and 95%, respectively. In conclusion, this study is apparently the first report of fetal sex determination in mares using ccffDNA.

  19. Biological Synthesis of Silver Nanoparticles by Cell-Free Extract of Spirulina platensis

    Directory of Open Access Journals (Sweden)

    Gaurav Sharma

    2015-01-01

    Full Text Available The present study explores biological synthesis of silver nanoparticles (AgNPs using the cell-free extract of Spirulina platensis. Biosynthesised AgNPs were characterised by UV-Vis spectroscopy, SEM, TEM, and FTIR analysis and finally evaluated for antibacterial activity. Extracellular synthesis using aqueous extract of S. platensis showed the formation of well scattered, highly stable, spherical AgNPs with an average size of 30–50 nm. The size and morphology of the nanoparticles were confirmed by SEM and TEM analysis. FTIR and UV-Vis spectra showed that biomolecules, proteins and peptides, are mainly responsible for the formation and stabilisation of AgNPs. Furthermore, the synthesised nanoparticles exhibited high antibacterial activity against pathogenic Gram-negative, that is, Escherichia coli, MTCC-9721; Proteus vulgaris, MTCC-7299; Klebsiella pneumoniae, MTCC-9751, and Gram-positive, that is, Staphylococcus aureus, MTCC-9542; S. epidermidis, MTCC-2639; Bacillus cereus, MTCC-9017, bacteria. The AgNPs had shown maximum zone of inhibition (ZOI that is 31.3±1.11 in P. vulgaris. Use of such a microalgal system provides a simple, cost-effective alternative template for the biosynthesis of nanomaterials of silver in a large scale that could be of great use in biomedical applications.

  20. High-throughput preparation methods of crude extract for robust cell-free protein synthesis.

    Science.gov (United States)

    Kwon, Yong-Chan; Jewett, Michael C

    2015-03-02

    Crude extract based cell-free protein synthesis (CFPS) has emerged as a powerful technology platform for high-throughput protein production and genetic part characterization. Unfortunately, robust preparation of highly active extracts generally requires specialized and costly equipment and can be labor and time intensive. Moreover, cell lysis procedures can be hard to standardize, leading to different extract performance across laboratories. These challenges limit new entrants to the field and new applications, such as comprehensive genome engineering programs to improve extract performance. To address these challenges, we developed a generalizable and easily accessible high-throughput crude extract preparation method for CFPS based on sonication. To validate our approach, we investigated two Escherichia coli strains: BL21 Star™ (DE3) and a K12 MG1655 variant, achieving similar productivity (defined as CFPS yield in g/L) by varying only a few parameters. In addition, we observed identical productivity of cell extracts generated from culture volumes spanning three orders of magnitude (10 mL culture tubes to 10 L fermentation). We anticipate that our rapid and robust extract preparation method will speed-up screening of genomically engineered strains for CFPS applications, make possible highly active extracts from non-model organisms, and promote a more general use of CFPS in synthetic biology and biotechnology.

  1. Substrate replenishment and byproduct removal improve yeast cell-free protein synthesis.

    Science.gov (United States)

    Schoborg, Jennifer A; Hodgman, C Eric; Anderson, Mark J; Jewett, Michael C

    2014-05-01

    Cell-free protein synthesis (CFPS) platforms are now considered a powerful tool for synthesizing a variety of proteins at scales from pL to 100 L with accelerated process development pipelines. We previously reported the advancement of a novel yeast-based CFPS platform. Here, we studied factors that cause termination of yeast CFPS batch reactions. Specifically, we characterized the substrate and byproduct concentrations in batch, fed-batch, and semi-continuous reaction formats through high-performance liquid chromatography (HPLC) and chemical assays. We discovered that creatine phosphate, the secondary energy substrate, and nucleoside triphosphates were rapidly degraded during batch CFPS, causing a significant drop in the reaction's energy charge (E.C.) and eventual termination of protein synthesis. As a consequence of consuming creatine phosphate, inorganic phosphate accumulated as a toxic byproduct. Additionally, we measured amino acid concentrations and found that aspartic acid was rapidly consumed. By adopting a semi-continuous reaction format, where passive diffusion enables substrate replenishment and byproduct removal, we achieved over a 70% increase in active superfolder green fluorescent protein (sfGFP) as compared with the batch system. This study identifies targets for the future improvement of the batch yeast CFPS reaction. Moreover, it outlines a detailed, generalized method to characterize and improve other CFPS platforms.

  2. Circulating Tumor Cell and Cell-free Circulating Tumor DNA in Lung Cancer.

    Science.gov (United States)

    Nurwidya, Fariz; Zaini, Jamal; Putra, Andika Chandra; Andarini, Sita; Hudoyo, Achmad; Syahruddin, Elisna; Yunus, Faisal

    2016-09-01

    Circulating tumor cells (CTCs) are tumor cells that are separated from the primary site or metastatic lesion and disseminate in blood circulation. CTCs are considered to be part of the long process of cancer metastasis. As a 'liquid biopsy', CTC molecular examination and investigation of single cancer cells create an important opportunity for providing an understanding of cancer biology and the process of metastasis. In the last decade, we have seen dramatic development in defining the role of CTCs in lung cancer in terms of diagnosis, genomic alteration determination, treatment response and, finally, prognosis prediction. The aims of this review are to understand the basic biology and to review methods of detection of CTCs that apply to the various types of solid tumor. Furthermore, we explored clinical applications, including treatment monitoring to anticipate therapy resistance as well as biomarker analysis, in the context of lung cancer. We also explored the potential use of cell-free circulating tumor DNA (ctDNA) in the genomic alteration analysis of lung cancer.

  3. Detection of Infertility-related Neutralizing Antibodies with a Cell-free Microfluidic Method

    Science.gov (United States)

    Eyer, Klaus; Root, Katharina; Verboket, Pascal E.; Dittrich, Petra S.

    2015-11-01

    The unwanted emergence of neutralizing antibodies (nAbs) against an endogenous or a therapeutic protein can result in deficiency diseases or therapy failure. Here, we developed a cell-free microfluidic method for the sensitive detection and quantification of nAbs in human serum that are associated with infertility. We used cell-derived vesicles containing the luteinizing hormone (LH)/choriogonadotropin receptor (LHHCGR) to detect nAbs against LH. The method exploits the entire cellular signal amplification mechanism, and facilitates the detection of as little as 0.44 nM of LH-nAb (Kd 1.5 nM) in human serum matrix within only 15 minutes. In addition, dose-response curves can be generated in less than 2 hours to evaluate the nAB concentration and dissociation constant. The developed system is devoid of problems associated with cell-based assays and we believe that this simple effect-directed analysis can be used in clinical environments, and is adaptable to other hormones or cytokines and their respective nAbs.

  4. A comparison of cell-free placental messenger ribonucleic acid and color Doppler ultrasound for the prediction of placental invasion in patients with placenta accreta

    Directory of Open Access Journals (Sweden)

    Elham Naghshineh

    2015-01-01

    Conclusions: Cell-free mRNA is an acceptable, easy made, functional test with sensitivity, specificity, PPV and NPV more than Doppler ultrasound for diagnosis and prediction of incidence of placenta accrete and we recommend the use of cell-free mRNA test for diagnosis of placenta accreta.

  5. Levels of plasma circulating cell free nuclear and mitochondrial DNA as potential biomarkers for breast tumors

    Directory of Open Access Journals (Sweden)

    Diesch Claude

    2009-11-01

    Full Text Available Abstract Background With the aim to simplify cancer management, cancer research lately dedicated itself more and more to discover and develop non-invasive biomarkers. In this connection, circulating cell-free DNA (ccf DNA seems to be a promising candidate. Altered levels of ccf nuclear DNA (nDNA and mitochondrial DNA (mtDNA have been found in several cancer types and might have a diagnostic value. Methods Using multiplex real-time PCR we investigated the levels of ccf nDNA and mtDNA in plasma samples from patients with malignant and benign breast tumors, and from healthy controls. To evaluate the applicability of plasma ccf nDNA and mtDNA as a biomarker for distinguishing between the three study-groups we performed ROC (Receiver Operating Characteristic curve analysis. We also compared the levels of both species in the cancer group with clinicopathological parameters. Results While the levels of ccf nDNA in the cancer group were significantly higher in comparison with the benign tumor group (P P P P = 0.022. The level of ccf nDNA was also associated with tumor-size (2 cmP = 0.034. Using ROC curve analysis, we were able to distinguish between the breast cancer cases and the healthy controls using ccf nDNA as marker (cut-off: 1866 GE/ml; sensitivity: 81%; specificity: 69%; P P Conclusion Our data suggests that nuclear and mitochondrial ccf DNA have potential as biomarkers in breast tumor management. However, ccf nDNA shows greater promise regarding sensitivity and specificity.

  6. Noninvasive Prenatal Diagnosis of Congenital Adrenal Hyperplasia Using Cell-Free Fetal DNA in Maternal Plasma

    Science.gov (United States)

    Tong, Yu K.; Yuen, Tony; Jiang, Peiyong; Pina, Christian; Chan, K. C. Allen; Khattab, Ahmed; Liao, Gary J. W.; Yau, Mabel; Kim, Se-Min; Chiu, Rossa W. K.; Sun, Li; Zaidi, Mone

    2014-01-01

    Context: Congenital adrenal hyperplasia (CAH) is an autosomal recessive condition that arises from mutations in CYP21A2 gene, which encodes for the steroidogenic enzyme 21-hydroxylase. To prevent genital ambiguity in affected female fetuses, prenatal treatment with dexamethasone must begin on or before gestational week 9. Currently used chorionic villus sampling and amniocentesis provide genetic results at approximately 14 weeks of gestation at the earliest. This means that mothers who want to undergo prenatal dexamethasone treatment will be unnecessarily treating seven of eight fetuses (males and three of four unaffected females), emphasizing the desirability of earlier genetic diagnosis in utero. Objective: The objective of the study was to develop a noninvasive method for early prenatal diagnosis of fetuses at risk for CAH. Patients: Fourteen families, each with a proband affected by phenotypically classical CAH, were recruited. Design: Cell-free fetal DNA was obtained from 3.6 mL of maternal plasma. Using hybridization probes designed to capture a 6-Mb region flanking CYP21A2, targeted massively parallel sequencing (MPS) was performed to analyze genomic DNA samples from parents and proband to determine parental haplotypes. Plasma DNA from pregnant mothers also underwent targeted MPS to deduce fetal inheritance of parental haplotypes. Results: In all 14 families, the fetal CAH status was correctly deduced by targeted MPS of DNA in maternal plasma, as early as 5 weeks 6 days of gestation. Conclusions: MPS on 3.6 mL plasma from pregnant mothers could potentially provide the diagnosis of CAH, noninvasively, before the ninth week of gestation. Only affected female fetuses will thus be treated. Our strategy represents a generic approach for noninvasive prenatal testing for an array of autosomal recessive disorders. PMID:24606108

  7. Biosensing and bioremediation of Cr(VI) by cell free extract of Enterobacter aerogenes T2.

    Science.gov (United States)

    Panda, Jigisha; Sarkar, Priyabrata

    2014-01-01

    Hexavalent chromium or Cr(VI) enters the environment through several anthropogenic activities and it is highly toxic and carcinogenic. Hence it is required to be detected and remediated from the environment. In this study, low-cost and environment-friendly methods of biosensing and bioremediation of Cr(VI) have been proposed. Crude cell free extract (CFE) of previously isolated Enterobacter aerogenes T2 (GU265554; NII 1111) was prepared and exploited to develop a stable biosensor for direct estimation of Cr(VI) in waste water, by using three electrodes via cyclic voltammetry. For bioremediation studies, a homogeneous solution of commercially available sodium alginate and CFE was added dropwise in a continuously stirred calcium chloride solution. Biologically modified calcium alginate beads were produced and these were further utilized for bioremediation studies. The proposed sensor showed linear response in the range of 10-40 μg L(-1) Cr(VI) and the limit of detection was found to be 6.6 μg L(-1) Cr(VI). No interference was observed in presence of metal ions, e.g., lead, cadmium, arsenic, tin etc., except for insignificant interference with molybdenum and manganese. In bioremediation studies, modified calcium alginate beads showed encouraging removal rate 900 mg Cr(VI)/m(3) water per day with a removal efficiency of 90%, much above than reported in literature. The proposed sensing system could be a viable alternative to costly measurement procedures. Calcium alginate beads, modified with CFE of E. aerogenes, could be used in bioremediation of Cr(VI) since it could work in real conditions with extraordinarily high capacity.

  8. Genome aberrations in canine mammary carcinomas and their detection in cell-free plasma DNA.

    Directory of Open Access Journals (Sweden)

    Julia Beck

    Full Text Available Mammary tumors are the most frequent cancers in female dogs exhibiting a variety of histopathological differences. There is lack of knowledge about the genomes of these common dog tumors. Five tumors of three different histological subtypes were evaluated. Massive parallel sequencing (MPS was performed in comparison to the respective somatic genome of each animal. Copy number and structural aberrations were validated using droplet digital PCR (ddPCR. Using mate-pair sequencing chromosomal aneuploidies were found in two tumors, frequent smaller deletions were found in one, inter-chromosomal fusions in one other, whereas one tumor was almost normal. These aberrations affect several known cancer associated genes such as cMYC, and KIT. One common deletion of the proximal end of CFA27, harboring the tumor suppressor gene PFDN5 was detected in four tumors. Using ddPCR, this deletion was validated and detected in 50% of tumors (N = 20. Breakpoint specific dPCRs were established for four tumors and tumor specific cell-free DNA (cfDNA was detected in the plasma. In one animal tumor-specific cfDNA was found >1 year after surgery, attributable to a lung metastasis. Paired-end sequencing proved that copy-number imbalances of the tumor are reflected by the cfDNA. This report on chromosomal instability of canine mammary cancers reveals similarities to human breast cancers as well as special canine alterations. This animal model provides a framework for using MPS for screening for individual cancer biomarkers with cost effective confirmation and monitoring using ddPCR. The possibility exists that ddPCR can be expanded to screening for common cancer related variants.

  9. Chimeric External Control to Quantify Cell Free DNA in Plasma Samples by Real Time PCR

    Science.gov (United States)

    Eini, Maryam; Behzad-Behbahani, Abbas; Takhshid, Mohammad Ali; Ramezani, Amin; Rafiei Dehbidi, Gholam Reza; Okhovat, Mohammad Ali; Farhadi, Ali; Alavi, Parniyan

    2016-01-01

    Background: DNA isolation procedure can significantly influence the quantification of DNA by real time PCR specially when cell free DNA (cfDNA) is the subject. To assess the extraction efficiency, linearity of the extraction yield, presence of co-purified inhibitors and to avoid problems with fragment size relevant to cfDNA, development of appropriate External DNA Control (EDC) is challenging. Using non-human chimeric nucleotide sequences, an EDC was developed for standardization of qPCR for monitoring stability of cfDNA concentration in blood samples over time. Methods: A0 DNA fragment of 167 bp chimeric sequence of parvovirus B19 and pBHA designated as EDC fragment was designed. To determine the impact of different factors during DNA extraction processing on quantification of cfDNA, blood samples were collected from normal subjects and divided into aliquots with and without specific treatment. In time intervals, the plasma samples were isolated. The amplicon of 167 bp EDC fragment in final concentration of 1.1 pg/500 μl was added to each plasma sample and total DNA was extracted by an in house method. Relative and absolute quantification real time PCR was performed to quantify both EDC fragment and cfDNA in extracted samples. Results: Comparison of real time PCR threshold cycle (Ct) for cfDNA fragment in tubes with and without specific treatment indicated a decrease in untreated tubes. In contrast, the threshold cycle was constant for EDC fragment in treated and untreated tubes, indicating the difference in Ct values of the cfDNA is because of specific treatments that were made on them. Conclusions: Spiking of DNA fragment size relevant to cfDNA into the plasma sample can be useful to minimize the bias due to sample preparation and extraction processing. Therefore, it is highly recommended that standard external DNA control be employed for the extraction and quantification of cfDNA for accurate data analysis. PMID:27141267

  10. Prolonging cell-free protein synthesis with a novel ATP regeneration system.

    Science.gov (United States)

    Kim, D M; Swartz, J R

    1999-01-01

    A new approach for the regeneration of adenosine triphosphate (ATP) during cell-free protein synthesis was developed to prolong the synthesis and also to avoid the accumulation of inorganic phosphate. This approach was demonstrated in a batch system derived from Escherichia coli. Contrary to the conventional methods in which exogenous energy sources contain high-energy phosphate bonds, the new system was designed to generate continuously the required high-energy phosphate bonds within the reaction mixture, thereby recycling the phosphate released during protein synthesis. If allowed to accumulate, phosphate inhibits protein synthesis, most likely by reducing the concentration of free magnesium ion. Pediococcus sp. pyruvate oxidase, when introduced in the reaction mixture along with thiamine pyrophosphate (TPP) and flavin adenine dinucleotide (FAD), catalyzed the generation of acetyl phosphate from pyruvate and inorganic phosphate. Acetyl kinase, already present with sufficient activity in Escherichia coli S30 extract, then catalyzed the regeneration of ATP. Oxygen is required for the generation of acetyl phosphate and the H(2)O(2) produced as a byproduct is sufficiently degraded by endogenous catalase activity. Through the continuous supply of chemical energy, and also through the prevention of inorganic phosphate accumulation, the duration of protein synthesis is extended up to 2 h. Protein accumulation levels also increase. The synthesis of human lymphotoxin receives greater benefit than than that of chloramphenicol acetyl transferase, because the former is more sensitive to phosphate inhibition. Finally, through repeated addition of pyruvate and amino acids during the reaction period, protein synthesis continued for 6 h in the new system, resulting in a final yield of 0.7 mg/mL.

  11. Effect of feeding whole compared with cell-free colostrum on calf immune status: Vaccination response.

    Science.gov (United States)

    Langel, S N; Wark, W A; Garst, S N; James, R E; McGilliard, M L; Petersson-Wolfe, C S; Kanevsky-Mullarky, I

    2016-05-01

    Vaccination contributes to improved herd health and production. Boosting immune development at a young age may have long-term effects by enhancing vaccine immune response and efficacy. In the bovine, colostrum is the sole source of maternal immunity, having a substantial effect on health status in the neonate. To date, colostral antibody concentration is used to evaluate colostrum quality. However, colostrum also contains proteins and cells, which may affect immune development and future responses to vaccines. To determine the effect of maternal colostral cells on immune development, 37 female Holstein and Jersey dairy calves were bottle-fed 4 quarts total of whole colostrum (WC) or cell-free colostrum (CFC) at birth. Calves were vaccinated with 2 series of multivalent vaccines. Series A consisted of vaccines given between 1 and 4mo of life. Series B consisted of vaccines given between 5 and 10mo of life. Calf peripheral blood samples were obtained before each vaccination series and monthly for 3mo after each vaccination series. Cellular blood parameters were determined by flow cytometry. Quantitative real-time PCR was used to determine cytokine gene expression in peripheral blood mononuclear cells before vaccination series B and once a month for 2mo after vaccination series B. Calves fed CFC had fewer numbers of B cells in mo 2 after vaccination series A when compared with WC-fed calves. Calves fed CFC had decreased gene expression levels of IL-2 in mo 1 and numbers of CD4(+)CD62L(+)CD45RO(-) and CD4(+)CD62L(+)CD45RO(+) T cells in mo 0 and 1 after vaccination series B as compared with WC-fed calves. Our findings indicate a greater response to vaccines up to 6 to 10mo post-WC feeding when compared with CFC. These data suggest that adoptive transfer of maternal colostral cells at birth has a long-term effect on development of the neonatal immune system.

  12. Generalized Fibonacci zone plates

    CERN Document Server

    Ke, Jie; Zhu, Jianqiang

    2015-01-01

    We propose a family of zone plates which are produced by the generalized Fibonacci sequences and their axial focusing properties are analyzed in detail. Compared with traditional Fresnel zone plates, the generalized Fibonacci zone plates present two axial foci with equal intensity. Besides, we propose an approach to adjust the axial locations of the two foci by means of different optical path difference, and further give the deterministic ratio of the two focal distances which attributes to their own generalized Fibonacci sequences. The generalized Fibonacci zone plates may allow for new applications in micro and nanophotonics.

  13. Membrane protein synthesis in cell-free systems: from bio-mimetic systems to bio-membranes.

    Science.gov (United States)

    Sachse, Rita; Dondapati, Srujan K; Fenz, Susanne F; Schmidt, Thomas; Kubick, Stefan

    2014-08-25

    When taking up the gauntlet of studying membrane protein functionality, scientists are provided with a plethora of advantages, which can be exploited for the synthesis of these difficult-to-express proteins by utilizing cell-free protein synthesis systems. Due to their hydrophobicity, membrane proteins have exceptional demands regarding their environment to ensure correct functionality. Thus, the challenge is to find the appropriate hydrophobic support that facilitates proper membrane protein folding. So far, various modes of membrane protein synthesis have been presented. Here, we summarize current state-of-the-art methodologies of membrane protein synthesis in biomimetic-supported systems. The correct folding and functionality of membrane proteins depend in many cases on their integration into a lipid bilayer and subsequent posttranslational modification. We highlight cell-free systems utilizing the advantages of biological membranes.

  14. Development of a Rapid Cell-free Method for Cytotoxicity Assessment of Vapor Phase of Cigarette Smoke

    Directory of Open Access Journals (Sweden)

    Cahours X

    2014-12-01

    Full Text Available Currently, several in vitro tests are widely used to measure toxicological properties of mainstream smoke (Neutral Red Uptake Assay, Micronucleus assay, Ames Test. These tests are necessary to assess cytotoxicity, genotoxicity, and mutagenicity, but are time consuming. This is essentially due to the preparation and the handling of cells. It is difficult to use these in vitro tests as screening method for product testing and development. For a better assessment of the cytotoxicity of the vapor phase, a rapid cell-free method has been developed. This paper describes a capillary electrophoresis cell-free method, based on the depletion of an anti-oxidant L-gamma-glutamyl-L-cysteinylglycine (GSH, applied to an aliquot of vapor phase phosphate buffered saline (PBS-trapped cigarette smoke (as recommended for in vitro testing. The correlation between this method and the survival/viability test (Neutral Red cytotoxicity is excellent (coefficient of correlation (r = 0.99.

  15. Reproducibility of Uniform Spheroid Formation in 384-Well Plates: The Effect of Medium Evaporation.

    Science.gov (United States)

    Das, Viswanath; Fürst, Tomáš; Gurská, Soňa; Džubák, Petr; Hajdúch, Marián

    2016-10-01

    Spheroid cultures of cancer cells reproduce the spatial dimension-induced in vivo tumor traits more effectively than the conventional two-dimensional cell cultures. With growing interest in spheroids for high-throughput screening (HTS) assays, there is an increasing demand for cost-effective miniaturization of reproducible spheroids in microtiter plates (MPs). However, well-to-well variability in spheroid size, shape, and growth is a frequently encountered problem with almost every culture method that has prevented the transfer of spheroids to the HTS platform. This variability partly arises due to increased susceptibility of MPs to edge effects and evaporation-induced changes in the growth of spheroids. In this study, we examined the effect of evaporation on the reproducibility of spheroids of tumor and nontumor cell lines in 384-well plates, and show that culture conditions that prevent evaporation-induced medium loss result in the formation of uniform spheroids across the plate. Additionally, we also present a few technical improvements to increase the scalability of the liquid-overlay spheroid culturing technique in MPs, together with a simple software routine for the quantification of spheroid size. We believe that these cost-effective improvements will aid in further improvement of spheroid cultures for HTS drug discovery.

  16. Enterococcus faecium LKE12 Cell-Free Extract Accelerates Host Plant Growth via Gibberellin and Indole-3-Acetic Acid Secretion.

    Science.gov (United States)

    Lee, Ko-Eun; Radhakrishnan, Ramalingam; Kang, Sang-Mo; You, Young-Hyun; Joo, Gil-Jae; Lee, In-Jung; Ko, Jae-Hwan; Kim, Jin-Ho

    2015-09-01

    The use of microbial extracts containing plant hormones is a promising technique to improve crop growth. Little is known about the effect of bacterial cell-free extracts on plant growth promotion. This study, based on phytohormonal analyses, aimed at exploring the potential mechanisms by which Enterococcus faecium LKE12 enhances plant growth in oriental melon. A bacterial strain, LKE12, was isolated from soil, and further identified as E. faecium by 16S rDNA sequencing and phylogenetic analysis. The plant growth-promoting ability of an LKE12 bacterial culture was tested in a gibberellin (GA)-deficient rice dwarf mutant (waito-C) and a normal GA biosynthesis rice cultivar (Hwayongbyeo). E. faecium LKE12 significantly improved the length and biomass of rice shoots in both normal and dwarf cultivars through the secretion of an array of gibberellins (GA1, GA3, GA7, GA8, GA9, GA12, GA19, GA20, GA24, and GA53), as well as indole-3-acetic acid (IAA). To the best of our knowledge, this is the first study indicating that E. faecium can produce GAs. Increases in shoot and root lengths, plant fresh weight, and chlorophyll content promoted by E. faecium LKE12 and its cell-free extract inoculated in oriental melon plants revealed a favorable interaction of E. faecium LKE12 with plants. Higher plant growth rates and nutrient contents of magnesium, calcium, sodium, iron, manganese, silicon, zinc, and nitrogen were found in cell-free extract-treated plants than in control plants. The results of the current study suggest that E. faecium LKE12 promotes plant growth by producing GAs and IAA; interestingly, the exogenous application of its cell-free culture extract can be a potential strategy to accelerate plant growth.

  17. Cell-free scaffolds with different stiffness but same microstructure promote bone regeneration in rabbit large bone defect model.

    Science.gov (United States)

    Chen, Guobao; Yang, Li; Lv, Yonggang

    2016-04-01

    To promote bone healing, bone repair biomaterials are increasingly designed to incorporate growth factors. However, the impact of matrix mechanics of cell-free scaffold independent of microstructure on the osteogenic differentiation of endogenous osteoprogenitor cells orchestrating bone repair and regeneration remains not to be fully understood. In our recent study, three-dimensional (3D) scaffolds with different stiffness but same microstructure have been successfully fabricated by coating decellularized bone with collagen/hydroxyapatite (HA) mixture with different collagen rations. It has been demonstrated that the scaffold with optimal stiffness can induce the osteogenic differentiation of MSCs in vitro and in the subcutaneous tissue. The present in vivo study further investigated the repair efficiency of these scaffolds in a rabbit radius with a critical-sized segmental defect model and its potential mechanism. Micro-computed tomography (μ-CT), X-ray and histological analysis were carried out to evaluate the repair capacity of these scaffolds. The results demonstrated that the cell-free scaffold with optimal stiffness incorporation of endogenous osteoprogenitor cells significantly promoted the repair and reconstruction quality of mass bone defect. One of the crucial mechanisms was that hypoxia and stromal cell-derived factor-1α (SDF-1α) mediated mesenchymal stem cells (MSCs) migration by which matrix mechanics exerted influence on bone fracture healing. These findings suggested that only modulating the matrix stiffness of cell-free scaffold can be one of the most attractive strategies for promoting the progression of bone healing.

  18. An extraordinary accumulation of (-)-pinoresinol in cell-free extracts of Forsythia intermedia: evidence for enantiospecific reduction of (+)-pinoresinol.

    Science.gov (United States)

    Katayama, T; Davin, L B; Lewis, N G

    1992-11-01

    Stereoselective and enantiospecific transformation mechanisms in lignan biogenesis are only now yielding to scientific inquiry: it has been shown that soluble cell-free preparations from Forsythia intermedia catalyse the formation of the enantiomerically pure lignan, (-)-secoisolariciresinol, when incubated with coniferyl alcohol in the presence of NAD(P)H and H2O2. Surprisingly, (-)-pinoresinol also accumulates in this soluble cell-free assay mixture in > 96% enantiomeric excess, even though it is not the naturally occurring antipode present in Forsythia sp. But these soluble cell-free preparations do not engender stereoselective coupling; instead, racemic pinoresinols are first formed, catalysed by an H2O2-dependent peroxidase reaction. An enantiospecific NAD(P)H reductase then converts (+)-pinoresinol, and not the (-)-antipode, into (-)-secoisolariciresinol. Stereoselective synthesis [correction of syntheis] of (+)-pinoresinol from E-coniferyl alcohol is, however, catalysed by an insoluble enzyme preparation in F. suspensa, obtained following removal of readily soluble and ionically bound enzymes; no exogenously supplied cofactors were required other than oxygen, although the reaction was stimulated by NAD-malate addition. Thus, the overall biochemical pathway to enantiomerically pure (-)-secoisolariciresinol has been delineated.

  19. Heterotrophic nature of the cell-free protein-synthesizing system from the strict chemolithotroph, Thiobacillus thiooxidans.

    Science.gov (United States)

    Amemiya, K; Umbreit, W W

    1974-02-01

    A cell-free protein-synthesizing system prepared from the strict chemolithotroph, Thiobacillus thiooxidans, was similar to that of heterotrophs. The poly-U directed system had a temperature optimum of 37 C, but in the presence of spermidine (3 mM) the optimum shifted to 45 C. Although growth of the chemolithotroph occurs only in acid conditions, the pH optimum for the cell-free system was pH 7.2. The endogenous-directed activity in the presence or absence of spermidine was maximal at pH 7.8. Spermidine had a stimulatory effect; however, this effect was dependent on the magnesium and tris(hydroxymethyl)aminomethane (Tris) concentrations. At low Tris concentrations (10 mM), spermidine (3 to 5 mM) could completely replace magnesium. When the Tris concentration was increased (50 mM), spermidine could not replace magnesium. Supernatant and ribosomal fractions from T. thiooxidans were exchanged with those of Bacillus thuringiensis and Escherichia coli, and the ribosomal fraction from the chemolithotroph gave good to moderate stimulation when exchanged with the supernatant from the heterotrophs. On the other hand, the supernatant from T. thiooxidans gave good stimulation when mixed with ribosomes from B. thuringiensis but poor activity with ribosomes from E. coli. Both supernatant and ribosomal fractions prepared from stationary phase extracts of T. thiooxidans were inactive in the cell-free system.

  20. The identification of 5'-fluoro-5-deoxyinosine as a shunt product in cell free extracts of Streptomyces cattleya.

    Science.gov (United States)

    Cobb, Steven L; Deng, Hai; Hamilton, John T G; McGlinchey, Ryan P; O'Hagan, David; Schaffrath, Christoph

    2005-10-01

    5'-Fluoro-5'-deoxyinosine (5'-FDI) is identified as an adventitious side product that accumulates in cell free incubations of SAM and fluoride ion in Streptomyces cattleya. 5'-FDI was identified by a combination of isotopic labelling studies and co-synthesis studies as well as enzymatic degradation. Although it is an efficiently generated end product of the cell free incubations, 5'-FDI is not a biosynthetic intermediate and it does not accumulate as a fluorometabolite with fluoroacetate and 4-fluorothreonine in whole cell incubations of S. cattleya. Clearly the purine deaminase which converts 5'-fluoro-5'-deoxyadenosine (5'-FDA) to 5'-FDI in the cell free extract does not come into contact with 5'-FDA in whole cells, suggesting some level of compartmentalisation in cells of S. cattleya. The biotransformation of 5'-FDI from fluoride ion extends the range of organofluorine products, beyond biosynthetic intermediates, that can be generated by this system, for applications such as enzymatic labelling with fluorine-18 for positron emission tomography applications.

  1. N-terminal fusion tags for effective production of g-protein-coupled receptors in bacterial cell-free systems.

    Science.gov (United States)

    Lyukmanova, E N; Shenkarev, Z O; Khabibullina, N F; Kulbatskiy, D S; Shulepko, M A; Petrovskaya, L E; Arseniev, A S; Dolgikh, D A; Kirpichnikov, M P

    2012-10-01

    G-protein-coupled receptors (GPCR) constitute one of the biggest families of membrane proteins. In spite of the fact that they are highly relevant to pharmacy, they have remained poorly explored. One of the main bottlenecks encountered in structural-functional studies of GPCRs is the difficulty to produce sufficient amounts of the proteins. Cell-free systems based on bacterial extracts fromE. colicells attract much attention as an effective tool for recombinant production of membrane proteins. GPCR production in bacterial cell-free expression systems is often inefficient because of the problems associated with the low efficiency of the translation initiation process. This problem could be resolved if GPCRs were expressed in the form of hybrid proteins with N-terminal polypeptide fusion tags. In the present work, three new N-terminal fusion tags are proposed for cell-free production of the human β2-adrenergic receptor, human M1 muscarinic acetylcholine receptor, and human somatostatin receptor type 5. It is demonstrated that the application of an N-terminal fragment (6 a.a.) of bacteriorhodopsin fromExiguobacterium sibiricum(ESR-tag), N-terminal fragment (16 а.о.) of RNAse A (S-tag), and Mistic protein fromB. subtilisallows to increase the CF synthesis of the target GPCRs by 5-38 times, resulting in yields of 0.6-3.8 mg from 1 ml of the reaction mixture, which is sufficient for structural-functional studies.

  2. Influence of erythrocyte aggregation at pathological levels on cell-free marginal layer in a narrow circular tube.

    Science.gov (United States)

    Namgung, Bumseok; Sakai, Hiromi; Kim, Sangho

    2015-01-01

    Human red blood cells (RBCs) were perfused in a circular micro-tube (inner diameter of 25 μm) to examine the dynamic changes of cell-free marginal region at both physiological (normal) and pathophysiological (hyper) levels of RBC aggregation. The cell-free area (CFA) was measured to provide additional information on the cell-free layer (CFL) width changes in space and time domains. A prominent enhancement in the mean CFL width was found in hyper-aggregating conditions as compared to that in non-aggregating conditions (P <  0.001). The frequent contacts between RBC and the tube wall were observed and the contact frequency was greatly decreased when the aggregation level was increased from none to normal (P <  0.05) and to hyper (P <  0.001) levels. In addition, the enhanced aggregation from none to hyper levels significantly enlarged the CFA (P <  0.01). We concluded that the RBC aggregation at pathophysiological levels could promote not only the CFL width (one-dimensional parameter) but also the spatiotemporal variation of CFA (two-dimensional parameter).

  3. Blue Willow Story Plates

    Science.gov (United States)

    Fontes, Kris

    2009-01-01

    In the December 1997 issue of "SchoolArts" is a lesson titled "Blue Willow Story Plates" by Susan Striker. In this article, the author shares how she used this lesson with her middle-school students many times over the years. Here, she describes a Blue Willow plate painting project that her students made.

  4. Generation of hydrogen peroxide from San Joaquin Valley particles in a cell-free solution

    Directory of Open Access Journals (Sweden)

    H. Shen

    2010-09-01

    Full Text Available Epidemiological studies have shown a correlation between exposure to ambient particulate matter (PM and adverse health effects. One proposed mechanism of PM-mediated health effects is the generation of reactive oxygen species (ROS – e.g., superoxide (•O2, hydrogen peroxide (HOOH, and hydroxyl radical (•OH – followed by oxidative stress. There are very few quantitative, specific measures of individual ROS generated from PM, but this information would help to more quantitatively address the link between ROS and the health effects of PM. To address this gap, we quantified the generation of HOOH by PM collected at an urban (Fresno and rural (Westside site in the San Joaquin Valley (SJV of California during summer and winter from 2006 to 2009. HOOH was quantified by HPLC after extracting the PM in a cell-free, phosphate-buffered saline (PBS solution with or without 50 μM ascorbate (Asc. Our results show that the urban PM generally generates much more HOOH than the rural PM but that there is no apparent seasonal difference in HOOH generation. In nearly all of the samples the addition of a physiologically relevant concentration of Asc greatly enhances HOOH formation, but a few of the coarse PM samples were able to generate a considerable amount of HOOH in the absence of added Asc, indicating the presence of unknown reductants. Normalized by air volume, the fine PM (PM2.5 generally makes more HOOH than the corresponding coarse PM (PMcf, i.e., 2.5 to 10 μm, primarily because the mass concentration of PM2.5 is much higher than that of PMcf. However, normalized by PM mass, the coarse PM typically generates more HOOH than the fine PM. The amount of HOOH produced by SJV PM is reduced on average by (78±15% when the transition metal chelator desferoxamine (DSF is added to the extraction solution, indicating that transition metals play a dominant role in HOOH generation. By

  5. Pre-analytical conditions in non-invasive prenatal testing of cell-free fetal RHD.

    Directory of Open Access Journals (Sweden)

    Frederik Banch Clausen

    Full Text Available BACKGROUND: Non-invasive prenatal testing of cell-free fetal DNA (cffDNA in maternal plasma can predict the fetal RhD type in D negative pregnant women. In Denmark, routine antenatal screening for the fetal RhD gene (RHD directs the administration of antenatal anti-D prophylaxis only to women who carry an RhD positive fetus. Prophylaxis reduces the risk of immunization that may lead to hemolytic disease of the fetus and the newborn. The reliability of predicting the fetal RhD type depends on pre-analytical factors and assay sensitivity. We evaluated the testing setup in the Capital Region of Denmark, based on data from routine antenatal RHD screening. METHODS: Blood samples were drawn at gestational age 25 weeks. DNA extracted from 1 mL of plasma was analyzed for fetal RHD using a duplex method for exon 7/10. We investigated the effect of blood sample transportation time (n = 110 and ambient outdoor temperatures (n = 1539 on the levels of cffDNA and total DNA. We compared two different quantification methods, the delta Ct method and a universal standard curve. PCR pipetting was compared on two systems (n = 104. RESULTS: The cffDNA level was unaffected by blood sample transportation for up to 9 days and by ambient outdoor temperatures ranging from -10 °C to 28 °C during transport. The universal standard curve was applicable for cffDNA quantification. Identical levels of cffDNA were observed using the two automated PCR pipetting systems. We detected a mean of 100 fetal DNA copies/mL at a median gestational age of 25 weeks (range 10-39, n = 1317. CONCLUSION: The setup for real-time PCR-based, non-invasive prenatal testing of cffDNA in the Capital Region of Denmark is very robust. Our findings regarding the transportation of blood samples demonstrate the high stability of cffDNA. The applicability of a universal standard curve facilitates easy cffDNA quantification.

  6. Hydrogen exchange during cell-free incorporation of deuterated amino acids and an approach to its inhibition

    Energy Technology Data Exchange (ETDEWEB)

    Tonelli, Marco; Singarapu, Kiran K. [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison (NMRFAM), Department of Biochemistry (United States); Makino, Shin-ichi; Sahu, Sarata C.; Matsubara, Yuko [University of Wisconsin-Madison, Center for Eukaryotic Structural Genomics (CESG), Department of Biochemistry (United States); Endo, Yaeta [Ehime University, Cell-Free Science and Technology Research Center (Japan); Kainosho, Masatsune [Tokyo Metropolitan University, Center for Priority Areas (Japan); Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison (NMRFAM), Department of Biochemistry (United States)

    2011-12-15

    Perdeuteration, selective deuteration, and stereo array isotope labeling (SAIL) are valuable strategies for NMR studies of larger proteins and membrane proteins. To minimize scrambling of the label, it is best to use cell-free methods to prepare selectively labeled proteins. However, when proteins are prepared from deuterated amino acids by cell-free translation in H{sub 2}O, exchange reactions can lead to contamination of {sup 2}H sites by {sup 1}H from the solvent. Examination of a sample of SAIL-chlorella ubiquitin prepared by Escherichia coli cell-free synthesis revealed that exchange had occurred at several residues (mainly at Gly, Ala, Asp, Asn, Glu, and Gln). We present results from a study aimed at identifying the exchanging sites and level of exchange and at testing a strategy for minimizing {sup 1}H contamination during wheat germ cell-free translation of proteins produced from deuterated amino acids by adding known inhibitors of transaminases (1 mM aminooxyacetic acid) and glutamate synthetase (0.1 mM l-methionine sulfoximine). By using a wheat germ cell-free expression system, we produced [U-{sup 2}H, {sup 15}N]-chlorella ubiquitin without and with added inhibitors, and [U-{sup 15}N]-chlorella ubiquitin as a reference to determine the extent of deuterium incorporation. We also prepared a sample of [U-{sup 13}C, {sup 15}N]-chlorella ubiquitin, for use in assigning the sites of exchange. The added inhibitors did not reduce the protein yield and were successful in blocking hydrogen exchange at C{sup {alpha}} sites, with the exception of Gly, and at C{sup {beta}} sites of Ala. We discovered, in addition, that partial exchange occurred with or without the inhibitors at certain side-chain methyl and methylene groups: Asn-H{sup {beta}}, Asp-H{sup {beta}}, Gln-H{sup {gamma}}, Glu-H{sup {gamma}}, and Lys-H{sup {epsilon}}. The side-chain labeling pattern, in particular the mixed chiral labeling resulting from partial exchange at certain sites, should be of

  7. Growth of the salt-tolerant yeast Zygosaccharomyces rouxii in microtiter plates : effects of NaCl, pH and temperature on growth and fusel alcohol production from branched-chain amino acids

    NARCIS (Netherlands)

    Jansen, Michael; Veurink, Janine H.; Euverink, Gert-Jan W.; Dijkhuizen, Lubbert

    2003-01-01

    Zygosaccharomyces rouxii, a salt-tolerant yeast isolated from the soy sauce process, produces fusel alcohols (isoamyl alcohol, active amyl alcohol and isobutyl alcohol) from branched-chain amino acids (leucine, isoleucine and valine, respectively) via the Ehrlich pathway. Using a high-throughput scr

  8. Pixelated neutron image plates

    Science.gov (United States)

    Schlapp, M.; Conrad, H.; von Seggern, H.

    2004-09-01

    Neutron image plates (NIPs) have found widespread application as neutron detectors for single-crystal and powder diffraction, small-angle scattering and tomography. After neutron exposure, the image plate can be read out by scanning with a laser. Commercially available NIPs consist of a powder mixture of BaFBr : Eu2+ and Gd2O3 dispersed in a polymer matrix and supported by a flexible polymer sheet. Since BaFBr : Eu2+ is an excellent x-ray storage phosphor, these NIPs are particularly sensitive to ggr-radiation, which is always present as a background radiation in neutron experiments. In this work we present results on NIPs consisting of KCl : Eu2+ and LiF that were fabricated into ceramic image plates in which the alkali halides act as a self-supporting matrix without the necessity for using a polymeric binder. An advantage of this type of NIP is the significantly reduced ggr-sensitivity. However, the much lower neutron absorption cross section of LiF compared with Gd2O3 demands a thicker image plate for obtaining comparable neutron absorption. The greater thickness of the NIP inevitably leads to a loss in spatial resolution of the image plate. However, this reduction in resolution can be restricted by a novel image plate concept in which a ceramic structure with square cells (referred to as a 'honeycomb') is embedded in the NIP, resulting in a pixelated image plate. In such a NIP the read-out light is confined to the particular illuminated pixel, decoupling the spatial resolution from the optical properties of the image plate material and morphology. In this work, a comparison of experimentally determined and simulated spatial resolutions of pixelated and unstructured image plates for a fixed read-out laser intensity is presented, as well as simulations of the properties of these NIPs at higher laser powers.

  9. ChooseMyPlate.gov

    Science.gov (United States)

    ... Topics Eating on a Budget Create a Grocery Game Plan Shop Smart to Fill Your Cart Prepare ... Eating on a Budget MyPlate Tip Sheets MyPlate Quiz Supertracker What's Cooking Tips Twitter What's New? MyPlate, ...

  10. Plate removal following orthognathic surgery.

    Science.gov (United States)

    Little, Mhairi; Langford, Richard Julian; Bhanji, Adam; Farr, David

    2015-11-01

    The objectives of this study are to determine the removal rates of orthognathic plates used during orthognathic surgery at James Cook University Hospital and describe the reasons for plate removal. 202 consecutive orthognathic cases were identified between July 2004 and July 2012. Demographics and procedure details were collected for these patients. Patients from this group who returned to theatre for plate removal between July 2004 and November 2012 were identified and their notes were analysed for data including reason for plate removal, age, smoking status, sex and time to plate removal. 3.2% of plates were removed with proportionally more plates removed from the mandible than the maxilla. 10.4% of patients required removal of one or more plate. Most plates were removed within the first post-operative year. The commonest reasons for plate removal were plate exposure and infection. The plate removal rates in our study are comparable to those seen in the literature.

  11. Plating in Top Agar

    OpenAIRE

    sprotocols

    2014-01-01

    1. Warm plates to room temperature before use. Cold plates causes the top agar to solidify irregularly. DO not warm plates to 37° as the top agar will take forever to solidify. - Prepare top agar as the appropriate liquid medium with 0.7% agar. Keeping 100 mL bottles is convenient. For phages, use λ top agar, which is less rich and yields bigger plaques. - Melt top agar in the microwave completely. Allow the agar to boil after liquification; incompletely melted agar looks liquid, but is...

  12. Anisotropic elastic plates

    CERN Document Server

    Hwu, Chyanbin

    2010-01-01

    As structural elements, anisotropic elastic plates find wide applications in modern technology. The plates here are considered to be subjected to not only in plane load but also transverse load. In other words, both plane and plate bending problems as well as the stretching-bending coupling problems are all explained in this book. In addition to the introduction of the theory of anisotropic elasticity, several important subjects have are discussed in this book such as interfaces, cracks, holes, inclusions, contact problems, piezoelectric materials, thermoelastic problems and boundary element a

  13. Circulating cell-free DNA: an up-coming molecular marker in exercise physiology.

    Science.gov (United States)

    Breitbach, Sarah; Tug, Suzan; Simon, Perikles

    2012-07-01

    The phenomenon of circulating cell-free DNA (cfDNA) concentrations is of importance for many biomedical disciplines including the field of exercise physiology. Increases of cfDNA due to exercise are described to be a potential hallmark for the overtraining syndrome and might be related to, or trigger adaptations of, immune function induced by strenuous exercise. At the same time, exercise provides a practicable model for studying the phenomenon of cfDNA that is described to be of pathophysiological relevance for different topics in clinical medicine like autoimmune diseases and cancer. In this review, we are summarizing the current knowledge of exercise-based acute and chronic alterations in cfDNA levels and their physiological significance. The effects of acute exercise on cfDNA concentrations have been investigated in resistance exercises and in continuous, stepwise and interval endurance exercises of different durations. cfDNA concentrations peaked immediately after acute exercise and showed a rapid return to baseline levels. Typical markers of skeletal muscle damage (creatine kinase, uric acid, C-reactive protein) show delayed kinetics compared with the cfDNA peak response. Exercise parameters such as intensity, duration or average energy expenditure do not explain the extent of increasing cfDNA concentrations after strenuous exercise. This could be due to complex processes inside the human organism during and after physical activity. Therefore, we hypothesize composite effects of different physiological stress parameters that come along with exercise to be responsible for increasing cfDNA concentrations. We suggest that due to acute stress, cfDNA levels increase rapidly by a spontaneous active or passive release mechanism that is not yet known. As a result of the rapid and parallel increase of cfDNA and lactate in an incremental treadmill test leading to exhaustion within 15-20 minutes, it is unlikely that cfDNA is released into the plasma by typical necrosis

  14. Designing Assemblies Of Plates

    Science.gov (United States)

    Williams, F. W.; Kennedy, D.; Butler, R.; Aston, G.; Anderson, M. S.

    1992-01-01

    VICONOPT calculates vibrations and instabilities of assemblies of prismatic plates. Designed for efficient, accurate analysis of buckling and vibration, and for optimum design of panels of composite materials. Written in FORTRAN 77.

  15. Tectonic Plate Movement.

    Science.gov (United States)

    Landalf, Helen

    1998-01-01

    Presents an activity that employs movement to enable students to understand concepts related to plate tectonics. Argues that movement brings topics to life in a concrete way and helps children retain knowledge. (DDR)

  16. Create Your Plate

    Medline Plus

    Full Text Available ... blood glucose levels and lose weight. With this method, you fill your plate with more non-starchy ... you have an easy portion control solution that works. Last Reviewed: October 8, 2015 Last Edited: September ...

  17. Fractal multifiber microchannel plates

    Science.gov (United States)

    Cook, Lee M.; Feller, W. B.; Kenter, Almus T.; Chappell, Jon H.

    1992-01-01

    The construction and performance of microchannel plates (MCPs) made using fractal tiling mehtods are reviewed. MCPs with 40 mm active areas having near-perfect channel ordering were produced. These plates demonstrated electrical performance characteristics equivalent to conventionally constructed MCPs. These apparently are the first MCPs which have a sufficiently high degree of order to permit single channel addressability. Potential applications for these devices and the prospects for further development are discussed.

  18. Origami - Folded Plate Structures

    OpenAIRE

    Buri, Hans Ulrich

    2010-01-01

    This research investigates new methods of designing folded plate structures that can be built with cross-laminated timber panels. Folded plate structures are attractive to both architects and engineers for their structural, spatial, and plastic qualities. Thin surfaces can be stiffened by a series of folds, and thus not only cover space, but also act as load bearing elements. The variation of light and shadow along the folded faces emphasizes the plas...

  19. Circulating levels of maternal plasma cell-free pregnancy-associated placenta-specific microRNAs are associated with placental weight.

    Science.gov (United States)

    Miura, K; Morisaki, S; Abe, S; Higashijima, A; Hasegawa, Y; Miura, S; Tateishi, S; Mishima, H; Yoshiura, K; Masuzaki, H

    2014-10-01

    The aim of this study was to investigate the relationship between plasma concentration of cell-free pregnancy-associated placenta-specific microRNAs and clinical variables (placental weight, maternal body mass index, and neonatal birth weight). Circulating levels of cell-free pregnancy-associated placenta-specific microRNAs (miR-515-3p, miR-517a, miR-517c and miR-518b) in maternal plasma were measured by quantitative real-time RT-PCR in sixty-two pregnant women. The levels of cell-free pregnancy-associated placenta-specific microRNAs were significantly associated with placental weight, but not associated with body mass index or birth weight. Therefore, the measurement of cell-free pregnancy-associated placenta-specific miRNAs levels in maternal plasma may reflect the pregnancy status related to placenta volume.

  20. Properties of catechol 1,2-dioxygenase in the cell free extract and immobilized extract of Mycobacterium fortuitum

    Directory of Open Access Journals (Sweden)

    A.S. Silva

    2013-01-01

    Full Text Available Polycyclic aromatic hydrocarbons (PAH are carcinogenic compounds which contaminate water and soil, and the enzymes can be used for bioremediation of these environments. This study aimed to evaluate some environmental conditions that affect the production and activity of the catechol 1,2-dioxygenase (C12O by Mycobacterium fortuitum in the cell free and immobilized extract in sodium alginate. The bacterium was grown in mineral medium and LB broth containing 250 mg L-1 of anthracene (PAH. The optimum conditions of pH (4.0-9.0, temperature (5-70 ºC, reaction time (10-90 min and the effect of ions in the enzyme activity were determined. The Mycobacterium cultivated in LB shown higher growth and the C12O activity was two-fold higher to that in the mineral medium. To both extracts the highest enzyme activity was at pH 8.0, however, the immobilized extract promoted the increase in the C12O activity in a pH range between 4.0 and 8.5. The immobilized extract increased the enzymatic activity time and showed the highest C12O activity at 45 ºC, 20 ºC higher than the greatest temperature in the cell free extract. The enzyme activity in both extracts was stimulated by Fe3+, Hg2+ and Mn2+ and inhibited by NH4+ and Cu2+, but the immobilization protected the enzyme against the deleterious effects of K+ and Mg2+ in tested concentrations. The catechol 1,2-dioxygenase of Mycobacterium fortuitum in the immobilized extract has greater stability to the variations of pH, temperature and reaction time, and show higher activity in presence of ions, comparing to the cell free extract.

  1. Exome Sequencing of Cell-Free DNA from Metastatic Cancer Patients Identifies Clinically Actionable Mutations Distinct from Primary Disease.

    Directory of Open Access Journals (Sweden)

    Timothy M Butler

    Full Text Available The identification of the molecular drivers of cancer by sequencing is the backbone of precision medicine and the basis of personalized therapy; however, biopsies of primary tumors provide only a snapshot of the evolution of the disease and may miss potential therapeutic targets, especially in the metastatic setting. A liquid biopsy, in the form of cell-free DNA (cfDNA sequencing, has the potential to capture the inter- and intra-tumoral heterogeneity present in metastatic disease, and, through serial blood draws, track the evolution of the tumor genome. In order to determine the clinical utility of cfDNA sequencing we performed whole-exome sequencing on cfDNA and tumor DNA from two patients with metastatic disease; only minor modifications to our sequencing and analysis pipelines were required for sequencing and mutation calling of cfDNA. The first patient had metastatic sarcoma and 47 of 48 mutations present in the primary tumor were also found in the cell-free DNA. The second patient had metastatic breast cancer and sequencing identified an ESR1 mutation in the cfDNA and metastatic site, but not in the primary tumor. This likely explains tumor progression on Anastrozole. Significant heterogeneity between the primary and metastatic tumors, with cfDNA reflecting the metastases, suggested separation from the primary lesion early in tumor evolution. This is best illustrated by an activating PIK3CA mutation (H1047R which was clonal in the primary tumor, but completely absent from either the metastasis or cfDNA. Here we show that cfDNA sequencing supplies clinically actionable information with minimal risks compared to metastatic biopsies. This study demonstrates the utility of whole-exome sequencing of cell-free DNA from patients with metastatic disease. cfDNA sequencing identified an ESR1 mutation, potentially explaining a patient's resistance to aromatase inhibition, and gave insight into how metastatic lesions differ from the primary tumor.

  2. Vibration and Buckling of Web Plate of the Plate Girder

    OpenAIRE

    高橋, 和雄; 呉, 明強; 中澤, 聡志; 筑紫, 宏之

    1998-01-01

    The vibration and buckling of the web of the plate girder are studied in this paper. The small deflection theory of the thin plate is used. The finite strip method is employed to solve vibration and buckling of the plate girder. Natural frequenies of buckling properties are shown for various plate girder bridges.

  3. Enzymatic activity of cell-free extracts from Burkholderia oxyphila OX-01 bio-converts (+)-catechin and (-)-epicatechin to (+)-taxifolin.

    Science.gov (United States)

    Otsuka, Yuichiro; Matsuda, Motoki; Sonoki, Tomonori; Sato-Izawa, Kanna; Goodell, Barry; Jelison, Jody; Navarro, Ronald R; Murata, Hitoshi; Nakamura, Masaya

    2016-12-01

    This study characterized the enzymatic ability of a cell-free extract from an acidophilic (+)-catechin degrader Burkholderia oxyphila (OX-01). The crude OX-01 extracts were able to transform (+)-catechin and (-)-epicatechin into (+)-taxifolin via a leucocyanidin intermediate in a two-step oxidation. Enzymatic oxidation at the C-4 position was carried out anaerobically using H2O as an oxygen donor. The C-4 oxidation occurred only in the presence of the 2R-catechin stereoisomer, with the C-3 stereoisomer not affecting the reaction. These results suggest that the OX-01 may have evolved to target both (+)-catechin and (-)-epicatechin, which are major structural units in plants.

  4. A pull-down method with a biotinylated bait protein prepared by cell-free translation using a puromycin linker.

    Science.gov (United States)

    Mochizuki, Yuki; Kohno, Fumiaki; Nishigaki, Koichi; Nemoto, Naoto

    2013-03-01

    In this paper, we demonstrate a novel pull-down method that dramatically reduces the cost and preparation time of a bait protein by cell-free translation with a puromycin linker. With the C-terminus of the bait protein linked to biotin through a puromycin molecule after the translation reaction and subsequent mRNA degradation by RNase, the prey protein was easily pulled down by streptavidin-coated magnetic beads in a test tube. Three fluorescent prey protein types were tested and confirmed by gel electrophoresis to be pulled down easily and rapidly, depending on their affinity.

  5. Establishment of Cell Free Conversion System With Biotin-labelled Recombinant PrPsen Expressed in E. Coli

    Institute of Scientific and Technical Information of China (English)

    JIN ZHANG; XIAO-PING DONG; JIAN-MEI GAO; FENG LI; JUN HAN; LAN CHEN; BAO-YUN ZHANG; XIAO-FAN WANG; WEI ZHOU; YONG LIU

    2006-01-01

    Objective To report a protocol using biotin-labelled PrP protein in cell free conversion assay instead of isotope. Methods A hamster PrP protein (HaPrP) was expressed in E. coli and purified with HIS-tag affinity chromatograph. After being labelled with biotin, HaPrP was mixed with PrPSc preparation from scrapie strain 263K. Results Protease-resistant bands were detected after four-day incubation. Conclusion The new conversion model provides a reliable, easily handling, and environment-friendly method for studies of prion and transmissible spongiform encephalopathies.

  6. Bending and stretching of plates

    CERN Document Server

    Mansfield, E H; Hemp, W S

    1964-01-01

    The Bending and Stretching of Plates deals with elastic plate theory, particularly on small- and large-deflexion theory. Small-deflexion theory concerns derivation of basic equations, rectangular plates, plates of various shapes, plates whose boundaries are amenable to conformal transformation, plates with variable rigidity, and approximate methods. Large-deflexion theory includes general equations and some exact solutions, approximate methods in large-deflexion theory, asymptotic large-deflexion theories for very thin plates. Asymptotic theories covers membrane theory, tension field theory, a

  7. High-throughput, cell-free, liposome-based approach for assessing in vitro activity of lipid kinases.

    Science.gov (United States)

    Demian, Douglas J; Clugston, Susan L; Foster, Meta M; Rameh, Lucia; Sarkes, Deborah; Townson, Sharon A; Yang, Lily; Zhang, Melvin; Charlton, Maura E

    2009-08-01

    Lipid kinases are central players in lipid signaling pathways involved in inflammation, tumorigenesis, and metabolic syndrome. A number of these kinase targets have proven difficult to investigate in higher throughput cell-free assay systems. This challenge is partially due to specific substrate interaction requirements for several of the lipid kinase family members and the resulting incompatibility of these substrates with most established, homogeneous assay formats. Traditional, cell-free in vitro investigational methods for members of the lipid kinase family typically involve substrate incorporation of [gamma-32P] and resolution of signal by thin-layer chromatography (TLC) and autoradiograph densitometry. This approach, although highly sensitive, does not lend itself to high-throughput testing of large numbers of small molecules (100 s to 1 MM+). The authors present the development and implementation of a fully synthetic, liposome-based assay for assessing in vitro activity of phosphatidylinositol-5-phosphate-4-kinase isoforms (PIP4KIIbeta and alpha) in 2 commonly used homogeneous technologies. They have validated these assays through compound testing in both traditional TLC and radioactive filterplate approaches as well as binding validation using isothermic calorimetry. A directed library representing known kinase pharmacophores was screened against type IIbeta phosphatidylinositol-phosphate kinase (PIPK) to identify small-molecule inhibitors. This assay system can be applied to other types and isoforms of PIPKs as well as a variety of other lipid kinase targets.

  8. Differential timing of antibody-mediated phagocytosis and cell-free killing of invasive African Salmonella allows immune evasion.

    Science.gov (United States)

    Siggins, Matthew K; O'Shaughnessy, Colette M; Pravin, John; Cunningham, Adam F; Henderson, Ian R; Drayson, Mark T; MacLennan, Calman A

    2014-04-01

    Nontyphoidal Salmonellae commonly cause fatal bacteraemia in African children lacking anti-Salmonella antibodies. These are facultative intracellular bacteria capable of cell-free and intracellular survival within macrophages. To better understand the relationship between extracellular and intracellular infection in blood and general mechanisms of Ab-related protection against Salmonella, we used human blood and sera to measure kinetics of Ab and complement deposition, serum-mediated bactericidal killing and phagocytosis of invasive African Salmonella enterica serovar Typhimurium D23580. Binding of antibodies peaked by 30 s, but C3 deposition lagged behind, peaking after 2-4 min. C5b-9 deposition was undetectable until between 2 and 6 min and peaked after 10 min, after which time an increase in serum-mediated killing occurred. In contrast, intracellular, opsonized Salmonellae were readily detectable within 5 min. By 10 min, around half of monocytes and most neutrophils contained bacteria. The same kinetics of serum-mediated killing and phagocytosis were observed with S. enterica Typhimurium laboratory strain SL1344, and the S. enterica Enteritidis African invasive isolate D24954 and laboratory strain PT4. The differential kinetics between cell-free killing and phagocytosis of invasive nontyphoidal Salmonella allows these bacteria to escape the blood and establish intracellular infection before they are killed by the membrane attack complex.

  9. Sodium nitrite induces acute central nervous system toxicity in guinea pigs exposed to systemic cell-free hemoglobin.

    Science.gov (United States)

    Buehler, Paul W; Butt, Omer I; D'Agnillo, Felice

    2011-06-10

    Systemic cell-free hemoglobin (Hb) released via hemolysis disrupts vascular homeostasis, in part, through the scavenging of nitric oxide (NO). Sodium nitrite (NaNO(2)) therapy can attenuate the hypertensive effects of Hb. However, the chemical reactivity of NaNO(2) with Hb may enhance heme- or iron-mediated toxicities. Here, we investigate the effect of NaNO(2) on the central nervous system (CNS) in guinea pigs exposed to systemic cell-free Hb. Intravascular infusion of NaNO(2), at doses sufficient to alleviate Hb-mediated blood pressure changes, reduced the expression of occludin, but not zona occludens-1 (ZO-1) or claudin-5, in cerebral tight junctions 4h after Hb infusion. This was accompanied by increased perivascular heme oxygenase-1 expression, neuronal iron deposition, increased astrocyte and microglial activation, and reduced expression of neuron-specific nuclear protein (NeuN). These CNS changes were not observed in animals treated with Hb or NaNO(2) alone. Taken together, these findings suggest that the use of nitrite salts to treat systemic Hb exposure may promote acute CNS toxicity.

  10. DASAF: An R Package for Deep Sequencing-Based Detection of Fetal Autosomal Abnormalities from Maternal Cell-Free DNA

    Directory of Open Access Journals (Sweden)

    Baohong Liu

    2016-01-01

    Full Text Available Background. With the development of massively parallel sequencing (MPS, noninvasive prenatal diagnosis using maternal cell-free DNA is fast becoming the preferred method of fetal chromosomal abnormality detection, due to its inherent high accuracy and low risk. Typically, MPS data is parsed to calculate a risk score, which is used to predict whether a fetal chromosome is normal or not. Although there are several highly sensitive and specific MPS data-parsing algorithms, there are currently no tools that implement these methods. Results. We developed an R package, detection of autosomal abnormalities for fetus (DASAF, that implements the three most popular trisomy detection methods—the standard Z-score (STDZ method, the GC correction Z-score (GCCZ method, and the internal reference Z-score (IRZ method—together with one subchromosome abnormality identification method (SCAZ. Conclusions. With the cost of DNA sequencing declining and with advances in personalized medicine, the demand for noninvasive prenatal testing will undoubtedly increase, which will in turn trigger an increase in the tools available for subsequent analysis. DASAF is a user-friendly tool, implemented in R, that supports identification of whole-chromosome as well as subchromosome abnormalities, based on maternal cell-free DNA sequencing data after genome mapping.

  11. An overview of circulating cell-free microRNAs as putative biomarkers in Alzheimer's and Parkinson's Diseases.

    Science.gov (United States)

    Batistela, Meire Silva; Josviak, Nalini Drieli; Sulzbach, Carla Daniela; de Souza, Ricardo Lehtonen Rodrigues

    2016-07-20

    Circulating cell-free microRNAs (miRNAs) are stable in many biological fluids and their expression profiles can suffer changes under different physiological and pathological conditions. In the last few years, miRNAs have been proposed as putative noninvasive biomarkers in diagnosis, prognosis and response to treatment for several diseases, including neurodegenerative disorders as Alzheimer's disease (AD) and Parkinson's disease (PD). Cognitive and/or motor impairments are usually considered for establishing clinical diagnosis, and at this stage, the majority of the neurons may already be lost making difficult attempts of novel therapies. In this review, we intend to survey the circulating cell-free miRNAs found as dysregulated in cerebrospinal fluid, serum and plasma samples in AD and PD patients, and show how those miRNAs can be useful for early and differential diagnosis. Beyond that, we highlighted the miRNAs that are possibly related to common molecular mechanisms in the neurodegeneration process, as well those miRNAs related to specific disease pathways.

  12. Asymmetric bioreduction of acetophenones by Baker's yeast and its cell-free extract encapsulated in sol-gel silica materials

    Science.gov (United States)

    Kato, Katsuya; Nakamura, Hitomi; Nakanishi, Kazuma

    2014-02-01

    Baker's yeast (BY) encapsulated in silica materials was synthesized using a yeast cell suspension and its cell-free extract during a sol-gel reaction of tetramethoxysilane with nitric acid as a catalyst. The synthesized samples were fully characterized using various methods, such as scanning electron microscopy, nitrogen adsorption-desorption, Fourier transform infrared spectroscopy, thermogravimetry, and differential thermal analysis. The BY cells were easily encapsulated inside silica-gel networks, and the ratio of the cells in the silica gel was approximately 75 wt%, which indicated that a large volume of BY was trapped with a small amount of silica. The enzyme activity (asymmetric reduction of prochiral ketones) of BY and its cell-free extract encapsulated in silica gel was investigated in detail. The activities and enantioselectivities of free and encapsulated BY were similar to those of acetophenone and its fluorine derivatives, which indicated that the conformation structure of BY enzymes inside silica-gel networks did not change. In addition, the encapsulated BY exhibited considerably better solvent (methanol) stability and recyclability compared to free BY solution. We expect that the development of BY encapsulated in sol-gel silica materials will significantly impact the industrial-scale advancement of high-efficiency and low-cost biocatalysts for the synthesis of valuable chiral alcohols.

  13. Anterior cervical plating

    Directory of Open Access Journals (Sweden)

    Gonugunta V

    2005-01-01

    Full Text Available Although anterior cervical instrumentation was initially used in cervical trauma, because of obvious benefits, indications for its use have been expanded over time to degenerative cases as well as tumor and infection of the cervical spine. Along with a threefold increase in incidence of cervical fusion surgery, implant designs have evolved over the last three decades. Observation of graft subsidence and phenomenon of stress shielding led to the development of the new generation dynamic anterior cervical plating systems. Anterior cervical plating does not conclusively improve clinical outcome of the patients, but certainly enhances the efficacy of autograft and allograft fusion and lessens the rate of pseudoarthrosis and kyphosis after multilevel discectomy and fusions. A review of biomechanics, surgical technique, indications, complications and results of various anterior cervical plating systems is presented here to enable clinicians to select the appropriate construct design.

  14. License plate detection algorithm

    Science.gov (United States)

    Broitman, Michael; Klopovsky, Yuri; Silinskis, Normunds

    2013-12-01

    A novel algorithm for vehicle license plates localization is proposed. The algorithm is based on pixel intensity transition gradient analysis. Near to 2500 natural-scene gray-level vehicle images of different backgrounds and ambient illumination was tested. The best set of algorithm's parameters produces detection rate up to 0.94. Taking into account abnormal camera location during our tests and therefore geometrical distortion and troubles from trees this result could be considered as passable. Correlation between source data, such as license Plate dimensions and texture, cameras location and others, and parameters of algorithm were also defined.

  15. Casimir force between metal plate and dielectric plate

    Institute of Scientific and Technical Information of China (English)

    刘中柱; 邵成刚; 罗俊

    1999-01-01

    The Casimir effect between metal plate and dielectric plate is discussed with 1+1-dimensional potential model without using cut-off method. Calculation shows that the Casimir force between metal plate and dielectric plate is determined not only by the potential V0, the dielectric thickness and the distance α between the metal plate and dielectric plate, but also by the dimension of the vessel. When α is far less than the dimension of the vessel, the Casimir force Fc∝α(-1); conversely Fc∝α-2. This result is significant for Casimir force experiment.

  16. Nuclear reactor alignment plate configuration

    Energy Technology Data Exchange (ETDEWEB)

    Altman, David A; Forsyth, David R; Smith, Richard E; Singleton, Norman R

    2014-01-28

    An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

  17. Create Your Plate

    Medline Plus

    Full Text Available ... 1 Type 2 About Us Online Community Meal Planning Sign In Search: Search More Sites Search ≡ Are ... Fitness Home Food MyFoodAdvisor Recipes Association Cookbook Recipes Planning Meals Diabetes Meal Plans Create Your Plate Gluten ...

  18. The Plate Tectonics Project

    Science.gov (United States)

    Hein, Annamae J.

    2011-01-01

    The Plate Tectonics Project is a multiday, inquiry-based unit that facilitates students as self-motivated learners. Reliable Web sites are offered to assist with lessons, and a summative rubric is used to facilitate the holistic nature of the project. After each topic (parts of the Earth, continental drift, etc.) is covered, the students will…

  19. INL HIP Plate Fabrication

    Energy Technology Data Exchange (ETDEWEB)

    B. H. Park; C. R. Clark; J. F. Jue

    2010-02-01

    This document outlines the process used to bond monolithic fuel plates by Hot Isostatic Pressing (HIP). This method was developed at Idaho National Laboratory (INL) for the Reduced Enrichment for Research and Test Reactors (RERTR) program. These foils have been used in a number of irradiation experiments in support of the United States Global Threat Reduction Initiative (GTRI) program.

  20. Cell-free synthesis of functional human epidermal growth factor receptor: Investigation of ligand-independent dimerization in Sf21 microsomal membranes using non-canonical amino acids

    Science.gov (United States)

    Quast, Robert B.; Ballion, Biljana; Stech, Marlitt; Sonnabend, Andrei; Varga, Balázs R.; Wüstenhagen, Doreen A.; Kele, Péter; Schiller, Stefan M.; Kubick, Stefan

    2016-01-01

    Cell-free protein synthesis systems represent versatile tools for the synthesis and modification of human membrane proteins. In particular, eukaryotic cell-free systems provide a promising platform for their structural and functional characterization. Here, we present the cell-free synthesis of functional human epidermal growth factor receptor and its vIII deletion mutant in a microsome-containing system derived from cultured Sf21 cells. We provide evidence for embedment of cell-free synthesized receptors into microsomal membranes and asparagine-linked glycosylation. Using the cricket paralysis virus internal ribosome entry site and a repetitive synthesis approach enrichment of receptors inside the microsomal fractions was facilitated thereby providing analytical amounts of functional protein. Receptor tyrosine kinase activation was demonstrated by monitoring receptor phosphorylation. Furthermore, an orthogonal cell-free translation system that provides the site-directed incorporation of p-azido-L-phenylalanine is characterized and applied to investigate receptor dimerization in the absence of a ligand by photo-affinity cross-linking. Finally, incorporated azides are used to generate stable covalently linked receptor dimers by strain-promoted cycloaddition using a novel linker system. PMID:27670253

  1. Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems.

    Science.gov (United States)

    Takahashi, Melissa K; Chappell, James; Hayes, Clarmyra A; Sun, Zachary Z; Kim, Jongmin; Singhal, Vipul; Spring, Kevin J; Al-Khabouri, Shaima; Fall, Christopher P; Noireaux, Vincent; Murray, Richard M; Lucks, Julius B

    2015-05-15

    RNA regulators are emerging as powerful tools to engineer synthetic genetic networks or rewire existing ones. A potential strength of RNA networks is that they may be able to propagate signals on time scales that are set by the fast degradation rates of RNAs. However, a current bottleneck to verifying this potential is the slow design-build-test cycle of evaluating these networks in vivo. Here, we adapt an Escherichia coli-based cell-free transcription-translation (TX-TL) system for rapidly prototyping RNA networks. We used this system to measure the response time of an RNA transcription cascade to be approximately five minutes per step of the cascade. We also show that this response time can be adjusted with temperature and regulator threshold tuning. Finally, we use TX-TL to prototype a new RNA network, an RNA single input module, and show that this network temporally stages the expression of two genes in vivo.

  2. Cell-free activation of phagocyte NADPH-oxidase: tissue and differentiation-specific expression of cytosolic cofactor activity.

    Science.gov (United States)

    Parkinson, J F; Akard, L P; Schell, M J; Gabig, T G

    1987-06-30

    We examined a variety of tissues for the presence of cytosolic cofactor activity that would support arachidonate-dependent cell-free activation of NADPH-oxidase in isolated human neutrophil membranes. Cofactor activity was not found in cytosol isolated from erythrocytes, lymphocytes, placenta, brain, liver, or the human promyelocytic leukemic cell line HL-60. Induction of differentiation in HL-60 cells led to expression of cytosolic cofactor activity. In dimethylsulphoxide-induced HL-60 cells the level of cytosolic cofactor activity was closely correlated with phorbol myristate acetate-stimulated whole cell superoxide production. These results strongly suggest that the cytosolic cofactor is a phagocyte-specific regulatory protein of physiologic importance in NADPH-oxidase activation.

  3. Cell-associated hemolytic activity in environmental strains of Plesiomonas shigelloides expressing cell-free, iron-influenced extracellular hemolysin.

    Science.gov (United States)

    González-Rodríguez, Nieves; Santos, Jesús A; Otero, Andrés; García-López, María-Luisa

    2007-04-01

    Hemolysis is a means of providing pathogenic bacteria with heme iron in vivo. In a previous work, iron-influenced hemolytic activity against sheep erythrocytes was detected in cell-free supernatants, but not in the cell fraction of two environmental Plesiomonas shigelloides strains incubated without shaking. Both strains have the hugA gene, which encodes an outer membrane receptor required for heme iron utilization. The present study was undertaken to investigate the expression of a second hemolytic activity detected during aerated incubation in normal and iron-depleted tryptone soya broth (id-TSB). An agar overlay procedure and doubling dilution titrations were employed to detect the hemolytic activity against several erythrocyte species. The kinetics of growth and hemolytic activity were assayed at 35 degrees C in aerated normal and id-TSB and salmon extract. Overlaid colonies showed a cell-associated beta-hemolytic activity within 4 h. For aerated cell-free supernatants, titers above 16 were not attained until 30 to 48 h of incubation; the best activity was noted with dog and mouse erythrocytes. After 24 h of aerated incubation, sonicated cells yielded high hemolytic activity against dog erythrocytes without activity in supernatants, but after 48 h, only 28 to 30% of the total activity remained cell associated. The hemolytic factor was released in broths during the death phase. Hemolytic activity was not detected in fish extract. This and other studies suggest that P. shigelloides may produce at least two hemolytic factors, their expression and detection being influenced by environmental growth conditions and testing procedures. The overlay assay appears to be the best routine method for detecting hemolytic activity in P. shigelloides.

  4. Recombinant Nox4 cytosolic domain produced by a cell or cell-free base systems exhibits constitutive diaphorase activity

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Minh Vu Chuong, E-mail: mvchuong@yahoo.fr [GREPI AGIM FRE 3405 CNRS-UJF, Universite Joseph Fourier, Grenoble (France); Zhang, Leilei [GREPI AGIM FRE 3405 CNRS-UJF, Universite Joseph Fourier, Grenoble (France); Lhomme, Stanislas; Mouz, Nicolas [PX' Therapeutics, MINATEC/Batiment de Haute Technologie, Grenoble (France); Lenormand, Jean-Luc [HumProTher Laboratory, TheReX/TIMC-IMAG UMR 5525 CNRS UJF, Universite Joseph Fourier, UFR de Medecine, Domaine de la Merci, 38706 La Tronche (France); Lardy, Bernard; Morel, Francoise [GREPI AGIM FRE 3405 CNRS-UJF, Universite Joseph Fourier, Grenoble (France)

    2012-03-16

    Highlights: Black-Right-Pointing-Pointer A comparison of two bacterial cell and cell-free protein expression systems is presented. Black-Right-Pointing-Pointer Soluble and active truncated Nox4 proteins are produced. Black-Right-Pointing-Pointer Nox4 has a constitutive diaphorase activity which is independent of cytosolic factors. Black-Right-Pointing-Pointer Isoform Nox4B is unable to initiate the first electronic transfer step. Black-Right-Pointing-Pointer Findings contribute to the understanding of the mechanism of Nox4 oxidase activity. -- Abstract: The membrane protein NADPH (nicotinamide adenine dinucleotide phosphate) oxidase Nox4 constitutively generates reactive oxygen species differing from other NADPH oxidases activity, particularly in Nox2 which needs a stimulus to be active. Although the precise mechanism of production of reactive oxygen species by Nox2 is well characterized, the electronic transfer throughout Nox4 remains unclear. Our study aims to investigate the initial electronic transfer step (diaphorase activity) of the cytosolic tail of Nox4. For this purpose, we developed two different approaches to produce soluble and active truncated Nox4 proteins. We synthesized soluble recombinant proteins either by in vitro translation or by bacteria induction. While proteins obtained by bacteria induction demonstrate an activity of 4.4 {+-} 1.7 nmol/min/nmol when measured against iodonitro tetrazolium chloride and 20.5 {+-} 2.8 nmol/min/nmol with cytochrome c, the soluble proteins produced by cell-free expression system exhibit a diaphorase activity with a turn-over of 26 {+-} 2.6 nmol/min/nmol when measured against iodonitro tetrazolium chloride and 48 {+-} 20.2 nmol/min/nmol with cytochrome c. Furthermore, the activity of the soluble proteins is constitutive and does not need any stimulus. We also show that the cytosolic tail of the isoform Nox4B lacking the first NADPH binding site is unable to demonstrate any diaphorase activity pointing out the

  5. Blood-Brain Barrier Disruption and Oxidative Stress in Guinea Pig after Systemic Exposure to Modified Cell-Free Hemoglobin

    Science.gov (United States)

    Butt, Omer I.; Buehler, Paul W.; D'Agnillo, Felice

    2011-01-01

    Systemic exposure to cell-free hemoglobin (Hb) or its breakdown products after hemolysis or with the use of Hb-based oxygen therapeutics may alter the function and integrity of the blood-brain barrier. Using a guinea pig exchange transfusion model, we investigated the effect of a polymerized cell-free Hb (HbG) on the expression of endothelial tight junction proteins (zonula occludens 1, claudin-5, and occludin), astrocyte activation, IgG extravasation, heme oxygenase (HO), iron deposition, oxidative end products (4-hydroxynonenal adducts and 8-hydroxydeoxyguanosine), and apoptosis (cleaved caspase 3). Reduced zonula occludens 1 expression was observed after HbG transfusion as evidenced by Western blot and confocal microscopy. Claudin-5 distribution was altered in small- to medium-sized vessels. However, total expression of claudin-5 and occludin remained unchanged except for a notable increase in occludin 72 hours after HbG transfusion. HbG-transfused animals also showed increased astrocytic glial fibrillary acidic protein expression and IgG extravasation after 72 hours. Increased HO activity and HO-1 expression with prominent enhancement of HO-1 immunoreactivity in CD163-expressing perivascular cells and infiltrating monocytes/macrophages were also observed. Consistent with oxidative stress, HbG increased iron deposition, 4-hydroxynonenal and 8-hydroxydeoxyguanosine immunoreactivity, and cleaved caspase-3 expression. Systemic exposure to an extracellular Hb triggers blood-brain barrier disruption and oxidative stress, which may have important implications for the use of Hb-based therapeutics and may provide indirect insight on the central nervous system vasculopathies associated with excessive hemolysis. PMID:21356382

  6. MyPlate Food Guide

    Science.gov (United States)

    ... Surgery? A Week of Healthy Breakfasts Shyness MyPlate Food Guide KidsHealth > For Teens > MyPlate Food Guide Print ... other sugary drinks. Avoid oversized portions. continue Five Food Groups Different food groups meet different nutrition needs. ...

  7. Controlling Laminate Plate Elastic Behavior

    OpenAIRE

    Mareš, T.

    2004-01-01

    This paper aims to express the relation of a measure of laminate plate stiffness with respect to the fiber orientation of its plies. The inverse of the scalar product of the lateral displacement of the central plane and lateral loading of the plate is the measure of laminate plate stiffness. In the case of a simply supported rectangular laminate plate this measure of stiffness is maximized, and the optimum orientation of its plies is searched.

  8. Microchannel plate streak camera

    Science.gov (United States)

    Wang, Ching L.

    1989-01-01

    An improved streak camera in which a microchannel plate electron multiplier is used in place of or in combination with the photocathode used in prior streak cameras. The improved streak camera is far more sensitive to photons (UV to gamma-rays) than the conventional x-ray streak camera which uses a photocathode. The improved streak camera offers gamma-ray detection with high temporal resolution. It also offers low-energy x-ray detection without attenuation inside the cathode. Using the microchannel plate in the improved camera has resulted in a time resolution of about 150 ps, and has provided a sensitivity sufficient for 1000 KeV x-rays.

  9. Elastic plate spallation

    Science.gov (United States)

    Oline, L.; Medaglia, J.

    1972-01-01

    The dynamic finite element method was used to investigate elastic stress waves in a plate. Strain displacement and stress strain relations are discussed along with the stiffness and mass matrix. The results of studying point load, and distributed load over small, intermediate, and large radii are reported. The derivation of finite element matrices, and the derivation of lumped and consistent matrices for one dimensional problems with Laplace transfer solutions are included. The computer program JMMSPALL is also included.

  10. Electronic Equipment Cold Plates

    Science.gov (United States)

    1976-04-01

    equations for such a flow regiae. For laainar flow and Moderate teaperature differwwe« between the well «nd coolant, a aodifled Sieder -Tate...con- figuration. The heat-transfer coefficients, therefore, were determined by using both the Sieder -Tate and McAdams equations and the coaputed...values used In the analytical predictions. As with th* previous cold Plates, the Sieder -Tate equation gave too low of values for the heat- transfer

  11. Vehicle License Plate Recognition Syst

    Directory of Open Access Journals (Sweden)

    Meenakshi,R. B. Dubey

    2012-12-01

    Full Text Available The vehicle license plate recognition system has greater efficiency for vehicle monitoring in automatic zone access control. This Plate recognition system will avoid special tags, since all vehicles possess a unique registration number plate. A number of techniques have been used for car plate characters recognition. This system uses neural network character recognition and pattern matching of characters as two character recognition techniques. In this approach multilayer feed-forward back-propagation algorithm is used. The performance of the proposed algorithm has been tested on several car plates and provides very satisfactory results.

  12. Plate tectonics conserves angular momentum

    Directory of Open Access Journals (Sweden)

    C. Bowin

    2009-03-01

    Full Text Available A new combined understanding of plate tectonics, Earth internal structure, and the role of impulse in deformation of the Earth's crust is presented. Plate accelerations and decelerations have been revealed by iterative filtering of the quaternion history for the Euler poles that define absolute plate motion history for the past 68 million years, and provide an unprecedented precision for plate angular rotation variations with time at 2-million year intervals. Stage poles represent the angular rotation of a plate's motion between adjacent Euler poles, and from which the maximum velocity vector for a plate can be determined. The consistent maximum velocity variations, in turn, yield consistent estimates of plate accelerations and decelerations. The fact that the Pacific plate was shown to accelerate and decelerate, implied that conservation of plate tectonic angular momentum must be globally conserved, and that is confirmed by the results shown here (total angular momentum ~1.4 E+27 kgm2s−1. Accordingly, if a plate decelerates, other plates must increase their angular momentums to compensate. In addition, the azimuth of the maximum velocity vectors yields clues as to why the "bend" in the Emperor-Hawaiian seamount trend occurred near 46 Myr. This report summarizes processing results for 12 of the 14 major tectonic plates of the Earth (except for the Juan de Fuca and Philippine plates. Plate accelerations support the contention that plate tectonics is a product of torques that most likely are sustained by the sinking of positive density anomalies due to phase changes in subducted gabbroic lithosphere at depth in the upper lower mantle (above 1200 km depth. The tectonic plates are pulled along by the sinking of these positive mass anomalies, rather than moving at near constant velocity on the crests of convection cells driven by rising heat. These results imply that spreading centers are primarily passive reactive

  13. Using plate mapping to examine portion size and plate composition for large and small divided plates.

    Science.gov (United States)

    Sharp, David E; Sobal, Jeffery; Wansink, Brian

    2014-12-01

    Does the size of a plate influence the serving of all items equally, or does it influence the serving of some foods - such as meat versus vegetables - differently? To examine this question, we used the new method of plate mapping, where people drew a meal on a paper plate to examine sensitivity to small versus large three-compartment divided plates in portion size and meal composition in a sample of 109 university students. The total drawn meal area was 37% bigger on large plates than small plates, which showed that the portion of plate coverage did not differ by plate size. Men and women drew bigger vegetable portions and men drew bigger meat portions on large plates when compared to small plates. These results suggest that men and women are differentially sensitive to plate size for overall meal size and for meal composition. Implications for decreasing portion size and improving meal balance are that plate size may influence portion size and change the proportions of foods served.

  14. Temperature field of steel plate cooling process after plate rolling

    Directory of Open Access Journals (Sweden)

    Huijun Feng, Lingen Chen, Fengrui Sun

    2015-01-01

    Full Text Available Based on numerical calculation with Matlab, the study on cooling process after plate rolling is carried out, and the temperature field distribution of the plate varying with the time is obtained. The effects of the plate thickness, final rolling temperature, cooling water temperature, average flow rate of the cooling water, carbon content of the plate and cooling method on the plate surface and central temperatures as well as final cooling temperature are discussed. For the same cooling time, the plate surface and central temperatures as well as their temperature difference increase; with the decrease in rolling temperature and the increase in average flow rate of the cooling water, the plate surface and central temperatures decrease. Compared with the single water cooling process, the temperature difference between the plate centre and surface based on intermittent cooling is lower. In this case, the temperature uniformity of the plate is better, and the corresponding thermal stress is lower. The fitting equation of the final cooling temperature with respect to plate thickness, final rolling temperature, cooling water temperature and average flow rate of the cooling water is obtained.

  15. Real Plates and Dubious Microplates

    Science.gov (United States)

    Kogan, M. G.; Steblov, G. M.

    2008-12-01

    From the onset of plate tectonics, the existence of most of the plates was never put in doubt, although the boundaries of some plates, like Africa, were later revised. There are however, two microplates in northeast Asia, the Amurian and Okhotsk, whose existence and the sense of rotation was revised several times. The rms value of plate-residual GPS velocities is 0.5-0.9 mm/a for sets of stations representing the motion of the following plates: Antarctic, Australian, Eurasian, North American, Nubian, Pacific, and South American. This value can be regarded as an upper bound on deviation of real plates from infinite stiffness. The rms value of plate-residual GPS velocities is 1.2-1.8 mm/a for the Indian, Nazca, and Somalian plates. Higher rms values for India and Nazca are attributed to the noisier data. The higher rms value for Somalia appears to arise from the distributed deformation to the east of the East African Rift; whether this statement is true can only be decided from observations of denser network in the future. From the analysis of plate-residual GPS velocities, the Canadian Arctic and northeastern Siberia belong to the North American plate. The detailed GPS survey on Sakhalin Island shows that the Sea of Okhotsk region also belongs to the North American plate while the region to the west of it belongs to the Eurasian plate. These results provide a constraint on the geometry of the North American plate and put in doubt the existence of smaller plates in northeast Asia.

  16. Sonocatalytic injury of cancer cells attached on the surface of a nickel-titanium dioxide alloy plate.

    Science.gov (United States)

    Ninomiya, Kazuaki; Maruyama, Hirotaka; Ogino, Chiaki; Takahashi, Kenji; Shimizu, Nobuaki

    2016-01-01

    The present study demonstrates ultrasound-induced cell injury using a nickel-titanium dioxide (Ni-TiO2) alloy plate as a sonocatalyst and a cell culture surface. Ultrasound irradiation of cell-free Ni-TiO2 alloy plates with 1 MHz ultrasound at 0.5 W/cm(2) for 30s led to an increased generation of hydroxyl (OH) radicals compared to nickel-titanium (Ni-Ti) control alloy plates with and without ultrasound irradiation. When human breast cancer cells (MCF-7 cells) cultured on the Ni-TiO2 alloy plates were irradiated with 1 MHz ultrasound at 0.5 W/cm(2) for 30s and then incubated for 48 h, cell density on the alloy plate was reduced to approximately 50% of the controls on the Ni-Ti alloy plates with and without ultrasound irradiation. These results indicate the injury of MCF-7 cells following sonocatalytic OH radical generation by Ni-TiO2. Further experiments demonstrated cell shrinkage and chromatin condensation after ultrasound irradiation of MCF-7 cells attached on the Ni-TiO2 alloy plates, indicating induction of apoptosis.

  17. Plate Full of Color

    Centers for Disease Control (CDC) Podcasts

    2008-08-04

    The Eagle Books are a series of four books that are brought to life by wise animal characters - Mr. Eagle, Miss Rabbit, and Coyote - who engage Rain That Dances and his young friends in the joy of physical activity, eating healthy foods, and learning from their elders about health and diabetes prevention. Plate Full of Color teaches the value of eating a variety of colorful and healthy foods.  Created: 8/4/2008 by National Center for Chronic Disease Prevention and Health Promotion (NCCDPHP).   Date Released: 8/5/2008.

  18. Dynamics of Tectonic Plates

    CERN Document Server

    Pechersky, E; Sadowski, G; Yambartsev, A

    2014-01-01

    We suggest a model that describes a mutual dynamic of tectonic plates. The dynamic is a sort of stick-slip one which is modeled by a Markov random process. The process defines a microlevel of the dynamic. A macrolevel is obtained by a scaling limit which leads to a system of integro-differential equations which determines a kind of mean field systems. Conditions when Gutenberg-Richter empirical law are presented on the mean field level. These conditions are rather universal and do not depend on features of resistant forces.

  19. Dynamics of Tectonic Plates

    OpenAIRE

    2014-01-01

    We suggest a model that describes a mutual dynamic of tectonic plates. The dynamic is a sort of stick-slip one which is modeled by a Markov random process. The process defines a microlevel of the dynamic. A macrolevel is obtained by a scaling limit which leads to a system of integro-differential equations which determines a kind of mean field systems. Conditions when Gutenberg-Richter empirical law are presented on the mean field level. These conditions are rather universal and do not depend ...

  20. Acaricidal activities of whole cell suspension, cell-free supernatant,and crude cell extract of Xenorhabdus stokiae against mushroom mite (Luciaphorus sp.)

    Institute of Scientific and Technical Information of China (English)

    Prapassom BUSSAMAN; Chirayu SA-UTH; Paweena RATTANAS ENA; Angsumarn CHANDRAPATYA

    2012-01-01

    Xenorhabdus bacterium has been used as a biological control agent against Luciaphorus sp.,a mushroom mite endemic in Thailand.To develop an effective formulation of Xenorhabdus stokiae,treatments using different parts of X.stokiae isolate PB09 culture,including whole cell suspension,cell-free supernatant,and crude cell extract,were performed.The results show that different parts ofX.stokiae isolate PB09 culture could induce variable effects on mite mortality and fecundity.Application with cell-free supernatant of X.stokiae culture resulted in both the highest mite mortality rate [(89.00+3.60)%] and the lowest mite fecundity [(41.33+23.69) eggs/gravid female].Whole cell suspension of X.stokiae isolate PB09 culture was found to be slightly less effective than its cell-free supernatant,suggesting that X.stokiae was more likely to release its metabolites with acaricidal activities to the surrounding culture media.Crude cell extract of X.stokiae was not effective against mites.Cell-free supernatant of X.stokiae isolate PB09 was the most effective biological control agent and it could be conveniently used in future formulations instead of live bacteria.

  1. Enhanced functional expression of aquaporin Z via fusion of in situ cleavable leader peptides in Escherichia coli cell-free system.

    Science.gov (United States)

    Zhang, Xu; Lian, Jiazhang; Kai, Lei; Huang, Lei; Cen, Peilin; Xu, Zhinan

    2014-02-05

    Aquaporin Z (AqpZ) is a water channel protein from Escherichia coli and has attracted many attentions to develop the biomimetic water filtration technology. Cell-free protein synthesis (CFPS) system, one of the most complex multi-enzymatic systems, has the ability of producing the integral membrane protein in vitro. To enhance the synthesis of AqpZ in E. coli cell-free system, several natural leader peptides were respectively fused at the N-terminus and were verified to enhance the expression level significantly. Moreover, the supplementation of detergents or liposome could activate leader peptidase from the cell-free extract and provide hydrophobic environment for proper folding of AqpZ. Thus, the release of mature AqpZ via the in situ removal of leader peptide was achieved, with a specific water transport activity of (2.1 ± 0.1) × 10⁻¹⁴ cm³ s⁻¹ monomer⁻¹. Using this in situ removable leader peptide strategy, the transcription-translation, leader sequence cleavage and membrane protein folding were integrated into a simple process in the cell-free system, providing a convenient approach to enhance the expression of target proteins, especially those membrane proteins difficult to achieve.

  2. Cell-free fetal DNA and intact fetal cells in maternal blood circulation: implications for first and second trimester non-invasive prenatal diagnosis.

    Science.gov (United States)

    Bischoff, Farideh Z; Sinacori, Mina K; Dang, Dianne D; Marquez-Do, Deborah; Horne, Cassandra; Lewis, Dorothy E; Simpson, Joe Leigh

    2002-01-01

    Both intact fetal cells as well as cell-free fetal DNA are present in the maternal circulation and can be recovered for non-invasive prenatal genetic diagnosis. Although methods for enrichment and isolation of rare intact fetal cells have been challenging, diagnosis of fetal chromosomal aneuploidy including trisomy 21 in first- and second-trimester pregnancies has been achieved with a 50-75% detection rate. Similarly, cell-free fetal DNA can be reliably recovered from maternal plasma and assessed by quantitative PCR to detect fetal trisomy 21 and paternally derived single gene mutations. Real-time PCR assays are robust in detecting low-level fetal DNA concentrations, with sensitivity of approximately 95-100% and specificity near 100%. Comparing intact fetal cell versus cell-free fetal DNA methods for non-invasive prenatal screening for fetal chromosomal aneuploidy reveals that the latter is at least four times more sensitive. These preliminary results do not support a relationship between frequency of intact fetal cells and concentration of cell-free fetal DNA. The above results imply that the concentration of fetal DNA in maternal plasma may not be dependent on circulating intact fetal cells but rather be a product of growth and cellular turnover during embryonic or fetal development.

  3. Quantitative cell-free DNA, KRAS, and BRAF mutations in plasma from patients with metastatic colorectal cancer during treatment with cetuximab and irinotecan

    DEFF Research Database (Denmark)

    Spindler, Karen-Lise Garm; Pallisgaard, Niels; Vogelius, Ivan Storgaard

    2012-01-01

    The present study investigated the levels of circulating cell-free DNA (cfDNA) in plasma from patients with metastatic colorectal cancer (mCRC) in relation to third-line treatment with cetuximab and irinotecan and the quantitative relationship of cfDNA with tumor-specific mutations in plasma....

  4. Broadening Horizons and Teaching Basic Biology through Cell-Free Synthesis of Green Fluorescent Protein in a High School Laboratory Course

    Science.gov (United States)

    Albayrak, Cem; Jones, K. C.; Swartz, James R.

    2013-01-01

    Cell-free protein synthesis (CFPS) has emerged as a practical method for producing a broad variety of proteins. In addition, the direct accessibility to the reaction environment makes CFPS particularly suitable as a learning vehicle for fundamental biological concepts. Here, we describe its implementation as a teaching tool for a high school…

  5. High-throughput synthesis of stable isotope-labeled transmembrane proteins for targeted transmembrane proteomics using a wheat germ cell-free protein synthesis system.

    Science.gov (United States)

    Takemori, Nobuaki; Takemori, Ayako; Matsuoka, Kazuhiro; Morishita, Ryo; Matsushita, Natsuki; Aoshima, Masato; Takeda, Hiroyuki; Sawasaki, Tatsuya; Endo, Yaeta; Higashiyama, Shigeki

    2015-02-01

    Using a wheat germ cell-free protein synthesis system, we developed a high-throughput method for the synthesis of stable isotope-labeled full-length transmembrane proteins as proteoliposomes to mimic the in vivo environment, and we successfully constructed an internal standard library for targeted transmembrane proteomics by using mass spectrometry.

  6. In vitro formation of the anthranoid scaffold by cell-free extracts from yeast-extract-treated Cassia bicapsularis cell cultures.

    Science.gov (United States)

    Abdel-Rahman, Iman A M; Beuerle, Till; Ernst, Ludger; Abdel-Baky, Afaf M; Desoky, Ezz El-Din K; Ahmed, Amany S; Beerhues, Ludger

    2013-04-01

    The anthranoid skeleton is believed to be formed by octaketide synthase (OKS), a member of the type III polyketide synthase (PKS) superfamily. Recombinant OKSs catalyze stepwise condensation of eight acetyl units to form a linear octaketide intermediate which, however, is incorrectly folded and cyclized to give the shunt products SEK4 and SEK4b. Here we report in vitro formation of the anthranoid scaffold by cell-free extracts from yeast-extract-treated Cassia bicapsularis cell cultures. Unlike field- and in vitro-grown shoots which accumulate anthraquinones, cell cultures mainly contained tetrahydroanthracenes, formation of which was increased 2.5-fold by the addition of yeast extract. The elicitor-stimulated accumulation of tetrahydroanthracenes was preceded by an approx. 35-fold increase in OKS activity. Incubation of cell-free extracts from yeast-extract-treated cell cultures with acetyl-CoA and [2-(14)C]malonyl-CoA led to formation of torosachrysone (tetrahydroanthracene) and emodin anthrone, beside two yet unidentified products. No product formation occurred in the absence of acetyl-CoA as starter substrate. To confirm the identities of the enzymatic products, cell-free extracts were incubated with acetyl-CoA and [U-(13)C(3)]malonyl-CoA and (13)C incorporation was analyzed by ESI-MS/MS. Detection of anthranoid biosynthesis in cell-free extracts indicates in vitro cooperation of OKS with a yet unidentified factor or enzyme for octaketide cyclization.

  7. CMS Resistive plate Champers

    CERN Document Server

    Zainab, Karam

    2013-01-01

    There are many types of gas detectors which are used in CERN in LHC project, There is a main parts for the gas detectors which must be in all gas detectors types like Multiwire proportional chambers, such as the micromesh gaseous structure chamber (the MicroMegas), Gas-electron multiplier (GEM) detector, Resistive Plate Champers... Compact Muon Solenoid (CMS) experiment detecting muons which are powerful tool for recognizing signatures of interesting physics processes. The CMS detector uses: drift tube (DT), cathode strip chamber (CSC) and resistive plate chamber (RPC). Building RPC’s was my project in summer student program (hardware). RPC’s have advantages which are triggering detector and Excellent time resolution which reinforce the measurement of the correct beam crossing time. RPC’s Organized in stations :  RPC barrel (RB) there are 4 stations, namely RB1, RB2, RB3, and RB4  While in the RPC endcap (RE) the 3 stations are RE1, RE2, and RE3. In the endcaps a new starion will be added and this...

  8. Breast milk from Tanzanian women has divergent effects on cell-free and cell-associated HIV-1 infection in vitro.

    Directory of Open Access Journals (Sweden)

    Magdalena A Lyimo

    Full Text Available Transmission of HIV-1 during breastfeeding is a significant source of new pediatric infections in sub-Saharan Africa. Breast milk from HIV-positive mothers contains both cell-free and cell-associated virus; however, the impact of breast milk on HIV-1 infectivity remains poorly understood. In the present study, breast milk was collected from HIV-positive and HIV-negative Tanzanian women attending antenatal clinics in Dar es Salaam. Milk was analyzed for activity in vitro against both cell-free and cell-associated HIV-1. Potent inhibition of cell-free R5 and X4 HIV-1 occurred in the presence of milk from all donors regardless of HIV-1 serostatus. Inhibition of cell-free HIV-1 infection positively correlated with milk levels of sialyl-Lewis(X from HIV-positive donors. In contrast, milk from 8 of 16 subjects enhanced infection with cell-associated HIV-1 regardless of donor serostatus. Milk from two of these subjects contained high levels of multiple pro-inflammatory cytokines including TNFα, IL-1β, IL-6, IL-8, MIP-1α, MIP-1β, MCP-1 and IP-10, and enhanced cell-associated HIV-1 infection at dilutions as high as 1∶500. These findings indicate that breast milk contains innate factors with divergent activity against cell-free and cell-associated HIV-1 in vitro. Enhancement of cell-associated HIV-1 infection by breast milk may be associated with inflammatory conditions in the mother and may contribute to infant infection during breastfeeding.

  9. Cell-free mitochondrial DNA in CSF is associated with early viral rebound, inflammation, and severity of neurocognitive deficits in HIV infection.

    Science.gov (United States)

    Pérez-Santiago, Josué; Schrier, Rachel D; de Oliveira, Michelli F; Gianella, Sara; Var, Susanna R; Day, Tyler R C; Ramirez-Gaona, Miguel; Suben, Jesse D; Murrell, Ben; Massanella, Marta; Cherner, Mariana; Smith, Davey M; Ellis, Ronald J; Letendre, Scott L; Mehta, Sanjay R

    2016-04-01

    Cell-free mitochondiral DNA (mtDNA) is an immunogenic molecule associated with many inflammatory conditions. We evaluated the relationship between cell-free mtDNA in cerebrospinal fluid (CSF) and neurocognitive performance and inflammation during HIV infection. In a cross-sectional analysis, we evaluated the association of mtDNA levels with clinical assessments, inflammatory markers, and neurocognitive performance in 28 HIV-infected individuals. In CSF, we measured mtDNA levels by droplet digital PCR, and soluble CD14 and CD163, neurofilament light, and neopterin by ELISA. In blood and CSF, we measured soluble IP-10, MCP-1, TNF-α, and IL-6 by ELISA, and intracellular expression of IL-2, IFN-γ, and TNF-α in CD4(+) and CD8(+) T cells by flow cytometry. We also evaluated the relationship between CSF pleocytosis and mtDNA longitudinally in another set of five individuals participating in an antiretroviral treatment (ART) interruption study. Cell-free CSF mtDNA levels strongly correlated with neurocognitive performance among individuals with neurocognitive impairment (NCI) (r = 0.77, p = 0.001). CSF mtDNA also correlated with levels of IP-10 in CSF (r = 0.70, p = 0.007) and MCP-1 in blood plasma (r = 0.66, p = 0.01) in individuals with NCI. There were no significant associations between inflammatory markers and mtDNA in subjects without NCI, and levels of mtDNA did not differ between subjects with and without NCI. MtDNA levels preceded pleocytosis and HIV RNA following ART interruption. Cell-free mtDNA in CSF was strongly associated with the severity of neurocognitive dysfunction and inflammation only in individuals with NCI. Our findings suggest that within a subset of subjects cell-free CSF mtDNA is associated with inflammation and degree of NCI.

  10. Use of a cell-free system to determine UDP-N-acetylglucosamine 2-epimerase and N-acetylmannosamine kinase activities in human hereditary inclusion body myopathy.

    Science.gov (United States)

    Sparks, Susan E; Ciccone, Carla; Lalor, Molly; Orvisky, Eduard; Klootwijk, Riko; Savelkoul, Paul J; Dalakas, Marinos C; Krasnewich, Donna M; Gahl, William A; Huizing, Marjan

    2005-11-01

    Hereditary inclusion body myopathy (HIBM) is an autosomal recessive neuromuscular disorder associated with mutations in uridine diphosphate (UDP)-N-acetylglucosamine (GlcNAc) 2-epimerase (GNE)/N-acetylmannosamine (ManNAc) kinase (MNK), the bifunctional and rate-limiting enzyme of sialic acid biosynthesis. We developed individual GNE and MNK enzymatic assays and determined reduced activities in cultured fibroblasts of patients, with HIBM harboring missense mutations in either or both the GNE and MNK enzymatic domains. To assess the effects of individual mutations on enzyme activity, normal and mutated GNE/MNK enzymatic domains were synthesized in a cell-free in vitro transcription-translation system and subjected to the GNE and MNK enzymatic assays. This cell-free system was validated for both GNE and MNK activities, and it revealed that mutations in one enzymatic domain (in GNE, G135V, V216A, and R246W; in MNK, A631V, M712T) affected not only that domain's enzyme activity, but also the activity of the other domain. Moreover, studies of the residual enzyme activity associated with specific mutations revealed a discrepancy between the fibroblasts and the cell-free systems. Fibroblasts exhibited higher residual activities of both GNE and MNK than the cell-free system. These findings add complexity to the tightly regulated system of sialic acid biosynthesis. This cell-free approach can be applied to other glycosylation pathway enzymes that are difficult to evaluate in whole cells because their substrate specificities overlap with those of ancillary enzymes.

  11. Symmetry recovery of cell-free layer after bifurcations of small arterioles in reduced flow conditions: effect of RBC aggregation.

    Science.gov (United States)

    Ng, Yan Cheng; Namgung, Bumseok; Tien, Sim Leng; Leo, Hwa Liang; Kim, Sangho

    2016-08-01

    Heterogeneous distribution of red blood cells (RBCs) in downstream vessels of arteriolar bifurcations can be promoted by an asymmetric formation of cell-free layer (CFL) in upstream vessels. Consequently, the CFL widths in subsequent downstream vessels become an important determinant for tissue oxygenation (O2) and vascular tone change by varying nitric oxide (NO) availability. To extend our previous understanding on the formation of CFL in arteriolar bifurcations, this study investigated the formation of CFL widths from 2 to 6 vessel-diameter (2D-6D) downstream of arteriolar bifurcations in the rat cremaster muscle (D = 51.5 ± 1.3 μm). As the CFL widths are highly influenced by RBC aggregation, the degree of aggregation was adjusted to simulate levels seen during physiological and pathological states. Our in vivo experimental results showed that the asymmetry of CFL widths persists along downstream vessels up to 6D from the bifurcating point. Moreover, elevated levels of RBC aggregation appeared to retard the recovery of CFL width symmetry. The required length of complete symmetry recovery was estimated to be greater than 11D under reduced flow conditions, which is relatively longer than interbifurcation distances of arterioles for vessel diameter of ∼50 μm. In addition, our numerical prediction showed that the persistent asymmetry of CFL widths could potentially result in a heterogeneous vasoactivity over the entire arteriolar network in such abnormal flow conditions.

  12. Cell-free supernatants from probiotic Lactobacillus casei and Lactobacillus rhamnosus GG decrease colon cancer cell invasion in vitro.

    Science.gov (United States)

    Escamilla, Juanita; Lane, Michelle A; Maitin, Vatsala

    2012-08-01

    Probiotics have been shown to have a preventative role in colorectal carcinogenesis but research concerning their prophylactic potential in the later stages of colorectal cancer, specifically metastasis is limited. This study explored the potential of cell-free supernatants (CFS) from 2 probiotic Lactobacillus sp., Lactobacillus casei and Lactobacillus rhamnosus GG, to inhibit colon cancer cell invasion by influencing matrix metalloproteinase-9 (MMP-9) activity and levels of the tight junction protein zona occludens-1 (ZO-1) in cultured metastatic human colorectal carcinoma cells. HCT-116 cells were treated with CFS from L. casei, L. rhamnosus, or Bacteroides thetaiotaomicron (a gut commensal); or with uninoculated bacterial growth media. Treatment with CFS from both Lactobacillus sp. decreased colorectal cell invasion but treatment with CFS from B. thetaiotaomicron did not. CFS from both Lactobacillus sp. decreased MMP-9 and increased ZO-1 protein levels. L. rhamnosus CFS also lowered MMP-9 activity. To begin elucidating the secreted bacterial factor conveying these responses, Lactobacillus sp. CFS were fractionated into defined molecular weight ranges and cell invasion assessed. Fractionation revealed that the inhibitory activity was contained primarily in the >100 kDa and 50-100 kDa fractions, suggesting the inhibitory compound may be a macromolecule such as a protein, nucleic acid, or a polysaccharide.

  13. Simultaneous quantitative assessment of circulating cell-free mitochondrial and nuclear DNA by multiplex real-time PCR

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    Peng Xia

    2009-01-01

    Full Text Available Quantification of circulating nucleic acids in plasma and serum could be used as a non-invasive diagnostic tool for monitoring a wide variety of diseases and conditions. We describe here a rapid, simple and accurate multiplex real-time PCR method for direct synchronized analysis of circulating cell-free (ccf mitochondrial (mtDNA and nuclear (nDNA DNA in plasma and serum samples. The method is based on one-step multiplex real-time PCR using a FAM-labeled MGB probe and primers to amplify the mtDNA sequence of the ATP 8 gene, and a VIC-labeled MGB probe and primers to amplify the nDNA sequence of the glycerinaldehyde-3-phosphate-dehydrogenase (GAPDH gene, in plasma and serum samples simultaneously. The efficiencies of the multiplex assays were measured in serial dilutions. Based on the simulation of the PCR reaction kinetics, the relative quantities of ccf mtDNA were calculated using a very simple equation. Using our optimised real-time PCR conditions, close to 100% efficiency was obtained from the two assays. The two assays performed in the dilution series showed very good and reproducible correlation to each other. This optimised multiplex real-time PCR protocol can be widely used for synchronized quantification of mtDNA and nDNA in different samples, with a very high rate of efficiency.

  14. Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin.

    Science.gov (United States)

    Snyder, Matthew W; Kircher, Martin; Hill, Andrew J; Daza, Riza M; Shendure, Jay

    2016-01-14

    Nucleosome positioning varies between cell types. By deep sequencing cell-free DNA (cfDNA), isolated from circulating blood plasma, we generated maps of genome-wide in vivo nucleosome occupancy and found that short cfDNA fragments harbor footprints of transcription factors. The cfDNA nucleosome occupancies correlate well with the nuclear architecture, gene structure, and expression observed in cells, suggesting that they could inform the cell type of origin. Nucleosome spacing inferred from cfDNA in healthy individuals correlates most strongly with epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA. We build on this observation to show how nucleosome footprints can be used to infer cell types contributing to cfDNA in pathological states such as cancer. Since this strategy does not rely on genetic differences to distinguish between contributing tissues, it may enable the noninvasive monitoring of a much broader set of clinical conditions than currently possible.

  15. Admission cell free DNA levels predict 28-day mortality in patients with severe sepsis in intensive care.

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    Avital Avriel

    Full Text Available The aim of the current study is to assess the mortality prediction accuracy of circulating cell-free DNA (CFD level at admission measured by a new simplified method.CFD levels were measured by a direct fluorescence assay in severe sepsis patients on intensive care unit (ICU admission. In-hospital and/or twenty eight day all-cause mortality was the primary outcome.Out of 108 patients with median APACHE II of 20, 32.4% have died in hospital/or at 28-day. CFD levels were higher in decedents: median 3469.0 vs. 1659 ng/ml, p<0.001. In multivariable model APACHE II score and CFD (quartiles were significantly associated with the mortality: odds ratio of 1.05, p = 0.049 and 2.57, p<0.001 per quartile respectively. C-statistics for the models was 0.79 for CFD and 0.68 for APACHE II. Integrated discrimination improvement (IDI analyses showed that CFD and CFD+APACHE II score models had better discriminatory ability than APACHE II score alone.CFD level assessed by a new, simple fluorometric-assay is an accurate predictor of acute mortality among ICU patients with severe sepsis. Comparison of CFD to APACHE II score and Procalcitonin (PCT, suggests that CFD has the potential to improve clinical decision making.

  16. Microbubble moving in blood flow in microchannels: effect on the cell-free layer and cell local concentration.

    Science.gov (United States)

    Bento, David; Sousa, Lúcia; Yaginuma, Tomoko; Garcia, Valdemar; Lima, Rui; Miranda, João M

    2017-03-01

    Gas embolisms can hinder blood flow and lead to occlusion of the vessels and ischemia. Bubbles in microvessels circulate as tubular bubbles (Taylor bubbles) and can be trapped, blocking the normal flow of blood. To understand how Taylor bubbles flow in microcirculation, in particular, how bubbles disturb the blood flow at the scale of blood cells, experiments were performed in microchannels at a low Capillary number. Bubbles moving with a stream of in vitro blood were filmed with the help of a high-speed camera. Cell-free layers (CFLs) were observed downstream of the bubble, near the microchannel walls and along the centerline, and their thicknesses were quantified. Upstream to the bubble, the cell concentration is higher and CFLs are less clear. While just upstream of the bubble the maximum RBC concentration happens at positions closest to the wall, downstream the maximum is in an intermediate region between the centerline and the wall. Bubbles within microchannels promote complex spatio-temporal variations of the CFL thickness along the microchannel with significant relevance for local rheology and transport processes. The phenomenon is explained by the flow pattern characteristic of low Capillary number flows. Spatio-temporal variations of blood rheology may have an important role in bubble trapping and dislodging.

  17. SNPase-ARMS qPCR: Ultrasensitive Mutation-Based Detection of Cell-Free Tumor DNA in Melanoma Patients.

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    Julia Stadler

    Full Text Available Cell-free circulating tumor DNA in the plasma of cancer patients has become a common point of interest as indicator of therapy options and treatment response in clinical cancer research. Especially patient- and tumor-specific single nucleotide variants that accurately distinguish tumor DNA from wild type DNA are promising targets. The reliable detection and quantification of these single-base DNA variants is technically challenging. Currently, a variety of techniques is applied, with no apparent "gold standard". Here we present a novel qPCR protocol that meets the conditions of extreme sensitivity and specificity that are required for detection and quantification of tumor DNA. By consecutive application of two polymerases, one of them designed for extreme base-specificity, the method reaches unprecedented sensitivity and specificity. Three qPCR assays were tested with spike-in experiments, specific for point mutations BRAF V600E, PTEN T167A and NRAS Q61L of melanoma cell lines. It was possible to detect down to one copy of tumor DNA per reaction (Poisson distribution, at a background of up to 200 000 wild type DNAs. To prove its clinical applicability, the method was successfully tested on a small cohort of BRAF V600E positive melanoma patients.

  18. Non-thermal radio frequency and static magnetic fields increase rate of hemoglobin deoxygenation in a cell-free preparation.

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    David Muehsam

    Full Text Available The growing body of clinical and experimental data regarding electromagnetic field (EMF bioeffects and their therapeutic applications has contributed to a better understanding of the underlying mechanisms of action. This study reports that two EMF modalities currently in clinical use, a pulse-modulated radiofrequency (PRF signal, and a static magnetic field (SMF, applied independently, increased the rate of deoxygenation of human hemoglobin (Hb in a cell-free assay. Deoxygenation of Hb was initiated using the reducing agent dithiothreitol (DTT in an assay that allowed the time for deoxygenation to be controlled (from several min to several hours by adjusting the relative concentrations of DTT and Hb. The time course of Hb deoxygenation was observed using visible light spectroscopy. Exposure for 10-30 min to either PRF or SMF increased the rate of deoxygenation occurring several min to several hours after the end of EMF exposure. The sensitivity and biochemical simplicity of the assay developed here suggest a new research tool that may help to further the understanding of basic biophysical EMF transduction mechanisms. If the results of this study were to be shown to occur at the cellular and tissue level, EMF-enhanced oxygen availability would be one of the mechanisms by which clinically relevant EMF-mediated enhancement of growth and repair processes could occur.

  19. Determining antioxidant activities of lactobacilli cell-free supernatants by cellular antioxidant assay: a comparison with traditional methods.

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    Jiali Xing

    Full Text Available Antioxidant activity of lactic acid bacteria is associated with multiple health-protective effects. Traditional indexes of chemical antioxidant activities poorly reflect the antioxidant effects of these bacteria in vivo. Cellular antioxidant activity (CAA assay was used in this study to determine the antioxidant activity of cell-free supernatants (CFSs of 10 Lactobacillus strains. The performance of the CAA assay was compared with that of four chemical antioxidant activity assays, namely, DPPH radical scavenging, hydroxyl radical scavenging (HRS, reducing power (RP, and inhibition of linoleic acid peroxidation (ILAP. Results of the CAA assay were associated with those of DPPH and ILAP assays, but not with those of RP and HRS assays. The inter- and intra-specific antioxidant activities of CFS were characterized by chemical and CAA assays. L. rhamnosus CCFM 1107 displayed a high antioxidative effect similar to positive control L. rhamnosus GG ATCC 53103 in all of the assays. The CAA assay is a potential method for the detection of antioxidant activities of lactobacilli CFSs.

  20. Direct Reprogramming of Human Bone Marrow Stromal Cells into Functional Renal Cells Using Cell-free Extracts

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    Evangelia Papadimou

    2015-04-01

    Full Text Available The application of cell-based therapies in regenerative medicine is gaining recognition. Here, we show that human bone marrow stromal cells (BMSCs, also known as bone-marrow-derived mesenchymal cells, can be reprogrammed into renal proximal tubular-like epithelial cells using cell-free extracts. Streptolysin-O-permeabilized BMSCs exposed to HK2-cell extracts underwent morphological changes—formation of “domes” and tubule-like structures—and acquired epithelial functional properties such as transepithelial-resistance, albumin-binding, and uptake and specific markers E-cadherin and aquaporin-1. Transmission electron microscopy revealed the presence of brush border microvilli and tight intercellular contacts. RNA sequencing showed tubular epithelial transcript abundance and revealed the upregulation of components of the EGFR pathway. Reprogrammed BMSCs integrated into self-forming kidney tissue and formed tubular structures. Reprogrammed BMSCs infused in immunodeficient mice with cisplatin-induced acute kidney injury engrafted into proximal tubuli, reduced renal injury and improved function. Thus, reprogrammed BMSCs are a promising cell resource for future cell therapy.

  1. Antioxidant role of amyloid β protein in cell-free and biological systems: implication for the pathogenesis of Alzheimer disease.

    Science.gov (United States)

    Sinha, Maitrayee; Bhowmick, Pritha; Banerjee, Anindita; Chakrabarti, Sasanka

    2013-03-01

    In contrast to many studies showing the pro-oxidative nature of amyloid peptide, this work shows that aggregated Aβ42 peptide in varying concentrations (2-20 μM) in cell-free systems inhibits the formation of hydroxyl radicals and H(2)O(2) from a mixture of iron (20 μM FeSO(4)) and ascorbate (2mM) as measured by benzoate hydroxylation assay and coumarin carboxylic acid assay. Aggregated Aβ42 in similar concentrations further prevents protein and lipid oxidation in isolated rat brain mitochondria incubated alone or with FeSO(4) and ascorbate. Moreover, mitochondria exposed to FeSO(4) and ascorbate show enhanced formation of reactive oxygen species and this phenomenon is also abolished by aggregated Aβ42. It is suggested that the antioxidant property of Aβ42 in various systems is mediated by metal chelation and it is nearly as potent as a typical metal chelator, such as diethylenetriaminepentaacetic acid, in preventing oxidative damage. However, aggregated Aβ42 causes mitochondrial functional impairment in the form of membrane depolarization and a loss of phosphorylation capacity without involving reactive oxygen species in the process. Thus, the present results suggest that the amyloid peptide exhibits a protective antioxidant role in biological systems, but also has toxic actions independent of oxidative stress.

  2. Novel Method of Cell-Free In Vitro Synthesis of the Human Fibroblast Growth Factor 1 Gene

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    Peijun Zuo

    2010-01-01

    Full Text Available Recombinant DNA projects generally involve cell-based gene cloning. However, because template DNA is not always readily available, in vitro chemical synthesis of complete genes from DNA oligonucleotides is becoming the preferred method for cloning. This article describes a new, rapid procedure based on Taq polymerase for the precise assembly of DNA oligonucleotides to yield the complete human fibroblast growth factor 1 (FGF1 gene, which is 468 bp long and has a G+C content of 51.5%. The new method involved two steps: (1 the design of the DNA oligonucleotides to be assembled and (2 the assembly of multiple oligonucleotides by PCR to generate the whole FGF1 gene. The procedure lasted a total of only 2 days, compared with 2 weeks for the conventional procedure. This method of gene synthesis is expected to facilitate various kinds of complex genetic engineering projects that require rapid gene amplification, such as cell-free whole-DNA library construction, as well as the construction of new genes or genes that contain any mutation, restriction site, or DNA tag.

  3. Structural and physico-mechanical characterization of bio-cellulose produced by a cell-free system.

    Science.gov (United States)

    Ullah, Muhammad Wajid; Ul-Islam, Mazhar; Khan, Shaukat; Kim, Yeji; Park, Joong Kon

    2016-01-20

    This study was aimed to characterize the structural and physico-mechanical properties of bio-cellulose produced through cell-free system. Fourier transform-infrared spectrum illustrated exact matching of structural peaks with microbial cellulose, used as reference. Field-emission scanning electron microscopy revealed that fibrils of bio-cellulose were thicker and more compact than microbial cellulose. The specific positions of peaks in the X-ray diffraction and nuclear magnetic resonance spectra indicated that bio-cellulose possessed cellulose II polymorphic structure. Bio-cellulose presented superior physico-mechanical properties than microbial cellulose. The water holding capacity of bio-cellulose and microbial cellulose were found to be 188.6 ± 5.41 and 167.4 ± 4.32 times their dry-weights, respectively. Tensile strengths and degradation temperature of bio-cellulose were 17.63 MPa and 352 °C, respectively compared to 14.71 MPa and 327 °C of microbial cellulose. Overall, the results indicated successful synthesis and superior properties of bio-cellulose that advocate its effectiveness for various applications.

  4. Elevated cell-free plasma DNA level as an independent predictor of mortality in patients with severe traumatic brain injury.

    Science.gov (United States)

    Rodrigues Filho, Edison Moraes; Simon, Daniel; Ikuta, Nilo; Klovan, Caroline; Dannebrock, Fernando Augusto; Oliveira de Oliveira, Carla; Regner, Andrea

    2014-10-01

    Trauma is the leading cause of death in individuals less than 45 years old worldwide, and up to 50% of trauma fatalities are because of brain injury. Prediction of outcome is one of the major problems associated with severe traumatic brain injury (TBI), and research efforts have focused on the investigation of biomarkers with prognostic value after TBI. Therefore, our aim was to investigate whether cell-free DNA concentrations correlated to short-term primary outcome (survival or death) and Glasgow Coma Scale (GCS) scores after severe TBI. A total of 188 patients with severe TBI were enrolled in this prospective study; outcome variables comprised survival and neurological assessment using the GCS at intensive care unit (ICU) discharge. Control blood samples were obtained from 25 healthy volunteers. Peripheral venous blood was collected at admission to the ICU. Plasma DNA was measured using a real-time quantitative polymerase chain reaction (PCR) assay for the β-globin gene. There was correlation between higher DNA levels and both fatal outcome and lower hospital admission GCS scores. Plasma DNA concentrations at the chosen cutoff point (≥171,381 kilogenomes-equivalents/L) predicted mortality with a specificity of 90% and a sensitivity of 43%. Logistic regression analysis showed that elevated plasma DNA levels were independently associated with death (pfree DNA concentration was a predictor of short-term mortality after severe TBI.

  5. Quantification of Cell-Free DNA in Red Blood Cell Units in Different Whole Blood Processing Methods

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    Andrew W. Shih

    2016-01-01

    Full Text Available Background. Whole blood donations in Canada are processed by either the red cell filtration (RCF or whole blood filtration (WBF methods, where leukoreduction is potentially delayed in WBF. Fresh WBF red blood cells (RBCs have been associated with increased in-hospital mortality after transfusion. Cell-free DNA (cfDNA is released by neutrophils prior to leukoreduction, degraded during RBC storage, and is associated with adverse patient outcomes. We explored cfDNA levels in RBCs prepared by RCF and WBF and different storage durations. Methods. Equal numbers of fresh (stored ≤14 days and older RBCs were sampled. cfDNA was quantified by spectrophotometry and PicoGreen. Separate regression models determined the association with processing method and storage duration and their interaction on cfDNA. Results. cfDNA in 120 RBC units (73 RCF, 47 WBF were measured. Using PicoGreen, WBF units overall had higher cfDNA than RCF units (p=0.0010; fresh WBF units had higher cfDNA than fresh RCF units (p=0.0093. Using spectrophotometry, fresh RBC units overall had higher cfDNA than older units (p=0.0031; fresh WBF RBCs had higher cfDNA than older RCF RBCs (p=0.024. Conclusion. Higher cfDNA in fresh WBF was observed compared to older RCF blood. Further study is required for association with patient outcomes.

  6. Immunoscreening of Plasmodium falciparum proteins expressed in a wheat germ cell-free system reveals a novel malaria vaccine candidate

    Science.gov (United States)

    Morita, Masayuki; Takashima, Eizo; Ito, Daisuke; Miura, Kazutoyo; Thongkukiatkul, Amporn; Diouf, Ababacar; Fairhurst, Rick M.; Diakite, Mahamadou; Long, Carole A.; Torii, Motomi; Tsuboi, Takafumi

    2017-01-01

    The number of malaria vaccine candidates in preclinical and clinical development is limited. To identify novel blood-stage malaria vaccine candidates, we constructed a library of 1,827P. falciparum proteins prepared using the wheat germ cell-free system (WGCFS). Also, a high-throughput AlphaScreen procedure was developed to measure antibody reactivity to the recombinant products. Purified IgGs from residents in malaria endemic areas have shown functional activity against blood-stage parasites as judged by an in vitro parasite Growth Inhibition Assay (GIA). Therefore, we evaluated the GIA activity of 51 plasma samples prepared from Malian adults living in a malaria endemic area against the WGCFS library. Using the AlphaScreen-based immunoreactivity measurements, antibody reactivity against 3 proteins was positively associated with GIA activity. Since anti-LSA3-C responses showed the strongest correlation with GIA activity, this protein was investigated further. Anti-LSA3-C-specific antibody purified from Malian adult plasmas showed GIA activity, and expression of LSA3 in blood-stage parasites was confirmed by western blotting. Taken together, we identified LSA3 as a novel blood-stage vaccine candidate, and we propose that this system will be useful for future vaccine candidate discovery. PMID:28378857

  7. GLUT-4 translocation in skeletal muscle studied with a cell-free assay: involvement of phospholipase D.

    Science.gov (United States)

    Kristiansen, S; Nielsen, J N; Bourgoin, S; Klip, A; Franco, M; Richter, E A

    2001-09-01

    GLUT-4-containing membranes immunoprecipitated from insulin-stimulated rat skeletal muscle produce the phospholipase D (PLD) product phosphatidic acid. In vitro stimulation of PLD in crude membrane with ammonium sulfate (5 mM) resulted in transfer of GLUT-4 (3.0-fold vs. control) as well as transferrin receptor proteins from large to small membrane structures. The in vitro GLUT-4 transfer could be blocked by neomycin (a PLD inhibitor), and neomycin also reduced insulin-stimulated glucose transport in intact incubated soleus muscles. Furthermore, protein kinase B(beta) (PKB(beta)) was found to associate with the GLUT-4 protein and was transferred to small vesicles in response to ammonium sulfate in vitro. Finally, addition of cytosolic proteins, prepared from basal skeletal muscle, and GTP nucleotides to an enriched GLUT-4 membrane fraction resulted in in vitro transfer of GLUT-4 to small membranes (6.8-fold vs. unstimulated control). The cytosol and nucleotide-induced GLUT-4 transfer could be blocked by neomycin and N-ethylmaleimide. In conclusion, we have developed a cell-free assay that demonstrates in vitro GLUT-4 transfer. This transfer may suggest release of GLUT-4-containing vesicles from donor GLUT-4 membranes involving PLD activity and binding of PKB(beta) to GLUT-4.

  8. Non-Invasive Prenatal Testing Using Cell Free DNA in Maternal Plasma: Recent Developments and Future Prospects.

    Science.gov (United States)

    Benn, Peter

    2014-05-21

    Recent advances in molecular genetic technologies have facilitated non-invasive prenatal testing (NIPT) through the analysis of cell-free fetal DNA in maternal plasma. NIPT can be used to identify monogenic disorders including the identification of autosomal recessive disorders where the maternally inherited mutation needs to be identified in the presence of an excess of maternal DNA that contains the same mutation. In the future, simultaneous screening for multiple monogenic disorders is anticipated. Several NIPT methods have been developed to screen for trisomy. These have been shown to be effective for fetal trisomy 21, 18 and 13. Although the testing has been extended to sex chromosome aneuploidy, robust estimates of the efficacy are not yet available and maternal mosaicism for gain or loss of an X-chromosome needs to be considered. Using methods based on the analysis of single nucleotide polymorphisms, diandric triploidy can be identified. NIPT is being developed to identify a number of microdeletion syndromes including α-globin gene deletion. NIPT is a profoundly important development in prenatal care that is substantially advancing the individual patient and public health benefits achieved through conventional prenatal screening and diagnosis.

  9. Fetal Aneuploidy Detection by Cell-Free DNA Sequencing for Multiple Pregnancies and Quality Issues with Vanishing Twins

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    Sebastian Grömminger

    2014-06-01

    Full Text Available Non-invasive prenatal testing (NIPT by random massively parallel sequencing of maternal plasma DNA for multiple pregnancies is a promising new option for prenatal care since conventional non-invasive screening for fetal trisomies 21, 18 and 13 has limitations and invasive diagnostic methods bear a higher risk for procedure related fetal losses in the case of multiple gestations compared to singletons. In this study, in a retrospective blinded analysis of stored twin samples, all 16 samples have been determined correctly, with four trisomy 21 positive and 12 trisomy negative samples. In the prospective part of the study, 40 blood samples from women with multiple pregnancies have been analyzed (two triplets and 38 twins, with two correctly identified trisomy 21 cases, confirmed by karyotyping. The remaining 38 samples, including the two triplet pregnancies, had trisomy negative results. However, NIPT is also prone to quality issues in case of multiple gestations: the minimum total amount of cell-free fetal DNA must be higher to reach a comparable sensitivity and vanishing twins may cause results that do not represent the genetics of the living sibling, as described in two case reports.

  10. A second rhodopsin-like protein in Cyanophora paradoxa: gene sequence and protein expression in a cell-free system.

    Science.gov (United States)

    Frassanito, Anna Maria; Barsanti, Laura; Passarelli, Vincenzo; Evangelista, Valtere; Gualtieri, Paolo

    2013-08-05

    Here we report the identification and expression of a second rhodopsin-like protein in the alga Cyanophora paradoxa (Glaucophyta), named Cyanophopsin_2. This new protein was identified due to a serendipity event, since the RACE reaction performed to complete the sequence of Cyanophopsin_1, (the first rhodopsin-like protein of C. paradoxa identified in 2009 by our group), amplified a 619 bp sequence corresponding to a portion of a new gene of the same protein family. The full sequence consists of 1175 bp consisting of 849 bp coding DNA sequence and 4 introns of 326 bp. The protein is characterized by an N-terminal region of 47 amino acids, followed by a region with 7 α-helices of 213 amino acids and a C-terminal region of 22 amino acids. This protein showed high identity with Cyanophopsin_1 and other rhodopsin-like proteins of Archea, Bacteria, Fungi and Algae. Cyanophosin_2 (CpR2) was expressed in a cell-free expression system, and characterized by means of absorption spectroscopy.

  11. Cell-free Protein Synthesis in an Autoinduction System for NMR Studies of Protein-Protein Interactions

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    Ozawa, Kiyoshi; Jergic, Slobodan; Crowther, Jeffrey A.; Thompson, Phillip R. [Australian National University, Research School of Chemistry (Australia); Wijffels, Gene [Queensland Bioscience Precinct, CSIRO Livestock Industries (Australia); Otting, Gottfried; Dixon, Nicholas A. [Australian National University, Research School of Chemistry (Australia)], E-mail: dixon@rsc.anu.edu.au

    2005-07-15

    Cell-free protein synthesis systems provide facile access to proteins in a nascent state that enables formation of soluble, native protein-protein complexes even if one of the protein components is prone to self-aggregation and precipitation. Combined with selective isotope-labeling, this allows the rapid analysis of protein-protein interactions with few {sup 15}N-HSQC spectra. The concept is demonstrated with binary and ternary complexes between the {chi}, {psi} and {gamma} subunits of Escherichia coli DNA polymerase III: nascent, selectively {sup 15}N-labeled {psi} produced in the presence of {chi} resulted in a soluble, correctly folded {chi}-{psi} complex, whereas {psi} alone precipitated irrespective of whether {gamma} was present or not. The {sup 15}N-HSQC spectra showed that the N-terminal segment of {psi} is mobile in the {chi}-{psi} complex, yet important for its binding to {gamma}. The sample preparation was greatly enhanced by an autoinduction strategy, where the T7 RNA polymerase needed for transcription of a gene in a T7-promoter vector was produced in situ.

  12. Non-Invasive Prenatal Testing Using Cell Free DNA in Maternal Plasma: Recent Developments and Future Prospects

    Directory of Open Access Journals (Sweden)

    Peter Benn

    2014-05-01

    Full Text Available Recent advances in molecular genetic technologies have facilitated non-invasive prenatal testing (NIPT through the analysis of cell-free fetal DNA in maternal plasma. NIPT can be used to identify monogenic disorders including the identification of autosomal recessive disorders where the maternally inherited mutation needs to be identified in the presence of an excess of maternal DNA that contains the same mutation. In the future, simultaneous screening for multiple monogenic disorders is anticipated. Several NIPT methods have been developed to screen for trisomy. These have been shown to be effective for fetal trisomy 21, 18 and 13. Although the testing has been extended to sex chromosome aneuploidy, robust estimates of the efficacy are not yet available and maternal mosaicism for gain or loss of an X-chromosome needs to be considered. Using methods based on the analysis of single nucleotide polymorphisms, diandric triploidy can be identified. NIPT is being developed to identify a number of microdeletion syndromes including α-globin gene deletion. NIPT is a profoundly important development in prenatal care that is substantially advancing the individual patient and public health benefits achieved through conventional prenatal screening and diagnosis.

  13. Concentration and Methylation of Cell-Free DNA from Blood Plasma as Diagnostic Markers of Renal Cancer.

    Science.gov (United States)

    Skrypkina, Inessa; Tsyba, Liudmyla; Onyshchenko, Kateryna; Morderer, Dmytro; Kashparova, Olena; Nikolaienko, Oleksii; Panasenko, Grigory; Vozianov, Sergii; Romanenko, Alina; Rynditch, Alla

    2016-01-01

    The critical point for successful treatment of cancer is diagnosis at early stages of tumor development. Cancer cell-specific methylated DNA has been found in the blood of cancer patients, indicating that cell-free DNA (cfDNA) circulating in the blood is a convenient tumor-associated DNA marker. Therefore methylated cfDNA can be used as a minimally invasive diagnostic marker. We analysed the concentration of plasma cfDNA and methylation of six tumor suppressor genes in samples of 27 patients with renal cancer and 15 healthy donors as controls. The cfDNA concentrations in samples from cancer patients and healthy donors was measured using two different methods, the SYBR Green I fluorescence test and quantitative real-time PCR. Both methods revealed a statistically significant increase of cfDNA concentrations in cancer patients. Hypermethylation on cfDNA was detected for the LRRC3B (74.1%), APC (51.9%), FHIT (55.6%), and RASSF1 (62.9%) genes in patients with renal cancer. Promoter methylation of VHL and ITGA9 genes was not found on cfDNA. Our results confirmed that the cfDNA level and methylation of CpG islands of RASSF1A, FHIT, and APC genes in blood plasma can be used as noninvasive diagnostic markers of cancer.

  14. Direct Reprogramming of Human Bone Marrow Stromal Cells into Functional Renal Cells Using Cell-free Extracts

    Science.gov (United States)

    Papadimou, Evangelia; Morigi, Marina; Iatropoulos, Paraskevas; Xinaris, Christodoulos; Tomasoni, Susanna; Benedetti, Valentina; Longaretti, Lorena; Rota, Cinzia; Todeschini, Marta; Rizzo, Paola; Introna, Martino; Grazia de Simoni, Maria; Remuzzi, Giuseppe; Goligorsky, Michael S.; Benigni, Ariela

    2015-01-01

    Summary The application of cell-based therapies in regenerative medicine is gaining recognition. Here, we show that human bone marrow stromal cells (BMSCs), also known as bone-marrow-derived mesenchymal cells, can be reprogrammed into renal proximal tubular-like epithelial cells using cell-free extracts. Streptolysin-O-permeabilized BMSCs exposed to HK2-cell extracts underwent morphological changes—formation of “domes” and tubule-like structures—and acquired epithelial functional properties such as transepithelial-resistance, albumin-binding, and uptake and specific markers E-cadherin and aquaporin-1. Transmission electron microscopy revealed the presence of brush border microvilli and tight intercellular contacts. RNA sequencing showed tubular epithelial transcript abundance and revealed the upregulation of components of the EGFR pathway. Reprogrammed BMSCs integrated into self-forming kidney tissue and formed tubular structures. Reprogrammed BMSCs infused in immunodeficient mice with cisplatin-induced acute kidney injury engrafted into proximal tubuli, reduced renal injury and improved function. Thus, reprogrammed BMSCs are a promising cell resource for future cell therapy. PMID:25754206

  15. Concentration and Methylation of Cell-Free DNA from Blood Plasma as Diagnostic Markers of Renal Cancer

    Science.gov (United States)

    Tsyba, Liudmyla; Onyshchenko, Kateryna; Kashparova, Olena; Nikolaienko, Oleksii; Panasenko, Grigory; Vozianov, Sergii; Romanenko, Alina; Rynditch, Alla

    2016-01-01

    The critical point for successful treatment of cancer is diagnosis at early stages of tumor development. Cancer cell-specific methylated DNA has been found in the blood of cancer patients, indicating that cell-free DNA (cfDNA) circulating in the blood is a convenient tumor-associated DNA marker. Therefore methylated cfDNA can be used as a minimally invasive diagnostic marker. We analysed the concentration of plasma cfDNA and methylation of six tumor suppressor genes in samples of 27 patients with renal cancer and 15 healthy donors as controls. The cfDNA concentrations in samples from cancer patients and healthy donors was measured using two different methods, the SYBR Green I fluorescence test and quantitative real-time PCR. Both methods revealed a statistically significant increase of cfDNA concentrations in cancer patients. Hypermethylation on cfDNA was detected for the LRRC3B (74.1%), APC (51.9%), FHIT (55.6%), and RASSF1 (62.9%) genes in patients with renal cancer. Promoter methylation of VHL and ITGA9 genes was not found on cfDNA. Our results confirmed that the cfDNA level and methylation of CpG islands of RASSF1A, FHIT, and APC genes in blood plasma can be used as noninvasive diagnostic markers of cancer.

  16. Recovery of cell-free layer and wall shear stress profile symmetry downstream of an arteriolar bifurcation.

    Science.gov (United States)

    Ye, Swe Soe; Ju, Meongkeun; Kim, Sangho

    2016-07-01

    Unequal RBC partitioning at arteriolar bifurcations contributes to dissimilar flow developments between daughter vessels in a bifurcation. Due to the importance of the cell-free layer (CFL) and the wall shear stress (WSS) to physiological processes such as vasoregulation and gas diffusion, we investigated the effects of a bifurcation disturbance on the development of the CFL width and WSS in bifurcation daughter branches. The analysis was performed on a two-dimensional (2-D) computational model of a transverse arteriole at three different flow rates corresponding to parent branch (PB) pseudoshear rates of 60, 170 and 470s(-1), while maintaining a 2-D hematocrit of about 55% in the PB. Flow symmetry was defined using the statistical similarity of the CFL and WSS distributions between the two walls of the vessel branch. In terms of the flow symmetry recovery, higher flow rates caused larger reductions in the flow symmetry indices in the MB and subsequently required longer vessel lengths for complete recovery. Lower tube hematocrits in the SB led to complete symmetry recovery for all flow rates despite the higher initial asymmetry in the SB than in the MB. Arteriolar bifurcations produce unavoidable local CFL asymmetry and the persistence of the asymmetry downstream may increase effective blood viscosity which is especially significant at higher physiological flow rates.

  17. A cell-free system for studying a priming factor involved in repair of bleomycin-damaged DNA.

    Directory of Open Access Journals (Sweden)

    Seki,Shuji

    1989-04-01

    Full Text Available A simple cell-free system for studying a priming factor involved in the repair of bleomycin-damaged DNA was established. The template-primer used for the repair DNA synthesis was prepared by treating the closed circular, superhelical form of pUC19 plasmid DNA with 2.2 microM bleomycin and 20 microM ferrous ions. Single-strand breaks were introduced into pUC19 DNA by the bleomycin treatment, and the DNA was consequently converted largely into the open circular form. A system for repair of this bleomycin-damaged DNA was constructed with a priming factor, DNA polymerase (DNA polymerase beta or Klenow fragment of DNA polymerase I, ATP, T4 DNA ligase and four deoxynucleoside triphosphates. After incubation, the conformation of the DNA was analyzed by agarose gel electrophoresis and electron microscopy. The open circular DNA was largely converted to the closed circular DNA, indicating that the single-strand breaks of DNA were repaired. When the priming factor was omitted, DNA repair did not occur. The present system seemed to be applicable to the study of priming factors involved in the repair of DNA with single-strand breaks caused not only by bleomycin but also by ionizing radiation or active oxygen.

  18. Cell-free expression of human glucosamine 6-phosphate N-acetyltransferase (HsGNA1) for inhibitor screening.

    Science.gov (United States)

    Ma, Yi; Ghoshdastider, Umesh; Wang, Jufang; Ye, Wei; Dötsch, Volker; Filipek, Slawomir; Bernhard, Frank; Wang, Xiaoning

    2012-12-01

    Glucosamine 6-phosphate N-acetyltransferase (GNA1; EC 2.3.1.4) is required for the de novo synthesis of N-acetyl-d-glucosamine-6-phosphate (GlcNAc-6P), which is an essential precursor in Uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) biosynthesis pathway. Therefore, GNA1 is indispensable for the viability of organisms. Here, a novel cell-free expression strategy was developed to efficiently produce large amounts of human GNA1(HsGNA1) and HsGNA1-sGFP for throughput inhibitor screening. The binding site of inhibitor glucose-6-phosphate (G6P) to hGNA was identified by simulated annealing. Subtle differences to the binding site of Aspergillius GNA1(AfGNA1) can be harnessed for inhibitor design. HsGNA1 may be also useful as an antimicrobial and chemotherapeutic target against cancer. Additionally HsGNA1 inhibitors/modulators can possibly be administered with other drugs in the next generation of personalized medicine.

  19. A New Model for Providing Cell-Free DNA and Risk Assessment for Chromosome Abnormalities in a Public Hospital Setting

    Directory of Open Access Journals (Sweden)

    Robert Wallerstein

    2014-01-01

    Full Text Available Objective. Cell-free DNA (cfDNA offers highly accurate noninvasive screening for Down syndrome. Incorporating it into routine care is complicated. We present our experience implementing a novel program for cfDNA screening, emphasizing patient education, genetic counseling, and resource management. Study Design. Beginning in January 2013, we initiated a new patient care model in which high-risk patients for aneuploidy received genetic counseling at 12 weeks of gestation. Patients were presented with four pathways for aneuploidy risk assessment and diagnosis: (1 cfDNA; (2 integrated screening; (3 direct-to-invasive testing (chorionic villus sampling or amniocentesis; or (4 no first trimester diagnostic testing/screening. Patients underwent follow-up genetic counseling and detailed ultrasound at 18–20 weeks to review first trimester testing and finalize decision for amniocentesis. Results. Counseling and second trimester detailed ultrasound were provided to 163 women. Most selected cfDNA screening (69% over integrated screening (0.6%, direct-to-invasive testing (14.1%, or no screening (16.6%. Amniocentesis rates decreased following implementation of cfDNA screening (19.0% versus 13.0%, P<0.05. Conclusion. When counseled about screening options, women often chose cfDNA over integrated screening. This program is a model for patient-directed, efficient delivery of a newly available high-level technology in a public health setting. Genetic counseling is an integral part of patient education and determination of plan of care.

  20. Prenatal diagnosis of Down syndrome using cell-free fetal DNA in amniotic fluid by quantitative fluorescent polymersase chain reaction

    Institute of Scientific and Technical Information of China (English)

    Wu Dan; Chi Hongbin; Shao Minjie; Wu Yao; Jin Hongyan; Wu Baiyan; Qiao Jie

    2014-01-01

    Backgroud Amniotic fluid (AF) supernatant contains cell-free fetal DNA (cffDNA) fragments.This study attempted to take advantage of cffDNA as a new material for prenatal diagnosis,which could be combined with simple quantitative fluorescent polymerase chain reaction (QF-PCR) to provide an ancillary method for the prenatal diagnosis of trisomy 21 syndrome.Methods AF supernatant samples were obtained from 27 women carrying euploid fetuses and 28 women carrying aneuploid fetuses with known cytogenetic karyotypes.Peripheral blood samples of the parents were collected at the same time.Short tandem repeat (STR) fragments on chromosome 21 were amplified by QF-PCR.Fetal condition and the parental source of the extra chromosome could be determined by the STR peaks.Results The sensitivity of the assay for the aneuploid was 93% (26/28; confidence interval,CI:77%-98%) and the specificity was 100% (26/26; CI:88%-100%).The determination rate of the origin of the extra chromosome was 69%.The sensitivity and the specificity of the assay in the euploid were 100% (27/27).Conclusions Trisomy 21 can be prenatally diagnosed by the QF-PCR method in AF supernatant.This karyotype analysis method greatly reduces the requirement for the specimen size.It will be a benefit for early amniocentesis and could avoid pregnancy complications.The method may become an ancillary method for prenatal diagnosis of trisomy 21.

  1. Tectonics of the Easter plate

    Science.gov (United States)

    Engeln, J. F.; Stein, S.

    1984-01-01

    A new model for the Easter plate is presented in which rift propagation has resulted in the formation of a rigid plate between the propagating and dying ridges. The distribution of earthquakes, eleven new focal mechanisms, and existing bathymetric and magnetic data are used to describe the tectonics of this area. Both the Easter-Nazca and Easter-Pacific Euler poles are sufficiently close to the Easter plate to cause rapid changes in rates and directions of motion along the boundaries. The east and west boundaries are propagating and dying ridges; the southwest boundary is a slow-spreading ridge and the northern boundary is a complex zone of convergent and transform motion. The Easter plate may reflect the tectonics of rift propagation on a large scale, where rigid plate tectonics requires boundary reorientation. Simple schematic models to illustrate the general features and processes which occur at plates resulting from large-scale rift propagation are used.

  2. Localised Plate Motion on Venus

    Science.gov (United States)

    Ghail, R. C.

    1996-03-01

    The volcanic and tectonic features observed in Dali Vinculum, Parga Vinculum and Imdr Regio are concentrated at long, narrow, curvilinear zones, with relatively minor volcanism and tectonism between these zones. These zones, whilst more diffuse than terrestrial plate boundaries, nevertheless define the margins of tectonic plates. In contrast to Earth, however, it appears that venusian plates are neither created nor destroyed by lateral motion. Rather, plates are thinned and intruded at vincula plate boundaries, vertically accreted by small-scale intra-plate (planitia) volcanism and perhaps destroyed by delamination of thickened crust in tesserae and montane regions such as Thetis Regio and Ishtar Terra. The diversity in age both between and within these three areas together with the evidence for infrequent, small scale resurfacing in the planitiae are difficult to reconcile with a non-uniformitarian geological process.

  3. Aluminum Manganese Molten Salt Plating

    Science.gov (United States)

    2006-06-01

    Dry fixture thoroughly with the air gun. Be especially careful to dry water out of crevices. Note: water is a contaminant to the plating process...easily destroyed if blown with the air. Be especially careful to dry water out of crevices. Note: water is a contaminant to the plating process and...especially careful to dry water out of crevices. 13. Carefully remove part from fixture. If residual plating solution is present at attachments points

  4. Glass-bead peen plating

    Science.gov (United States)

    Graves, J. R.

    1974-01-01

    Peen plating of aluminum, copper, and nickel powders was investigated. Only aluminum was plated successfully within the range of peen plating conditions studied. Optimum plating conditions for aluminum were found to be: (1) bead/powder mixture containing 25 to 35% powder by weight, (2) peening intensity of 0.007A as measured by Almen strip, and (3) glass impact bead diameter of at least 297 microns (0.0117 inches) for depositing-100 mesh aluminum powder. No extensive cleaning or substrate preparation is required beyond removing loose dirt or heavy oil.

  5. Intermittent plate tectonics?

    Science.gov (United States)

    Silver, Paul G; Behn, Mark D

    2008-01-01

    Although it is commonly assumed that subduction has operated continuously on Earth without interruption, subduction zones are routinely terminated by ocean closure and supercontinent assembly. Under certain circumstances, this could lead to a dramatic loss of subduction, globally. Closure of a Pacific-type basin, for example, would eliminate most subduction, unless this loss were compensated for by comparable subduction initiation elsewhere. Given the evidence for Pacific-type closure in Earth's past, the absence of a direct mechanism for termination/initiation compensation, and recent data supporting a minimum in subduction flux in the Mesoproterozoic, we hypothesize that dramatic reductions or temporary cessations of subduction have occurred in Earth's history. Such deviations in the continuity of plate tectonics have important consequences for Earth's thermal and continental evolution.

  6. VISAS AND GREEN PLATES

    CERN Multimedia

    2000-01-01

    From 3 April 2000, all questions relating to visa requests for Switzerland, France, or Russia for a member of the personnel must be addressed to Ms. Agnita Querrou (telephone 72838, office 5-2-019, e-mail Agnita.Querrou@cern.ch).The Users' Office continues to deal with requests for letters of invitation and questions concerning visas for users in EP Division.Questions relating to removals, requests for green plates, to privileges of members of the personnel and to the importation of vehicles are still dealt with by Ms Zuzana Miller (telephone 79257, office 33-1-017, e-mail Zuzana.Muller@cern.ch) and Ms Joëlle Belleman (telephone 73962, office 33-1-019, e-mail Joelle.Belleman@cern.ch).

  7. Plate osteosynthesis of simple forearm fractures : LCP versus DC plates

    NARCIS (Netherlands)

    Stevens, Charles Tjerk; Ten Duis, Henk Jan

    2008-01-01

    The aim of this study was to compare the time to radiological bony union of simple A-type fractures of the forearm, treated with either a locking compression plate (LCP) or a dynamic compression plate (DCP). For each fracture, the relation between the use of compression and radiological healing time

  8. Plate tectonics, damage and inheritance.

    Science.gov (United States)

    Bercovici, David; Ricard, Yanick

    2014-04-24

    The initiation of plate tectonics on Earth is a critical event in our planet's history. The time lag between the first proto-subduction (about 4 billion years ago) and global tectonics (approximately 3 billion years ago) suggests that plates and plate boundaries became widespread over a period of 1 billion years. The reason for this time lag is unknown but fundamental to understanding the origin of plate tectonics. Here we suggest that when sufficient lithospheric damage (which promotes shear localization and long-lived weak zones) combines with transient mantle flow and migrating proto-subduction, it leads to the accumulation of weak plate boundaries and eventually to fully formed tectonic plates driven by subduction alone. We simulate this process using a grain evolution and damage mechanism with a composite rheology (which is compatible with field and laboratory observations of polycrystalline rocks), coupled to an idealized model of pressure-driven lithospheric flow in which a low-pressure zone is equivalent to the suction of convective downwellings. In the simplest case, for Earth-like conditions, a few successive rotations of the driving pressure field yield relic damaged weak zones that are inherited by the lithospheric flow to form a nearly perfect plate, with passive spreading and strike-slip margins that persist and localize further, even though flow is driven only by subduction. But for hotter surface conditions, such as those on Venus, accumulation and inheritance of damage is negligible; hence only subduction zones survive and plate tectonics does not spread, which corresponds to observations. After plates have developed, continued changes in driving forces, combined with inherited damage and weak zones, promote increased tectonic complexity, such as oblique subduction, strike-slip boundaries that are subparallel to plate motion, and spalling of minor plates.

  9. Towards standardisation of cell-free DNA measurement in plasma: controls for extraction efficiency, fragment size bias and quantification.

    Science.gov (United States)

    Devonshire, Alison S; Whale, Alexandra S; Gutteridge, Alice; Jones, Gerwyn; Cowen, Simon; Foy, Carole A; Huggett, Jim F

    2014-10-01

    Circulating cell-free DNA (cfDNA) is becoming an important clinical analyte for prenatal testing, cancer diagnosis and cancer monitoring. The extraction stage is critical in ensuring clinical sensitivity of analytical methods measuring minority nucleic acid fractions, such as foetal-derived sequences in predominantly maternal cfDNA. Consequently, quality controls are required for measurement of extraction efficiency, fragment size bias and yield for validation of cfDNA methods. We evaluated the utility of an external DNA spike for monitoring these parameters in a study comparing three specific cfDNA extraction methods [QIAamp circulating nucleic acid (CNA) kit, NucleoSpin Plasma XS (NS) kit and FitAmp plasma/serum DNA isolation (FA) kit] with the commonly used QIAamp DNA blood mini (DBM) kit. We found that the extraction efficiencies of the kits ranked in the order CNA kit > DBM kit > NS kit > FA kit, and the CNA and NS kits gave a better representation of smaller DNA fragments in the extract than the DBM kit. We investigated means of improved reporting of cfDNA yield by comparing quantitative PCR measurements of seven different reference gene assays in plasma samples and validating these with digital PCR. We noted that the cfDNA quantities based on measurement of some target genes (e.g. TERT) were, on average, more than twofold higher than those of other assays (e.g. ERV3). We conclude that analysis and averaging of multiple reference genes using a GeNorm approach gives a more reliable estimate of total cfDNA quantity.

  10. Genome-wide DNA methylation profiling of cell-free serum DNA in esophageal adenocarcinoma and Barrett esophagus.

    Science.gov (United States)

    Zhai, Rihong; Zhao, Yang; Su, Li; Cassidy, Lauren; Liu, Geoffrey; Christiani, David C

    2012-01-01

    Aberrant DNA methylation (DNAm) is a feature of most types of cancers. Genome-wide DNAm profiling has been performed successfully on tumor tissue DNA samples. However, the invasive procedure limits the utility of tumor tissue for epidemiological studies. While recent data indicate that cell-free circulating DNAm (cfDNAm) profiles reflect DNAm status in corresponding tumor tissues, no studies have examined the association of cfDNAm with cancer or precursors on a genome-wide scale. The objective of this pilot study was to evaluate the putative significance of genome-wide cfDNAm profiles in esophageal adenocarcinoma (EA) and Barrett esophagus (BE, EA precursor). We performed genome-wide DNAm profiling in EA tissue DNA (n = 8) and matched serum DNA (n = 8), in serum DNA of BE (n = 10), and in healthy controls (n = 10) using the Infinium HumanMethylation27 BeadChip that covers 27,578 CpG loci in 14,495 genes. We found that cfDNAm profiles were highly correlated to DNAm profiles in matched tumor tissue DNA (r = 0.92) in patients with EA. We selected the most differentially methylated loci to perform hierarchical clustering analysis. We found that 911 loci can discriminate perfectly between EA and control samples, 554 loci can separate EA from BE samples, and 46 loci can distinguish BE from control samples. These results suggest that genome-wide cfDNAm profiles are highly consistent with DNAm profiles detected in corresponding tumor tissues. Differential cfDNAm profiling may be a useful approach for the noninvasive screening of EA and EA premalignant lesions.

  11. KRAS G12V Mutation Detection by Droplet Digital PCR in Circulating Cell-Free DNA of Colorectal Cancer Patients.

    Science.gov (United States)

    Olmedillas López, Susana; García-Olmo, Dolores C; García-Arranz, Mariano; Guadalajara, Héctor; Pastor, Carlos; García-Olmo, Damián

    2016-04-01

    KRAS mutations are responsible for resistance to anti-epidermal growth factor receptor (EGFR) therapy in colorectal cancer patients. These mutations sometimes appear once treatment has started. Detection of KRAS mutations in circulating cell-free DNA in plasma ("liquid biopsy") by droplet digital PCR (ddPCR) has emerged as a very sensitive and promising alternative to serial biopsies for disease monitoring. In this study, KRAS G12V mutation was analyzed by ddPCR in plasma DNA from 10 colorectal cancer patients and compared to six healthy donors. The percentage of KRAS G12V mutation relative to wild-type sequences in tumor-derived DNA was also determined. KRAS G12V mutation circulating in plasma was detected in 9 of 10 colorectal cancer patients whose tumors were also mutated. Colorectal cancer patients had 35.62 copies of mutated KRAS/mL plasma, whereas in healthy controls only residual copies were found (0.62 copies/mL, p = 0.0066). Interestingly, patients with metastatic disease showed a significantly higher number of mutant copies than M0 patients (126.25 versus 9.37 copies/mL, p = 0.0286). Wild-type KRAS was also significantly elevated in colorectal cancer patients compared to healthy controls (7718.8 versus 481.25 copies/mL, p = 0.0002). In conclusion, KRAS G12V mutation is detectable in plasma of colorectal cancer patients by ddPCR and could be used as a non-invasive biomarker.

  12. Effect of L. plantarum cell-free extract and co-trimoxazole against Salmonella Typhimurium: a possible adjunct therapy

    Directory of Open Access Journals (Sweden)

    Kaur Prabhjot

    2011-02-01

    Full Text Available Abstract Background Frequent and indiscriminate use of antibiotics has led to the development of multi-drug resistant bacterial strains. It necessitates the exploitation of alternative therapeutic strategies. In order to reduce the dose of antibiotic required and to decrease the associated side effects, the present study was aimed at evaluating the synergism, if any, between a conventional antibiotic, co-trimoxazole (CTZ and cell free supernatant (CFS of a probiotic (L. plantarum against S. Typhimurium NCTC 74. This antimicrobial combination was selected on the basis of antibiotic susceptibility pattern of Salmonella and L. plantarum. Methods The synergy was evaluated in terms of size of zone of inhibition, fractional inhibitory concentration index, time-kill assay (in-vitro as well as macrophage functions (ex-vivo. Results The concentration producing the same or higher antibacterial effect (size of zone of inhibition was reduced to half when both the agents were used in combination with respect to the concentrations required when used separately. CTZ and CFS exhibited synergetic activity against Salmonella by checkerboard microtitre test and the time-kill test. Ex-vivo studies demonstrated a significantly higher intracellular killing of bacteria by macrophages treated with CFS (80 AU/ml + (CTZ (2 μg/ml as compared to when treated with both separately at higher concentrations. Significant reduction in the extent of lipid peroxidation and nitrite levels generated by macrophages in presence of CFS and CTZ, in conjunction, further substantiated the synergistic efficacy of the combination. Conclusions The antimicrobial efficacy of this combination indicates that it may serve as the basis in developing alternative strategies to combat Salmonella infections.

  13. Completion of proteomic data sets by Kd measurement using cell-free synthesis of site-specifically labeled proteins.

    Science.gov (United States)

    Majkut, Paul; Claußnitzer, Iris; Merk, Helmut; Freund, Christian; Hackenberger, Christian P R; Gerrits, Michael

    2013-01-01

    The characterization of phosphotyrosine mediated protein-protein interactions is vital for the interpretation of downstream pathways of transmembrane signaling processes. Currently however, there is a gap between the initial identification and characterization of cellular binding events by proteomic methods and the in vitro generation of quantitative binding information in the form of equilibrium rate constants (Kd values). In this work we present a systematic, accelerated and simplified approach to fill this gap: using cell-free protein synthesis with site-specific labeling for pull-down and microscale thermophoresis (MST) we were able to validate interactions and to establish a binding hierarchy based on Kd values as a completion of existing proteomic data sets. As a model system we analyzed SH2-mediated interactions of the human T-cell phosphoprotein ADAP. Putative SH2 domain-containing binding partners were synthesized from a cDNA library using Expression-PCR with site-specific biotinylation in order to analyze their interaction with fluorescently labeled and in vitro phosphorylated ADAP by pull-down. On the basis of the pull-down results, selected SH2's were subjected to MST to determine Kd values. In particular, we could identify an unexpectedly strong binding of ADAP to the previously found binding partner Rasa1 of about 100 nM, while no evidence of interaction was found for the also predicted SH2D1A. Moreover, Kd values between ADAP and its known binding partners SLP-76 and Fyn were determined. Next to expanding data on ADAP suggesting promising candidates for further analysis in vivo, this work marks the first Kd values for phosphotyrosine/SH2 interactions on a phosphoprotein level.

  14. Prediction of the efficacy of immunotherapy by measuring the integrity of cell-free DNA in plasma in colorectal cancer.

    Science.gov (United States)

    Kitahara, Masahiro; Hazama, Shoichi; Tsunedomi, Ryouichi; Takenouchi, Hiroko; Kanekiyo, Shinsuke; Inoue, Yuka; Nakajima, Masao; Tomochika, Shinobu; Tokuhisa, Yoshihiro; Iida, Michihisa; Sakamoto, Kazuhiko; Suzuki, Nobuaki; Takeda, Shigeru; Ueno, Tomio; Yamamoto, Shigeru; Yoshino, Shigefumi; Nagano, Hiroaki

    2016-12-01

    We previously reported a phase II study of a cancer vaccine using five novel peptides recognized by HLA-A*2402-restricted CTL in combination with oxaliplatin-containing chemotherapy (FXV study) as first-line therapy for patients with metastatic colorectal cancer and demonstrated the safety and promising potential of our five-peptide cocktail. The objective of this analysis was to identify predictive biomarkers for identifying patients who are likely to receive a clinical benefit from immunochemotherapy. Circulating cell-free DNA (cfDNA) in plasma has been reported to be a candidate molecular biomarker for the efficacy of anticancer therapy. Unlike uniformly truncated small-sized DNA released from apoptotic normal cells, DNA released from necrotic cancer cells varies in size. The integrity of plasma cfDNA (i.e. the ratio of longer fragments [400 bp] to shorter fragments [100 bp] of cfDNA), may be clinically useful for detecting colorectal cancer progression. We assessed plasma samples collected from 93 patients prior to receiving immunochemotherapy. The cfDNA levels and integrity were analyzed by semi-quantitative real-time PCR. Progression-free survival was significantly better in patients with a low plasma cfDNA integrity value than in those with a high value (P = 0.0027). Surprisingly, in the HLA-A*2402-matched group, patients with a low plasma cfDNA integrity value had significantly better progression-free survival than those with a high value (P = 0.0015). This difference was not observed in the HLA-A*2402-unmatched group. In conclusion, the integrity of plasma cfDNA may provide important clinical information and may be a useful predictive biomarker of the outcome of immunotherapy in metastatic colorectal cancer.

  15. KRAS G12V Mutation Detection by Droplet Digital PCR in Circulating Cell-Free DNA of Colorectal Cancer Patients

    Directory of Open Access Journals (Sweden)

    Susana Olmedillas López

    2016-04-01

    Full Text Available KRAS mutations are responsible for resistance to anti-epidermal growth factor receptor (EGFR therapy in colorectal cancer patients. These mutations sometimes appear once treatment has started. Detection of KRAS mutations in circulating cell-free DNA in plasma (“liquid biopsy” by droplet digital PCR (ddPCR has emerged as a very sensitive and promising alternative to serial biopsies for disease monitoring. In this study, KRAS G12V mutation was analyzed by ddPCR in plasma DNA from 10 colorectal cancer patients and compared to six healthy donors. The percentage of KRAS G12V mutation relative to wild-type sequences in tumor-derived DNA was also determined. KRAS G12V mutation circulating in plasma was detected in 9 of 10 colorectal cancer patients whose tumors were also mutated. Colorectal cancer patients had 35.62 copies of mutated KRAS/mL plasma, whereas in healthy controls only residual copies were found (0.62 copies/mL, p = 0.0066. Interestingly, patients with metastatic disease showed a significantly higher number of mutant copies than M0 patients (126.25 versus 9.37 copies/mL, p = 0.0286. Wild-type KRAS was also significantly elevated in colorectal cancer patients compared to healthy controls (7718.8 versus 481.25 copies/mL, p = 0.0002. In conclusion, KRAS G12V mutation is detectable in plasma of colorectal cancer patients by ddPCR and could be used as a non-invasive biomarker.

  16. Production of monoclonal antibodies against GPCR using cell-free synthesized GPCR antigen and biotinylated liposome-based interaction assay.

    Science.gov (United States)

    Takeda, Hiroyuki; Ogasawara, Tomio; Ozawa, Tatsuhiko; Muraguchi, Atsushi; Jih, Pei-Ju; Morishita, Ryo; Uchigashima, Motokazu; Watanabe, Masahiko; Fujimoto, Toyoshi; Iwasaki, Takahiro; Endo, Yaeta; Sawasaki, Tatsuya

    2015-06-10

    G-protein-coupled receptors (GPCRs) are one of the most important drug targets, and anti-GPCR monoclonal antibody (mAb) is an essential tool for functional analysis of GPCRs. However, it is very difficult to develop GPCR-specific mAbs due to difficulties in production of recombinant GPCR antigens, and lack of efficient mAb screening method. Here we describe a novel approach for the production of mAbs against GPCR using two original methods, bilayer-dialysis method and biotinylated liposome-based interaction assay (BiLIA), both of which are developed using wheat cell-free protein synthesis system and liposome technology. Using bilayer-dialysis method, various GPCRs were successfully synthesized with quality and quantity sufficient for immunization. For selection of specific mAb, we designed BiLIA that detects interaction between antibody and membrane protein on liposome. BiLIA prevented denaturation of GPCR, and then preferably selected conformation-sensitive antibodies. Using this approach, we successfully obtained mAbs against DRD1, GHSR, PTGER1 and T1R1. With respect to DRD1 mAb, 36 mouse mAbs and 6 rabbit mAbs were obtained which specifically recognized native DRD1 with high affinity. Among them, half of the mAbs were conformation-sensitive mAb, and two mAbs recognized extracellular loop 2 of DRD1. These results indicated that this approach is useful for GPCR mAb production.

  17. An adaptive detection method for fetal chromosomal aneuploidy using cell-free DNA from 447 Korean women

    Directory of Open Access Journals (Sweden)

    Sunshin Kim

    2016-10-01

    Full Text Available Abstract Background Noninvasive prenatal testing (NIPT using massively parallel sequencing of cell-free DNA (cfDNA is increasingly being used to predict fetal chromosomal abnormalities. However, concerns over erroneous predictions which occur while performing NIPT still exist in pregnant women at high risk for fetal aneuploidy. We performed the largest-scale clinical NIPT study in Korea to date to assess the risk of false negatives and false positives using next-generation sequencing. Methods A total of 447 pregnant women at high risk for fetal aneuploidy were enrolled at 12 hospitals in Korea. They underwent definitive diagnoses by full karyotyping by blind analysis and received aneuploidy screening at 11–22 weeks of gestation. Three steps were employed for cfDNA analyses. First, cfDNA was sequenced. Second, the effect of GC bias was corrected using normalization of samples as well as LOESS and linear regressions. Finally, statistical analysis was performed after selecting a set of reference samples optimally adapted to a test sample from the whole reference samples. We evaluated our approach by performing cfDNA testing to assess the risk of trisomies 13, 18, and 21 using the sets of extracted reference samples. Results The adaptive selection algorithm presented here was used to choose a more optimized reference sample, which was evaluated by the coefficient of variation (CV, demonstrated a lower CV and higher sensitivity than standard approaches. Our adaptive approach also showed that fetal aneuploidies could be detected correctly by clearly splitting the z scores obtained for positive and negative samples. Conclusions We show that our adaptive reference selection algorithm for optimizing trisomy detection showed improved reliability and will further support practitioners in reducing both false negative and positive results.

  18. An Economic Analysis of Cell-Free DNA Non-Invasive Prenatal Testing in the US General Pregnancy Population.

    Directory of Open Access Journals (Sweden)

    Peter Benn

    Full Text Available Analyze the economic value of replacing conventional fetal aneuploidy screening approaches with non-invasive prenatal testing (NIPT in the general pregnancy population.Using decision-analysis modeling, we compared conventional screening to NIPT with cell-free DNA (cfDNA analysis in the annual US pregnancy population. Sensitivity and specificity for fetal aneuploidies, trisomy 21, trisomy 18, trisomy 13, and monosomy X, were estimated using published data and modeling of both first- and second trimester screening. Costs were assigned for each prenatal test component and for an affected birth. The overall cost to the healthcare system considered screening costs, the number of aneuploid cases detected, invasive procedures performed, procedure-related euploid losses, and affected pregnancies averted. Sensitivity analyses evaluated the effect of variation in parameters. Costs were reported in 2014 US Dollars.Replacing conventional screening with NIPT would reduce healthcare costs if it can be provided for $744 or less in the general pregnancy population. The most influential variables were timing of screening entry, screening costs, and pregnancy termination rates. Of the 13,176 affected pregnancies undergoing screening, NIPT detected 96.5% (12,717/13,176 of cases, compared with 85.9% (11,314/13,176 by conventional approaches. NIPT reduced invasive procedures by 60.0%, with NIPT and conventional methods resulting in 24,596 and 61,430 invasive procedures, respectively. The number of procedure-related euploid fetal losses was reduced by 73.5% (194/264 in the general screening population.Based on our analysis, universal application of NIPT would increase fetal aneuploidy detection rates and can be economically justified. Offering this testing to all pregnant women is associated with substantial prenatal healthcare benefits.

  19. Effect of feeding whole compared with cell-free colostrum on calf immune status: The neonatal period.

    Science.gov (United States)

    Langel, S N; Wark, W A; Garst, S N; James, R E; McGilliard, M L; Petersson-Wolfe, C S; Kanevsky-Mullarky, I

    2015-06-01

    Mortality and decreased weight gain resulting from infection and disease in dairy calves are problems within the dairy industry. The bovine neonate relies solely on colostrum to acquire antibodies through passive transfer. To date, colostrum quality is determined by the concentration of antibodies. However, proteins and cells in the colostrum might also enhance immune development in the neonate. To determine the effect of maternal colostral immune cells on calf health and immune status, maternal colostrum was fed either fresh or after lysis of cells by flash-freezing in liquid nitrogen. Thirty-seven female Holstein and Jersey dairy calves were fed 4 quarts total of whole colostrum (WC) or cell-free colostrum (CFC) at birth. Respiratory and fecal scores were measured from birth to d 45 of life. Calf peripheral blood samples were obtained before and after feeding colostrum as well as on d 1, 3, 7, 14, 21, and 28 of life. Peripheral blood mononuclear cells were collected and analyzed for cellular parameters by flow cytometry. Total respiratory scores were greater in CFC-fed calves compared with WC-fed calves on d 38 of life. There were fewer CD4+ T cells and CD4+CD62L+CD45RO- T cells on d 1 and fewer CD4+CD62L+CD45RO+ T cells on d 1 and 3 in CFC-fed calves compared with WC-fed calves. Compared with WC-fed calves, CFC-fed calves had a greater percentage of CD4+CD62L-CD45RO+ T cells on d 0.25, 1, 3, and 7, and a greater percentage of monocytes on d 7. Our data suggest that colostral cells adoptively transfer and enhance neonatal immunity during the first month of life.

  20. Completion of proteomic data sets by Kd measurement using cell-free synthesis of site-specifically labeled proteins.

    Directory of Open Access Journals (Sweden)

    Paul Majkut

    Full Text Available The characterization of phosphotyrosine mediated protein-protein interactions is vital for the interpretation of downstream pathways of transmembrane signaling processes. Currently however, there is a gap between the initial identification and characterization of cellular binding events by proteomic methods and the in vitro generation of quantitative binding information in the form of equilibrium rate constants (Kd values. In this work we present a systematic, accelerated and simplified approach to fill this gap: using cell-free protein synthesis with site-specific labeling for pull-down and microscale thermophoresis (MST we were able to validate interactions and to establish a binding hierarchy based on Kd values as a completion of existing proteomic data sets. As a model system we analyzed SH2-mediated interactions of the human T-cell phosphoprotein ADAP. Putative SH2 domain-containing binding partners were synthesized from a cDNA library using Expression-PCR with site-specific biotinylation in order to analyze their interaction with fluorescently labeled and in vitro phosphorylated ADAP by pull-down. On the basis of the pull-down results, selected SH2's were subjected to MST to determine Kd values. In particular, we could identify an unexpectedly strong binding of ADAP to the previously found binding partner Rasa1 of about 100 nM, while no evidence of interaction was found for the also predicted SH2D1A. Moreover, Kd values between ADAP and its known binding partners SLP-76 and Fyn were determined. Next to expanding data on ADAP suggesting promising candidates for further analysis in vivo, this work marks the first Kd values for phosphotyrosine/SH2 interactions on a phosphoprotein level.

  1. Nonionic homopolymeric amphipols: application to membrane protein folding, cell-free synthesis, and solution nuclear magnetic resonance.

    Science.gov (United States)

    Bazzacco, Paola; Billon-Denis, Emmanuelle; Sharma, K Shivaji; Catoire, Laurent J; Mary, Sophie; Le Bon, Christel; Point, Elodie; Banères, Jean-Louis; Durand, Grégory; Zito, Francesca; Pucci, Bernard; Popot, Jean-Luc

    2012-02-21

    Nonionic amphipols (NAPols) synthesized by homotelomerization of an amphiphatic monomer are able to keep membrane proteins (MPs) stable and functional in the absence of detergent. Some of their biochemical and biophysical properties and applications have been examined, with particular attention being paid to their complementarity with the classical polyacrylate-based amphipol A8-35. Bacteriorhodopsin (BR) from Halobacterium salinarum and the cytochrome b(6)f complex from Chlamydomonas reinhardtii were found to be in their native state and highly stable following complexation with NAPols. NAPol-trapped BR was shown to undergo its complete photocycle. Because of the pH insensitivity of NAPols, solution nuclear magnetic resonance (NMR) two-dimensional (1)H-(15)N heteronuclear single-quantum coherence spectra of NAPol-trapped outer MP X from Escherichia coli (OmpX) could be recorded at pH 6.8. They present a resolution similar to that of the spectra of OmpX/A8-35 complexes recorded at pH 8.0 and give access to signals from solvent-exposed rapidy exchanging amide protons. Like A8-35, NAPols can be used to fold MPs to their native state as demonstrated here with BR and with the ghrelin G protein-coupled receptor GHS-R1a, thus extending the range of accessible folding conditions. Following NAPol-assisted folding, GHS-R1a bound four of its specific ligands, recruited arrestin-2, and activated binding of GTPγS by the G(αq) protein. Finally, cell-free synthesis of MPs, which is inhibited by A8-35 and sulfonated amphipols, was found to be very efficient in the presence of NAPols. These results open broad new perspectives on the use of amphipols for MP studies.

  2. Genetic alteration andmutation proifling ofcirculating cell-free tumor DNA (cfDNA) fordiagnosis andtargeted therapy ofgastrointestinal stromal tumors

    Institute of Scientific and Technical Information of China (English)

    WeixinYan; AiguoZhang; MichaelJPowell

    2016-01-01

    Gastrointestinal stromal tumors (GISTs) have been recognized as a biologically distinctive type of tumor, different from smooth muscle and neural tumors of the gastrointestinal tract. The identiifcation of genetic aberrations in proto-oncogenes that drive the growth of GISTs is critical for improving the effcacy of cancer therapy by match-ing targeted drugs to speciifc mutations. Research into the oncogenic mechanisms of GISTs has found that these tumors frequently contain activating gene mutations in either platelet-derived growth factor receptor A (PDGFRA) or a receptor tyrosine protein associated with a mast cell growth factor receptor encoded by theKIT gene. Mutant cancer subpopulations have the potential to disrupt durable patient responses to molecularly targeted therapy for GISTs, yet the prevalence and size of subpopulations remain largely unexplored. Detection of the cancer subpopulations that harbor low-frequency mutant alleles of target proto-oncogenes through the use of molecular genetic methods, such as polymerase chain reaction (PCR) target ampliifcation technology, is hampered by the high abundance of wild-type alleles, which limit the sensitivity of detection of these minor mutant alleles. This is especially true in the case of mutant tumor DNA derived “driver” and “drug-resistant” alleles that are present in the circulating cell-free tumor DNA (cfDNA) in the peripheral blood circulation of GIST patients. So-called “liquid biopsy” allows for the dynamic monitor-ing of the patients’ tumor status during treatment using minimally invasive sampling. New methodologies, such as a technology that employs a xenonucleic acid (XNA) clamping probe to block the PCR ampliifcation of wild-type templates, have allowed improved molecular detection of these low-frequency alleles both in tissue biopsy samples and in cfDNA. These new methodologies could be widely applied for minimally invasive molecular testing in the therapeutic management of GISTs.

  3. Genome-wide DNA Methylation Profiling of Cell-Free Serum DNA in Esophageal Adenocarcinoma and Barrett Esophagus

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    Rihong Zhai

    2012-01-01

    Full Text Available Aberrant DNA methylation (DNAm is a feature of most types of cancers. Genome-wide DNAm profiling has been performed successfully on tumor tissue DNA samples. However, the invasive procedure limits the utility of tumor tissue for epidemiological studies. While recent data indicate that cell-free circulating DNAm (cfDNAm profiles reflect DNAm status in corresponding tumor tissues, no studies have examined the association of cfDNAm with cancer or precursors on a genome-wide scale. The objective of this pilot study was to evaluate the putative significance of genome-wide cfDNAm profiles in esophageal adenocarcinoma (EA and Barrett esophagus (BE, EA precursor. We performed genome-wide DNAm profiling in EA tissue DNA (n = 8 and matched serum DNA (n = 8, in serum DNA of BE (n = 10, and in healthy controls (n = 10 using the Infinium HumanMethylation27 BeadChip that covers 27,578 CpG loci in 14,495 genes. We found that cfDNAm profiles were highly correlated to DNAm profiles in matched tumor tissue DNA (r = 0.92 in patients with EA. We selected the most differentially methylated loci to perform hierarchical clustering analysis. We found that 911 loci can discriminate perfectly between EA and control samples, 554 loci can separate EA from BE samples, and 46 loci can distinguish BE from control samples. These results suggest that genome-wide cfDNAm profiles are highly consistent with DNAm profiles detected in corresponding tumor tissues. Differential cfDNAm profiling may be a useful approach for the noninvasive screening of EA and EA premalignant lesions.

  4. Casimir Effect for Dielectric Plates

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    We generalize Kupisewska method to the three-dimensional system and another derivation of the Casimir effect between two dielectric plates is presented based on the explicit quantization of the electromagnetic field in the presence of dielectrics, where the physical meaning of "evanescent mode" is discussed. The Lifshitz's formula is rederived perfect metallic plates will the evanescent modes become unimportant.

  5. Gold plating on spectacle frames.

    Science.gov (United States)

    Kenny, I; Mitchell, J W; Walsh, G

    1997-05-01

    An investigation was carried out into the thickness and standard of application of the plating and lacquer coatings applied to three metal spectacle frames. All conform to BS 6625 (1991) for plating thickness, but there was considerable variation in regularity and porosity.

  6. SAMI Automated Plug Plate Configuration

    CERN Document Server

    Lorente, Nuria P F; Goodwin, Michael

    2012-01-01

    The Sydney-AAO Multi-object Integral field spectrograph (SAMI) is a prototype wide-field system at the Anglo-Australian Telescope (AAT) which uses a plug-plate to mount its 13 x 61-core imaging fibre bundles (hexabundles) in the optical path at the telescope's prime focus. In this paper we describe the process of determining the positions of the plug-plate holes, where plates contain three or more stacked observation configurations. The process, which up until now has involved several separate processes and has required significant manual configuration and checking, is now being automated to increase efficiency and reduce error. This is carried out by means of a thin Java controller layer which drives the configuration cycle. This layer controls the user interface and the C++ algorithm layer where the plate configuration and optimisation is carried out. Additionally, through the Aladin display package, it provides visualisation and facilitates user verification of the resulting plates.

  7. The moving plate capacitor paradox

    Science.gov (United States)

    Davis, B. R.; Abbott, D.; Parrondo, J. M. R.

    2000-03-01

    For the first time we describe an apparent paradox concerning a moving plate capacitor driven by thermal noise from a resistor. A demon restores the plates of the capacitor to their original position, only when the voltage across the capacitor is small—hence only small forces are present for the demon to work against. The demon has to work harder than this to avoid the situation of perpetual motion, but the question is how? We explore the concept of a moving plate capacitor, driven by noise, a step further by examining the case where the restoring force on the capacitor plates is provided by a simple spring, rather than some unknown demon. We display simulation results with interesting behavior, particularly where the capacitor plates collide with each other.

  8. Underwater electrical discharge in plate to plate configuration

    Science.gov (United States)

    Stelmashuk, Vitaliy

    2016-09-01

    Two main configurations of high voltage electrodes submersed in water have been used for an electrical discharge generation: pin to pin and pin to plate. An electrical breakdown between plate electrodes is generally difficult to reproduce, because there is a uniform and weak electric field. One major advantage of using plate electrodes is their greater ``wear hardness'' to high-energy discharges. The plate electrodes can withstand extremely high energy deposition at which the pin electrode is quickly destroyed. The electrical discharge between plate electrodes can be initiated by creating an inhomogeneity in the electrical field. Two methods of discharge initiation between plate electrodes are proposed for this aim: 1) focusing of a shock wave in the interelectrode region; 2) a bubble injection into the electrode gap. The shock wave creates favourable conditions for the electrical breakdown between the two plate electrodes: it causes that numerous microbubbles of dissolved air start to grow and serve as locations for streamer initiation. In the second method the gas bubble is injected from the one of the electrodes, which has a gas inlet hole on the lateral face for this purpose. A ``volcano'' like morphology of positive streamers are observed in the experiments with weak electric field. The authors are grateful to MEYS grant INGO LG 15013.

  9. Canonical and Alternative Pathways in Cyclin-Dependent Kinase 1/Cyclin B Inactivation upon M-Phase Exit in Xenopus laevis Cell-Free Extracts

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    Jacek Z. Kubiak

    2011-01-01

    Full Text Available Cyclin-Dependent Kinase 1 (CDK1 is the major M-phase kinase known also as the M-phase Promoting Factor or MPF. Studies performed during the last decade have shown many details of how CDK1 is regulated and also how it regulates the cell cycle progression. Xenopus laevis cell-free extracts were widely used to elucidate the details and to obtain a global view of the role of CDK1 in M-phase control. CDK1 inactivation upon M-phase exit is a primordial process leading to the M-phase/interphase transition during the cell cycle. Here we discuss two closely related aspects of CDK1 regulation in Xenopus laevis cell-free extracts: firstly, how CDK1 becomes inactivated and secondly, how other actors, like kinases and phosphatases network and/or specific inhibitors, cooperate with CDK1 inactivation to assure timely exit from the M-phase.

  10. Highly curved microchannel plates

    Science.gov (United States)

    Siegmund, O. H. W.; Cully, S.; Warren, J.; Gaines, G. A.; Priedhorsky, W.; Bloch, J.

    1990-01-01

    Several spherically curved microchannel plate (MCP) stack configurations were studied as part of an ongoing astrophysical detector development program, and as part of the development of the ALEXIS satellite payload. MCP pairs with surface radii of curvature as small as 7 cm, and diameters up to 46 mm have been evaluated. The experiments show that the gain (greater than 1.5 x 10 exp 7) and background characteristics (about 0.5 events/sq cm per sec) of highly curved MCP stacks are in general equivalent to the performance achieved with flat MCP stacks of similar configuration. However, gain variations across the curved MCP's due to variations in the channel length to diameter ratio are observed. The overall pulse height distribution of a highly curved surface MCP stack (greater than 50 percent FWHM) is thus broader than its flat counterpart (less than 30 percent). Preconditioning of curved MCP stacks gives comparable results to flat MCP stacks, but it also decreases the overall gain variations. Flat fields of curved MCP stacks have the same general characteristics as flat MCP stacks.

  11. Detection and prognostic value of recurrent exportin 1 mutations in tumor and cell-free circulating DNA of patients with classical Hodgkin lymphoma

    Science.gov (United States)

    Camus, Vincent; Stamatoullas, Aspasia; Mareschal, Sylvain; Viailly, Pierre-Julien; Sarafan-Vasseur, Nasrin; Bohers, Elodie; Dubois, Sydney; Picquenot, Jean Michel; Ruminy, Philippe; Maingonnat, Catherine; Bertrand, Philippe; Cornic, Marie; Tallon-Simon, Valérie; Becker, Stéphanie; Veresezan, Liana; Frebourg, Thierry; Vera, Pierre; Bastard, Christian; Tilly, Hervé; Jardin, Fabrice

    2016-01-01

    Classical Hodgkin lymphoma is one of the most common lymphomas and shares clinical and genetic features with primary mediastinal B-cell lymphoma. In this retrospective study, we analyzed the recurrent hotspot mutation of the exportin 1 (XPO1, p.E571K) gene, previously identified in primary mediastinal B-cell lymphoma, in biopsies and plasma circulating cell-free DNA from patients with classical Hodgkin lymphoma using a highly sensitive digital PCR technique. A total of 94 patients were included in the present study. This widely expressed XPO1 E571K mutation is present in one quarter of classical Hodgkin lymphoma patients (24.2%). Mutated and wild-type classical Hodgkin lymphomas were similar regarding the main clinical features. Patients with a detectable XPO1 mutation at the end of treatment displayed a tendency toward shorter progression-free survival, as compared to patients with undetectable mutation in plasma cell-free DNA (2-year progression-free survival: 57.1%, 95% confidence interval: 30.1–100% versus 2-year progression-free survival: 90.5%, 95% confidence interval: 78.8–100%, respectively, P=0.0601). To conclude, the detection of the XPO1 E571K mutation in biopsy and plasma cell-free DNA by digital PCR may be used as a novel biomarker in classical Hodgkin lymphoma for both diagnosis and minimal residual disease, and pinpoints a crucial role of XPO1 in classical Hodgkin lymphoma pathogenesis. The detection of somatic mutation in the plasma cell-free DNA of patients represents a major technological advance in the context of liquid biopsies and noninvasive management of classical Hodgkin lymphoma. PMID:27479820

  12. Detection and prognostic value of recurrent exportin 1 mutations in tumor and cell-free circulating DNA of patients with classical Hodgkin lymphoma.

    Science.gov (United States)

    Camus, Vincent; Stamatoullas, Aspasia; Mareschal, Sylvain; Viailly, Pierre-Julien; Sarafan-Vasseur, Nasrin; Bohers, Elodie; Dubois, Sydney; Picquenot, Jean Michel; Ruminy, Philippe; Maingonnat, Catherine; Bertrand, Philippe; Cornic, Marie; Tallon-Simon, Valérie; Becker, Stéphanie; Veresezan, Liana; Frebourg, Thierry; Vera, Pierre; Bastard, Christian; Tilly, Hervé; Jardin, Fabrice

    2016-09-01

    Classical Hodgkin lymphoma is one of the most common lymphomas and shares clinical and genetic features with primary mediastinal B-cell lymphoma. In this retrospective study, we analyzed the recurrent hotspot mutation of the exportin 1 (XPO1, p.E571K) gene, previously identified in primary mediastinal B-cell lymphoma, in biopsies and plasma circulating cell-free DNA from patients with classical Hodgkin lymphoma using a highly sensitive digital PCR technique. A total of 94 patients were included in the present study. This widely expressed XPO1 E571K mutation is present in one quarter of classical Hodgkin lymphoma patients (24.2%). Mutated and wild-type classical Hodgkin lymphomas were similar regarding the main clinical features. Patients with a detectable XPO1 mutation at the end of treatment displayed a tendency toward shorter progression-free survival, as compared to patients with undetectable mutation in plasma cell-free DNA (2-year progression-free survival: 57.1%, 95% confidence interval: 30.1-100% versus 2-year progression-free survival: 90.5%, 95% confidence interval: 78.8-100%, respectively, P=0.0601). To conclude, the detection of the XPO1 E571K mutation in biopsy and plasma cell-free DNA by digital PCR may be used as a novel biomarker in classical Hodgkin lymphoma for both diagnosis and minimal residual disease, and pinpoints a crucial role of XPO1 in classical Hodgkin lymphoma pathogenesis. The detection of somatic mutation in the plasma cell-free DNA of patients represents a major technological advance in the context of liquid biopsies and noninvasive management of classical Hodgkin lymphoma.

  13. Acceptance of non-invasive prenatal testing by cell free foetal DNA for foetal aneuploidy in a developing country: experience at a tertiary care centre in India

    Directory of Open Access Journals (Sweden)

    Namrata Kashyap

    2016-03-01

    Conclusions: Newer genomic technology involving cell free maternal DNA is a new storm in prenatal diagnosis. Its application in clinical practice is the need of the hour, however, the lack of awareness, high cost and unavailability of the test in the country appears to be a major limiting factor for its poor acceptability. [Int J Reprod Contracept Obstet Gynecol 2016; 5(3.000: 705-710

  14. Indonesian Landforms and Plate Tectonics

    Directory of Open Access Journals (Sweden)

    Herman Th. Verstappen

    2014-06-01

    Full Text Available DOI: 10.17014/ijog.v5i3.103The horizontal configuration and vertical dimension of the landforms occurring in the tectonically unstable parts of Indonesia were resulted in the first place from plate tectonics. Most of them date from the Quaternary and endogenous forces are ongoing. Three major plates – the northward moving Indo-Australian Plate, the south-eastward moving SE-Asian Plate and the westward moving Pacific Plate - meet at a plate triple-junction situated in the south of New Guinea’s Bird’s Head. The narrow North-Moluccan plate is interposed between the Asia and Pacific. It tapers out northward in the Philippine Mobile Belt and is gradually disappearing. The greatest relief amplitudes occur near the plate boundaries: deep ocean trenches are associated with subduction zones and mountain ranges with collision belts. The landforms of the more stable areas of the plates date back to a more remote past and, where emerged, have a more subdued relief that is in the first place related to the resistance of the rocks to humid tropical weathering Rising mountain ranges and emerging island arcs are subjected to rapid humid-tropical river erosions and mass movements. The erosion products accumulate in adjacent sedimentary basins where their increasing weight causes subsidence by gravity and isostatic compensations. Living and raised coral reefs, volcanoes, and fault scarps are important geomorphic indicators of active plate tectonics. Compartmental faults may strongly affect island arcs stretching perpendicular to the plate movement. This is the case on Java. Transcurrent faults and related pull-apart basins are a leading factor where plates meet at an angle, such as on Sumatra. The most complicated situation exists near the triple-junction and in the Moluccas. Modern research methods, such as GPS measurements of plate movements and absolute dating of volcanic outbursts and raised coral reefs are important tools. The mega-landforms resulting

  15. Four-base codon-mediated incorporation of non-natural amino acids into proteins in a eukaryotic cell-free translation system.

    Science.gov (United States)

    Taira, Hikaru; Fukushima, Masaharu; Hohsaka, Takahiro; Sisido, Masahiko

    2005-05-01

    Various four-base codons have been shown to work for the introduction of non-natural amino acids into proteins in an Escherichia coli cell-free translation system. Here, a four-base codon-mediated non-natural mutagenesis was applied to a eukaryotic rabbit reticulocyte cell-free translation system. Mutated streptavidin mRNAs containing four-base codons were prepared and added to a rabbit reticulocyte lysate in the presence of tRNAs that were aminoacylated with a non-natural amino acid and had the corresponding four-base anticodons. A Western blot analysis of translation products indicated that the four-base codons CGGU, CGCU, CCCU, CUCU, CUAU, and GGGU were efficiently decoded by the aminoacyl-tRNAs having the corresponding four-base anticodons. In contrast, the four-base codons AGGU, AGAU, CGAU, UUGU, UCGU, and ACGU were not decoded. The stop codon-derived four-base codons UAGU, UAAU, and UGAU were found to be inefficient, whereas the amber codon UAG and opal codon UGA were efficient for the incorporation of non-natural amino acids. The application of the expanded genetic code in a eukaryotic cell-free system opens the possibility of a four-base codon-mediated incorporation of non-natural amino acids into proteins in living eukaryotic cells.

  16. An amino acid depleted cell-free protein synthesis system for the incorporation of non-canonical amino acid analogs into proteins.

    Science.gov (United States)

    Singh-Blom, Amrita; Hughes, Randall A; Ellington, Andrew D

    2014-05-20

    Residue-specific incorporation of non-canonical amino acids into proteins is usually performed in vivo using amino acid auxotrophic strains and replacing the natural amino acid with an unnatural amino acid analog. Herein, we present an efficient amino acid depleted cell-free protein synthesis system that can be used to study residue-specific replacement of a natural amino acid by an unnatural amino acid analog. This system combines a simple methodology and high protein expression titers with a high-efficiency analog substitution into a target protein. To demonstrate the productivity and efficacy of a cell-free synthesis system for residue-specific incorporation of unnatural amino acids in vitro, we use this system to show that 5-fluorotryptophan and 6-fluorotryptophan substituted streptavidin retain the ability to bind biotin despite protein-wide replacement of a natural amino acid for the amino acid analog. We envisage this amino acid depleted cell-free synthesis system being an economical and convenient format for the high-throughput screening of a myriad of amino acid analogs with a variety of protein targets for the study and functional characterization of proteins substituted with unnatural amino acids when compared to the currently employed in vivo methodologies.

  17. The concept of locking plates.

    Science.gov (United States)

    Cronier, P; Pietu, G; Dujardin, C; Bigorre, N; Ducellier, F; Gerard, R

    2010-05-01

    After a short historical review of locking bone plates since their inception more than a century ago to the success of the concept less than 15 years ago with today's plates, the authors present the main locking mechanisms in use. In the two broad categories - plates with fixed angulation and those with variable angulation - the screw head is locked in the plate with a locknut by screwing in a threaded chamber on the plate or by screwing through an adapted ring. The authors then provide a concrete explanation, based on simple mechanical models, of the fundamental differences between conventional bone plates and locking plates and why a locking screw system presents greater resistance at disassembly, detailing the role played by the position and number of screws. The advantages of epiphyseal fixation are then discussed, including in cases of mediocre-quality bone. For teaching purposes, the authors also present assembly with an apple fixed with five locking screws withstanding a 47-kg axial load with no resulting disassembly. The principles of plate placement are detailed for both the epiphysis and diaphysis, including the number and position of screws and respect of the soft tissues, with the greatest success assured by the minimally invasive and even percutaneous techniques. The authors then present the advantages of locking plates in fixation of periprosthetic fractures where conventional osteosynthesis often encounters limited success. Based on simplified theoretical cases, the economic impact in France of this type of implant is discussed, showing that on average it accounts for less than 10% of the overall cost of this pathology to society. Finally, the possible problems of material ablation are discussed as well as the means to remediate these problems.

  18. Functional expression of a single-chain antibody to ErbB-2 in plants and cell-free systems

    Directory of Open Access Journals (Sweden)

    Benevolo Maria

    2006-09-01

    Full Text Available Abstract Background Aberrant signaling by ErbB-2 (HER 2, Neu, a member of the human Epidermal Growth Factor (EGF receptor family, is associated with an aggressive clinical behaviour of carcinomas, particularly breast tumors. Antibodies targeting the ErbB-2 pathway are a preferred therapeutic option for patients with advanced breast cancer, but a worldwide deficit in the manufacturing capacities of mammalian cell bioreactors is foreseen. Methods Herein, we describe a multi-platform approach for the production of recombinant Single chain Fragments of antibody variable regions (ScFvs to ErbB-2 that involves their functional expression in (a bacteria, (b transient as well as stable transgenic tobacco plants, and (c a newly developed cell-free transcription-translation system. Results An ScFv (ScFv800E6 was selected by cloning immunoglobulin sequences from murine hybridomas, and was expressed and fully functional in all the expression platforms, thereby representing the first ScFv to ErbB-2 produced in hosts other than bacteria and yeast. ScFv800E6 was optimized with respect to redox synthesis conditions. Different tags were introduced flanking the ScFv800E6 backbone, with and without spacer arms, including a novel Strep II tag that outperforms conventional streptavidin-based detection systems. ScFv800E6 was resistant to standard chemical radiolabeling procedures (i.e. Chloramine T, displayed a binding ability extremely similar to that of the parental monovalent Fab' fragment, as well as a flow cytometry performance and an equilibrium binding affinity (Ka approximately 2 × 108 M-1 only slightly lower than those of the parental bivalent antibody, suggesting that its binding site is conserved as compared to that of the parental antibody molecule. ScFv800E6 was found to be compatible with routine reagents for immunohistochemical staining. Conclusion ScFv800E6 is a useful reagent for in vitro biochemical and immunodiagnostic applications in oncology

  19. Differences in regulation of the first two M-phases in Xenopus laevis embryo cell-free extracts.

    Science.gov (United States)

    Chesnel, Franck; Vignaux, Françoise; Richard-Parpaillon, Laurent; Huguet, Antoine; Kubiak, Jacek Z

    2005-09-15

    The first embryonic M-phase is special, being the time when paternal and maternal chromosomes mix together for the first time. Reports from a variety of species suggest that the regulation of first M-phase has many particularities; however, no systematic comparative study of the biochemical aspects of first and the following M-phases has been previously undertaken. Here, we ask whether the regulation of the first embryonic M-phase is modified, using Xenopus cell-free extracts. We developed new types of extract specific for the first and the second M-phase obtained either from parthenogenetic or from in vitro fertilized embryos. Analyses of these extracts confirmed that the amplitude of histone H1 kinase activity reflecting CDK1/cyclin B (or MPF for M-phase Promoting Factor) activity is higher and persists longer than during the second M-phase, and that levels of cyclins B1 and B2 are correspondingly higher during the first than the second embryonic M-phase. Inhibition of protein synthesis shortly before M-phase entry reduced mitotic histone H1 kinase amplitude, shortened the period of mitotic phosphorylation of chosen marker proteins, and reduced cyclin B1 and B2 levels, suggesting a role of B-type cyclins in regulating the duration of mitotic events. Moreover, addition of exogenous cyclin B to the extract prior the second mitosis brought forward the activation of mitotic histone H1 kinase but prolonged the duration of this activity. We also confirmed that the inhibitory phosphorylation of CDK1 on tyrosine 15 oscillates between the first two embryonic M-phases, but is clearly more pronounced before the first than the second mitosis, while the MAP kinase ERK2 tended to show greater activation during the first embryonic M-phase but with a similar duration of activation. We conclude that discrete differences exist between the first two M-phases in Xenopus embryo and that higher CDK1/cyclin B activity and B-type cyclin levels could account for the different

  20. Plate shell structures of glass

    DEFF Research Database (Denmark)

    Bagger, Anne

    to their curved shape. A plate shell structure maintains a high stiffness-to-weight ratio, while facilitating the use of plane structural elements. The study focuses on using laminated glass panes for the load bearing facets. Various methods of generating a plate shell geometry are suggested. Together with Ghent......, such as facet size, imperfections, and connection characteristics. The critical load is compared to that of a similar, but smoothly curved, shell structure. Based on the investigations throughout the study, a set of guidelines for the structural design of plate shells of glass is proposed....

  1. Hierarchical self-organization of tectonic plates

    OpenAIRE

    2010-01-01

    The Earth's surface is subdivided into eight large tectonic plates and many smaller ones. We reconstruct the plate tessellation history and demonstrate that both large and small plates display two distinct hierarchical patterns, described by different power-law size-relationships. While small plates display little organisational change through time, the structure of the large plates oscillate between minimum and maximum hierarchical tessellations. The organization of large plates rapidly chan...

  2. Tectonics: Changing of the plates

    Science.gov (United States)

    Brandon, Alan

    2016-10-01

    The composition of Earth's crust depends on the style of plate tectonics and of the melting regimes in the mantle. Analyses of the oldest identified rocks suggest that these styles and the resulting crust have changed over Earth's history.

  3. An efficient rectangular plate element

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A new 12-parameter rectangular plate element is presented by useof the double set parameter method. The error in the energy norm is of order O(h2), one order higher than the commonly used Adini nonconforming element.

  4. The multigap resistive plate chamber

    Energy Technology Data Exchange (ETDEWEB)

    Zeballos, E. Cerron [European Organization for Nuclear Research (CERN), Geneva (Switzerland); World Lab., Lausanne (Switzerland); Crotty, I. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Hatzifotiadou, D. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); World Lab., Lausanne (Switzerland); Valverde, J. Lamas [European Organization for Nuclear Research (CERN), Geneva (Switzerland); World Lab., Lausanne (Switzerland); Univ. Louis Pasteur, Strasbourg (France); Neupane, S. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); World Lab., Lausanne (Switzerland); Williams, M. C. S. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Zichichi, A. [Univ. of Bologna, Bologna (Italy)

    2015-02-03

    The paper describes the multigap resistive plate chamber (RPC). This is a variant of the wide gap RPC. However it has much improved time resolution, while keeping all the other advantages of the wide gap RPC design.

  5. Rhodium platings – experimental study

    Directory of Open Access Journals (Sweden)

    R. Rudolf

    2013-07-01

    Full Text Available Modern rhodium plating solutions are based on either sulphate or phosphate. Although in theory there are four possible combinations, in practice only three different rhodium electrolytes are used. These are based on dilutions of rhodium sulphate or phosphate concentrates with added sulphuric or phosphoric acid. These processes are be discussed in this paper with a demonstration of Rh platings in the Slovenian firm Zlatarna Celje d.d.

  6. Horizontally oriented plates in clouds

    CERN Document Server

    Bréon, François-Marie

    2011-01-01

    Horizontally oriented plates in clouds generate a sharp specular reflectance signal in the glint direction, often referred to as "subsun". This signal (amplitude and width) may be used to analyze the relative area fraction of oriented plates in the cloud top layer and their characteristic tilt angle to the horizontal. We make use of spaceborne measurements from the POLDER instrument to provide a statistical analysis of these parameters. More than half of the clouds show a detectable maximum reflectance in the glint direction, although this maximum may be rather faint. The typical effective fraction (area weighted) of oriented plates in clouds lies between 10-3 and 10-2. For those oriented plates, the characteristic tilt angle is less than 1 degree in most cases. These low fractions imply that the impact of oriented plates on the cloud albedo is insignificant. The largest proportion of clouds with horizontally oriented plates is found in the range 500-700 hPa, in agreement with typical in situ observation of p...

  7. Horizontal versus vertical plate motions

    Directory of Open Access Journals (Sweden)

    M. Cuffaro

    2006-07-01

    Full Text Available We review both present and past motions at major plate boundaries, which have the horizontal component in average 10 to 100 times faster (10–100 mm/yr than the vertical component (0.01–1 mm/yr in all geodynamic settings. The steady faster horizontal velocity of the lithosphere with respect to the upward or downward velocities at plate boundaries supports dominating tangential forces acting on plates. This suggests a passive role of plate boundaries with respect to far field forces determining the velocity of plates. The forces acting on the lithosphere can be subdivided in coupled and uncoupled, as a function of the shear at the lithosphere base. Higher the asthenosphere viscosity, more significant should be the coupled forces, i.e., the mantle drag and the trench suction. Lower the asthenosphere viscosity, more the effects of uncoupled forces might result determinant, i.e., the ridge push, the slab pull and the tidal drag. Although a combination of all forces acting on the lithosphere is likely, the decoupling between lithosphere and mantle suggests that a torque acts on the lithosphere independently of the mantle drag. Slab pull and ridge push are candidates for generating this torque, but, unlike these boundary forces, the advantage of the tidal drag is to be a volume force, acting simultaneously on the whole plates, and being the decoupling at the lithosphere base controlled by lateral variations in viscosity of the low-velocity layer.

  8. How mantle slabs drive plate tectonics.

    Science.gov (United States)

    Conrad, Clinton P; Lithgow-Bertelloni, Carolina

    2002-10-04

    The gravitational pull of subducted slabs is thought to drive the motions of Earth's tectonic plates, but the coupling between slabs and plates is not well established. If a slab is mechanically attached to a subducting plate, it can exert a direct pull on the plate. Alternatively, a detached slab may drive a plate by exciting flow in the mantle that exerts a shear traction on the base of the plate. From the geologic history of subduction, we estimated the relative importance of "pull" versus "suction" for the present-day plates. Observed plate motions are best predicted if slabs in the upper mantle are attached to plates and generate slab pull forces that account for about half of the total driving force on plates. Slabs in the lower mantle are supported by viscous mantle forces and drive plates through slab suction.

  9. Geometry of the Cocos Plate Under North American Plate

    Science.gov (United States)

    Perez-Campos, X.

    2015-12-01

    The Cocos plate subducts under the North American plate with a complex geometry, and previous seismicity studies revealed some of this complexity. However, details of the geometry and the depth that the plate penetrates werelargely unknown. Since 2004, temporary experiments and the expansion of the permanent network of the Servicio Sismológico Nacional (SSN, Mexican National Seismological Service) have improved resolution of the plate geometry and have helped to map its descent into the upper mantle. Going from northwest to southeast, the Cocos plate appears to be fragmenting into north and south segments. The north segment subducts with an angle of ~30º and the south with an angle of ~10-15º. The transition is smooth near the trench and progresses to a tear at depth; this coincides with the projection of the Orozco Fracture Zone to depth. Also, this transition marks the limit of the presence to the south of an ultra slow velocity layer (USL) on top of the slab.South of this transition, the Cocos plate subducts horizontally , underplating the North American plate for a distance of ~140 to ~300 km from the trench. Along this horizontal region, silent slow events (SSE) and tectonic tremor (TT) have been observed. At a distance of 300 km from the trench (beneath central Mexico), the plate dives into the mantle with an angle of 76º to a depth of 500 km. This geometry changes abruptly to the south, marking the eastern limit of the USL. This change seems to be also characterized by a tear on the slab. Finally to the south, the Cocos plate subducts with a constant angle of 26º. This presentation summarizes the work of many contributors including A. Arciniega-Ceballos, M. Brudzinski, E. Cabral-Cano, T. Chen, R. Clayton,F. Cordoba-Montiel,P. Davis,S. Dougherty,F. Green, M. Gurnis, D. V. Helmberger, A. Husker,A. Iglesias, Y. Kim, V. Manea, D. Melgar, M. Rodríguez-Domínguez,S. K. Singh, T.-R. A. Song, C. M. Valdés-González, D. Valencia-Cabrera

  10. Synthesis and decay of calmodulin-ubiquitin conjugates in cell-free extracts of various rabbit tissues.

    Science.gov (United States)

    Laub, M; Jennissen, H P

    1997-06-27

    of 30 min was followed in liver crude extracts by the addition of EGTA, which specifically inhibits ubiquityl-calmodulin synthesis, a half-life of calmodulin-conjugate decay of 15-20 min is observed. A similar conjugate half-life of ca. 30 min was observed after addition of EDTA excluding that conjugate decay is due to an ATP-dependent proteolytic process. Studying the decay of purified ubiquitin-125I-BH-calmodulin conjugates in cell-free reticulocyte extracts led to the discovery of an ATP-independent isopeptidase activity which splits ubiquitin-calmodulin conjugates without leading to detectable calmodulin fragments. The rapid decay of ubiquitin-calmodulin conjugates in tissue extracts can therefore be plausibly explained by a ubiquityl-calmodulin splitting isopeptidase activity.

  11. Analytical solution for multilayer plates using general layerwise plate theory

    Directory of Open Access Journals (Sweden)

    Vuksanović Đorđe M.

    2005-01-01

    Full Text Available This paper deals with closed-form solution for static analysis of simply supported composite plate, based on generalized laminate plate theory (GLPT. The mathematical model assumes piece-wise linear variation of in-plane displacement components and a constant transverse displacement through the thickness. It also include discrete transverse shear effect into the assumed displacement field, thus providing accurate prediction of transverse shear stresses. Namely, transverse stresses satisfy Hook's law, 3D equilibrium equations and traction free boundary conditions. With assumed displacement field, linear strain-displacement relation, and constitutive equations of the lamina, equilibrium equations are derived using principle of virtual displacements. Navier-type closed form solution of GLPT, is derived for simply supported plate, made of orthotropic laminae, loaded by harmonic and uniform distribution of transverse pressure. Results are compared with 3D elasticity solutions and excellent agreement is found.

  12. Plate tectonics of the Mediterranean region.

    Science.gov (United States)

    McKenzie, D P

    1970-04-18

    The seismicity and fault plane solutions in the Mediterranean area show that two small rapidly moving plates exist in the Eastern Mediterranean, and such plates may be a common feature of contracting ocean basins. The results show that the concepts of plate tectonics apply to instantaneous motions across continental plate boundaries.

  13. 胎儿游离核酸与子痫前期的研究进展%Research on Cell Free Fetal Nucleic Acid in Preeclampsia

    Institute of Scientific and Technical Information of China (English)

    沈彦婷

    2012-01-01

    Preeclampsia (PE) is one of the leading causes of maternal and fetal/neonatal mortality and deformity around the world. At present,there are no exact early diagnostic standard of it. Once preeclampsia is diagnosed,it has caused damage to the health of mothers and infants in different degrees. For this reason,making early diagnosis before preeclampsia clinical symptoms appearance is very necessary. The existing regular prenatal diagnosis is reliable, but it would endanger the health of mothers and infants. So .exploring a specific noninvasive fast diagnosis technology is very important and has clinical significance. Circulating cell free fetal nucleic acid, including cell free fetal DNA (cffDNA) ,cell free fetal mRNA (cffmRNA), and microRNA, as a novel and non-invasive biomarker, which not only can effectively predict the incidence of preeclampsia but also create new path for non-invasive prenatal diagnosis, has good prospect of development. In the recent years,many researches on the relationship between the cell free fetal nucleic acid and the preeclampsia screening have been conducted. This review will summarize the related content about the discovery, tissue origin, and detection methods of cell free fetal DNA, cell free fetal mRNA, and microRNA, and their roles in preeclampsia screening.%子痫前期(preeclampsia,PE)是全球范围内致母婴或新生儿死亡与致残的主要原因之一.目前尚无早期的诊断标准.一经检出,母婴已受到不同程度的损伤.因此,在PE临床症状出现前做出早期诊断对降低孕产妇与围生儿病死率、提高母婴健康具有重要意义.现有的常规产前诊断技术虽然可靠但可能危及母婴安全,因此寻找一种特异、无创、快速的诊断方法具有重要的临床意义.循环的胎儿细胞游离核酸,包括胎儿游离DNA、胎儿游离RNA以及微RNA(miRNA),作为一种特异性的无创性生物学标记物,其不仅可以有效地对PE进行预测,而且为无创性产

  14. Characterization of cell-free extracts from fenpropathrin-degrading strain Bacillus cereus ZH-3 and its potential for bioremediation of pyrethroid-contaminated soils.

    Science.gov (United States)

    Liu, Jie; Huang, Wenwen; Han, Haitao; She, Changchun; Zhong, Guohua

    2015-08-01

    Synthetic pyrethroid fenpropathrin has received increasing attention because of its environmental contamination and toxic effects on non-target organisms including human beings. Here we report the degradation characteristics of cell-free extracts from fenpropathrin-degrading strain Bacillus cereus ZH-3 and its potential for pyrethroid bioremediation in soils. 50mg·L(-1) of fenpropathrin was decreased to 20.6mg·L(-1) by the enzymatic extracts (869.4mg·L(-1)) within 30min. Kinetic constants Km and Vm were determined to be 1006.7nmol·L(-1) and 56.8nmol·min(-1), respectively. Degradation products were identified as 3-phenoxybenzaldehyde, α-hydroxy-3-phenoxy-benzeneacetonitrile and phenol by gas chromatography-mass spectrometry (GC-MS). In addition to degradation of fenpropathrin, the cell-free extracts could degrade other pyrethroids including beta-cypermethrin, cyfluthrin, deltamethrin and cypermethrin. Additionally, the reaction conditions were optimized. In the sterile and non-sterile soils, 50mg·kg(-1) of fenpropathrin was reduced to 15.3 and 13.9mg·L(-1) in 1d, respectively. Sprayed 100 and 300mg·kg(-1) of fenpropathrin emulsifiable concentrate (EC), up to 84.6% and 92.1% of soil fenpropathrin were removed from soils within 7d, respectively. Taken together, our results depict the biodegradation characteristics of cell-free extracts from B. cereus ZH-3, highlight its promising potential in bioremediation of pyrethroid-contaminated soils and also provide new insights into the utilization of degrading microbes.

  15. Plating on some difficult-to-plate metals and alloys

    Energy Technology Data Exchange (ETDEWEB)

    Dini, J.W.; Johnson, H.R.

    1980-02-01

    Electrodeposition of coatings on metals such as beryllium, beryllium-copper, Kovar, lead, magnesium, thorium, titanium, tungsten, uranium, zirconium, and their alloys can be problematic. This is due in most cases to a natural oxide surface film that readily reforms after being removed. The procedures we recommend for plating on these metals rely on replacing the oxide film with a displacement coating, or etching to allow mechanical keying between the substrate and plated deposit. The effectiveness of the procedures is demonstrated by interface bond strengths found in ring-shear and conical-head tensile tests.

  16. Beyond plate tectonics - Looking at plate deformation with space geodesy

    Science.gov (United States)

    Jordan, Thomas H.; Minster, J. Bernard

    1988-01-01

    The requirements that must be met by space-geodetic systems in order to constrain the horizontal secular motions associated with the geological deformation of the earth's surface are explored. It is suggested that in order to improve existing plate-motion models, the tangential components of relative velocities on interplate baselines must be resolved to an accuracy of less than 3 mm/yr. Results indicate that measuring the velocities between crustal blocks to + or - 5 mm/yr on 100-km to 1000-km scales can produce geologically significant constraints on the integrated deformation rates across continental plate-boundary zones such as the western United States.

  17. Chladni's law for vibrating plates

    Science.gov (United States)

    Rossing, Thomas D.

    1982-03-01

    The normal vibrational modes of free circular plates can be classified according to the number of nodal diameters m and the number of nodal circles n. Chladni observed that the addition of one nodal circle raised the frequency f about the same amount as adding two nodal diameters, and Rayleigh pointed out that f is proportional to (m+2n)2 for large f. Waller, however, concluded that the number of nodal diameters necessary to raise the frequency as much as a nodal circle varies from two to five. We have examined data on the vibrations of flat and non-flat circular plates and fitted their vibration frequencies to the relationship f = c(m+bn)k. By proper choice of c it is possible to satisfy Chladni's law (b = 2, k = 2) over quite a wide range of frequency in flat plates. Non-flat plates such as cymbals and bells, require different choices of b and k. A brief history of Chladni patterns, and suggestions for observing and demonstrating the vibrational modes of plates are included (AIP).

  18. Detection of Clonal and Subclonal Copy-Number Variants in Cell-Free DNA from Patients with Breast Cancer Using a Massively Multiplexed PCR Methodology

    OpenAIRE

    Eser Kirkizlar; Bernhard Zimmermann; Tudor Constantin; Ryan Swenerton; Bin Hoang; Nicholas Wayham; Babiarz, Joshua E; Zachary Demko; Pelham, Robert J.; Stephanie Kareht; Simon, Alexander L.; Kristine N. Jinnett; Matthew Rabinowitz; Styrmir Sigurjonsson; Matthew Hill

    2015-01-01

    We demonstrate proof-of-concept for the use of massively multiplexed PCR and next-generation sequencing (mmPCR-NGS) to identify both clonal and subclonal copy-number variants (CNVs) in circulating tumor DNA. This is the first report of a targeted methodology for detection of CNVs in plasma. Using an in vitro model of cell-free DNA, we show that mmPCR-NGS can accurately detect CNVs with average allelic imbalances as low as 0.5%, an improvement over previously reported whole-genome sequencin...

  19. A1M Ameliorates Preeclampsia-Like Symptoms in Placenta and Kidney Induced by Cell-Free Fetal Hemoglobin in Rabbit.

    Science.gov (United States)

    Nääv, Åsa; Erlandsson, Lena; Axelsson, Josefin; Larsson, Irene; Johansson, Martin; Wester-Rosenlöf, Lena; Mörgelin, Matthias; Casslén, Vera; Gram, Magnus; Åkerström, Bo; Hansson, Stefan R

    2015-01-01

    Preeclampsia is one of the most serious pregnancy-related diseases and clinically manifests as hypertension and proteinuria after 20 gestational weeks. The worldwide prevalence is 3-8% of pregnancies, making it the most common cause of maternal and fetal morbidity and mortality. Preeclampsia lacks an effective therapy, and the only "cure" is delivery. We have previously shown that increased synthesis and accumulation of cell-free fetal hemoglobin (HbF) in the placenta is important in the pathophysiology of preeclampsia. Extracellular hemoglobin (Hb) and its metabolites induce oxidative stress, which may lead to acute renal failure and vascular dysfunction seen in preeclampsia. The human endogenous protein, α1-microglobulin (A1M), removes cell-free heme-groups and induces natural tissue repair mechanisms. Exogenously administered A1M has been shown to alleviate the effects of Hb-induced oxidative stress in rat kidneys. Here we attempted to establish an animal model mimicking the human symptoms at stage two of preeclampsia by administering species-specific cell-free HbF starting mid-gestation until term, and evaluated the therapeutic effect of A1M on the induced symptoms. Female pregnant rabbits received HbF infusions i.v. with or without A1M every second day from gestational day 20. The HbF-infused animals developed proteinuria and a significantly increased glomerular sieving coefficient in kidney that was ameliorated by co-administration of A1M. Transmission electron microscopy analysis of kidney and placenta showed both intracellular and extracellular tissue damages after HbF-treatment, while A1M co-administration resulted in a significant reduction of the structural and cellular changes. Neither of the HbF-treated animals displayed any changes in blood pressure during pregnancy. In conclusion, infusion of cell-free HbF in the pregnant rabbits induced tissue damage and organ failure similar to those seen in preeclampsia, and was restored by co-administration of A

  20. Multiregional evaluation of the SimPlate heterotrophic plate count method compared to the standard plate count agar pour plate method in water.

    Science.gov (United States)

    Jackson, R W; Osborne, K; Barnes, G; Jolliff, C; Zamani, D; Roll, B; Stillings, A; Herzog, D; Cannon, S; Loveland, S

    2000-01-01

    A new SimPlate heterotrophic plate count (HPC) method (IDEXX Laboratories, Westbrook, Maine) was compared with the pour plate method at 35 degrees C for 48 h. Six laboratories tested a total of 632 water samples. The SimPlate HPC method was found to be equivalent to the pour plate method by regression analysis (r = 0. 95; y = 0.99X + 0.06).

  1. Multiple-Dynode-Layer Microchannel Plate

    Science.gov (United States)

    Woodgate, Bruce E.

    1990-01-01

    Improved microchannel-plate electron image amplifier made of stack of discrete microchannel-plate layers. New plates easier to manufacture because no need to etch long, narrow holes, to draw and bundle thin glass tubes, or to shear plates to give microchannels curvatures necessary for reduction of undesired emission of ions. Discrete dynode layers stacked with slight offset from layer to layer to form microchannel plate with curved channels. Provides for relatively fast recharging of microchannel dynodes, with consequent enhancement of performance.

  2. Multiregional Evaluation of the SimPlate Heterotrophic Plate Count Method Compared to the Standard Plate Count Agar Pour Plate Method in Water

    OpenAIRE

    Jackson, R. Wayne; Osborne, Karen; Barnes, Gary; Jolliff, Carol; Zamani, Dianna; Roll, Bruce; Stillings, Amy; Herzog, David; Cannon, Shelly; Loveland, Scott

    2000-01-01

    A new SimPlate heterotrophic plate count (HPC) method (IDEXX Laboratories, Westbrook, Maine) was compared with the pour plate method at 35°C for 48 h. Six laboratories tested a total of 632 water samples. The SimPlate HPC method was found to be equivalent to the pour plate method by regression analysis (r = 0.95; y = 0.99X + 0.06).

  3. Plate Tearing by a Cone

    DEFF Research Database (Denmark)

    Simonsen, Bo Cerup

    1998-01-01

    The present paper is concerned with steady-state plate tearing by a cone. This is a scenario where a cone is forced through a ductile metal plate with a constant lateral tip penetration in a motion in the plane of the plate. The considered process could be an idealisation of the damage, which...... develops in a ship bottom raking accident or a collision with a floating object. The deformation involves a complex mixture of large plastic deformations, fracture and friction. The observed mode of deformation is idealised by a simplified, kinematically admissible deformation mode, and the rate...... of internal energy dissipation in plasticity, fracture and friction is quantified accordingly by analytical expressions. The idealised mode has two free parameters which are determined from the postulate that they adjust to give the least rate of energy dissipation. The theory is compared to a series...

  4. Plate Tearing by a Cone

    DEFF Research Database (Denmark)

    Simonsen, Bo Cerup

    1997-01-01

    The present paper is concerned with steady-state plate tearing by a cone. This is a scenario where a cone is forced through a ductile metal plate with a constant lateral tip penetration in a motion in the plane of the plate. The considered process could be an idealisaton of the damage, which...... of internal energy dissipation in plasticity,fracture and friction is quantified accordingly by analytical expressions. The idealised mode has two free parameters which are determined from the postulate that they adjust to give the least rate of energy dissipation. The theory is compared to a series...... of measurements. The coefficient of friction was not measured, so the calculation are presented for different realistic values and it is shown that for a coefficient of friction of about 0,2, there is a reasonably good agreement between theory and measurements for the inplane resistance force as well...

  5. Ultimately Thin Metasurface Wave Plates

    CERN Document Server

    Keene, David; Durach, Maxim

    2015-01-01

    Optical properties of a metasurface which can be considered a monolayer of two classical uniaxial metamaterials, parallel-plate and nanorod arrays, are investigated. It is shown that such metasurface acts as an ultimately thin sub-50 nm wave plate. This is achieved via an interplay of epsilon-near-zero and epsilon-near-pole behavior along different axes in the plane of the metasurface allowing for extremely rapid phase difference accumulation in very thin metasurface layers. These effects are shown to not be disrupted by non-locality and can be applied to the design of ultrathin wave plates, Pancharatnam-Berry phase optical elements and plasmon-carrying optical torque wrench devices.

  6. Plate-like osteoma cutis.

    Science.gov (United States)

    Orme, Charisse M; Hale, Christopher S; Meehan, Shane A; Long, Wendy

    2014-12-16

    Osteoma cutis is the aberrant development of bone within the skin. The bone formation may be de novo (primary) or result from an injury to the skin (secondary). Here we present a healthy 53-year-old man with no known abnormalities in calcium or phosphate metabolism with plate-like osteoma cutis of the scalp. Plate- or plaque-like osteoma cutis was initially described as a congenital condition but has now been reported several times in the literature as an idiopathic process that occurs in adults. Treatment options are limited and are only required if the lesion is bothersome to the patient.

  7. Hydroelasticity of a Floating Plate

    DEFF Research Database (Denmark)

    Chen, X.; Jensen, Jørgen Juncher; Cui, W.;

    2003-01-01

    The membrane forces are included in the hydroelastic analysis of a floating plate undergoing large vertical deflections in regular monochromatic multidirectional waves. The first-order vertical displacements induced by the linear wave exciting forces are calculated by the mode expansion method...... in the frequency domain. The second-order vertical displacements induced by the membrane forces are calculated by the von Karman plate theory. The results show that the membrane contribution both in terms of the axial stresses and the effect on the bending stresses can be important...

  8. Orifice plates and venturi tubes

    CERN Document Server

    Reader-Harris, Michael

    2015-01-01

    This book gives the background to differential-pressure flow measurement and goes through the requirements explaining the reason for them. For those who want to use an orifice plate or a Venturi tube the standard ISO 5167 and its associated Technical Reports give the instructions required.  However, they rarely tell the users why they should follow certain instructions.  This book helps users of the ISO standards for orifice plates and Venturi tubes to understand the reasons why the standards are as they are, to apply them effectively, and to understand the consequences of deviations from the standards.

  9. Outer rise seismicity of the subducting Nazca Plate: Plate stress distribution, fault orientation and plate hydration

    Science.gov (United States)

    Barama, Louisa

    Subduction of the Nazca plate beneath the South American plate drives frequent and sometimes large magnitude earthquakes. During the past 40 years, significant numbers of outer rise earthquakes have occurred in the offshore regions of Colombia and Chile. In this study, we investigate the distribution of stress due to lithospheric bending and the extent of faults within the subducting plate. To calculate more accurate epicenters and to constrain which earthquakes occurred within the outer rise, we use hypocentroidal decomposition to relocate earthquakes with Global Centroid Moment Tensor (GCMT) solutions occurring after 1976 offshore Colombia and Chile. We determine centroid depths of outer rise earthquakes by inverting teleseismic P-, SH-, and SV- waveforms for earthquakes occurring from 1993 to 2014 with Mw ≥ 5.5. In order to further constrain the results of the waveform inversion, we estimate depths by comparing earthquake duration, amplitude, and arrival times for select stations with waveforms with good signal to noise ratios. Our results indicate that tensional earthquakes occur at depths down to 13 km and 24 km depth beneath the surface in the Colombia and Chile regions, respectively. Since faulting within the outer rise can make the plate susceptible to hydration and mantle serpentinization, we therefore infer the extent of possible hydration of the Nazca plate to extend no deeper than the extent of tensional outer rise earthquakes.

  10. Impact of Cell-free Supernatant of Lactic Acid Bacteria on Putrescine and Other Polyamine Formation by Foodborne Pathogens in Ornithine Decarboxylase Broth.

    Science.gov (United States)

    Ozogul, Fatih; Tabanelli, Giulia; Toy, Nurten; Gardini, Fausto

    2015-06-24

    Conversion of ornithine to putrescine by Salmonella Paratyphi A, Listeria monocytogenes, Staphylococcus aureus, and Escherichia coli was investigated in ornithine decarboxylase broth (ODB) using cell-free supernatants (CFSs) obtained from Leuconostoc mesenterodies subsp. cremoris, Pediococcus acidilactici, Lactococcus lactis subsp. lactis, Streptococcus thermophilus. Two groups of cell-free supernatants (25 or 50%) and control (only ODB) were prepared to investigate putrescine (PUT) and other polyamine formation by foodborne pathogens (FBPs). Significant differences (p < 0.05) were observed among the species for each amine. All of the CFSs reduced the formation of PUT by ≥65%. The production of cadaverine (CAD) was scarcely affected by the presence of CFSs, with the exception of the samples inoculated with L. monocytogenes. The variation in polyamine was found with respect to the control samples. Spermidine (SPD) was produced in lower amount in many samples, especially in Gram-negative FBPs, whereas spermine (SPN) increased drastically in the major part of the samples concerning the control. Histamine (HIS) was characterized by a marked concentration decrease in all of the samples, and tyramine (TYR) was accumulated in very low concentrations in the controls. Therefore, the ability of bacteria to produce certain biogenic amines such as HIS, TYR, PUT, and CAD has been studied to assess their risk and prevent their formation in food products. The results obtained from this study concluded that the lactic acid bacteria (LAB) strains with non-decarboxylase activity are capable of avoiding or limiting biogenic amine formation by FBP.

  11. Asymmetric bioreduction of acetophenones by Baker's yeast and its cell-free extract encapsulated in sol–gel silica materials

    Energy Technology Data Exchange (ETDEWEB)

    Kato, Katsuya, E-mail: katsuya-kato@aist.go.jp [National Institute of Advanced Industrial Science and Technology (AIST), 2266-98 Anagahora, Shimoshidami, Moriyama-ku, Nagoya, 463-8560 (Japan); Nakamura, Hitomi [National Institute of Advanced Industrial Science and Technology (AIST), 2266-98 Anagahora, Shimoshidami, Moriyama-ku, Nagoya, 463-8560 (Japan); Nakanishi, Kazuma [Department of Chemistry for Materials, Graduate School of Engineering, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie, 514-8570 (Japan)

    2014-02-28

    Baker's yeast (BY) encapsulated in silica materials was synthesized using a yeast cell suspension and its cell-free extract during a sol–gel reaction of tetramethoxysilane with nitric acid as a catalyst. The synthesized samples were fully characterized using various methods, such as scanning electron microscopy, nitrogen adsorption–desorption, Fourier transform infrared spectroscopy, thermogravimetry, and differential thermal analysis. The BY cells were easily encapsulated inside silica-gel networks, and the ratio of the cells in the silica gel was approximately 75 wt%, which indicated that a large volume of BY was trapped with a small amount of silica. The enzyme activity (asymmetric reduction of prochiral ketones) of BY and its cell-free extract encapsulated in silica gel was investigated in detail. The activities and enantioselectivities of free and encapsulated BY were similar to those of acetophenone and its fluorine derivatives, which indicated that the conformation structure of BY enzymes inside silica-gel networks did not change. In addition, the encapsulated BY exhibited considerably better solvent (methanol) stability and recyclability compared to free BY solution. We expect that the development of BY encapsulated in sol–gel silica materials will significantly impact the industrial-scale advancement of high-efficiency and low-cost biocatalysts for the synthesis of valuable chiral alcohols.

  12. Nod2-Nodosome in a Cell-Free System: Implications in Pathogenesis and Drug Discovery for Blau Syndrome and Early-Onset Sarcoidosis

    Directory of Open Access Journals (Sweden)

    Tomoyuki Iwasaki

    2016-01-01

    Full Text Available Nucleotide-binding oligomerization domain-containing protein (Nod 2 is an intracellular pattern recognition receptor, which recognizes muramyl dipeptide (N-Acetylmuramyl-L-Alanyl-D-Isoglutamine: MDP, a bacterial peptidoglycan component, and makes a NF-κB-activating complex called nodosome with adaptor protein RICK (RIP2/RIPK2. Nod2 mutants are associated with the autoinflammatory diseases, Blau syndrome (BS/early-onset sarcoidosis (EOS. For drug discovery of BS/EOS, we tried to develop Nod2-nodosome in a cell-free system. FLAG-tagged RICK, biotinylated-Nod2, and BS/EOS-associated Nod2 mutants were synthesized, and proximity signals between FLAG-tagged and biotinylated proteins were detected by amplified luminescent proximity homogeneous assay (ALPHA. Upon incubation with MDP, the ALPHA signal of interaction between Nod2-WT and RICK was increased in a dose-dependent manner. The ALPHA signal of interaction between RICK and the BS/EOS-associated Nod2 mutants was more significantly increased than Nod2-WT. Notably, the ALPHA signal between Nod2-WT and RICK was increased upon incubation with MDP, but not when incubated with the same concentrations, L-alanine, D-isoglutamic acid, or the MDP-D-isoform. Thus, we successfully developed Nod2-nodosome in a cell-free system reflecting its function in vivo, and it can be useful for screening Nod2-nodosome-targeted therapeutic molecules for BS/EOS and granulomatous inflammatory diseases.

  13. Expression, Purification, and Characterization of a Sucrose Nonfermenting 1-Related Protein Kinases 2 of Arabidopsis thaliana in E. coli-Based Cell-Free System

    Directory of Open Access Journals (Sweden)

    Xu Zhang

    2016-01-01

    Full Text Available The plant-specific sucrose nonfermenting 1-related protein kinase 2 (SnRK2 family is considered an important regulator of plant responses to abiotic stresses such as drought, cold, salinity, and nutrition deficiency. However, little information is available on how SnRK2s regulate sulfur deprivation responses in Arabidopsis. Large-scale production of SnRK2 kinases in vitro can help to elucidate the biochemical properties and physiological functions of this protein family. However, heterogenous expression of SnRK2s usually leads to inactive proteins. In this study, we expressed a recombinant Arabidopsis SnRK2.1 in a modified E. coli cell-free system, which combined two kinds of extracts allowing for a convenient and affordable protein preparation. The recombinant SnRK2.1 was produced in large-scale and the autophosphorylation activity of purified SnRK2.1 was characterized, allowing for further biochemical and substrate binding analysis in sulfur signaling. The application of this improved E. coli cell-free system provides us a promising and convenient platform to enhance expression of the target proteins economically.

  14. Monitoring multiple myeloma by next-generation sequencing of V(D)J rearrangements from circulating myeloma cells and cell-free myeloma DNA.

    Science.gov (United States)

    Oberle, Anna; Brandt, Anna; Voigtlaender, Minna; Thiele, Benjamin; Radloff, Janina; Schulenkorf, Anita; Alawi, Malik; Akyüz, Nuray; März, Manuela; Ford, Christopher T; Krohn-Grimberghe, Artus; Binder, Mascha

    2017-02-09

    Recent studies suggest that circulating tumor cells and cell-free DNA may represent powerful non-invasive tools for disease monitoring in patients with solid and hematological malignancies. Here, we conducted a pilot study in 27 myeloma patients to explore the clonotypic V(D)J rearrangement for monitoring of circulating myeloma cells (cmc-V(D)J) and cell-free myeloma DNA (cfm-V(D)J). Next-generation sequencing was used to define the myeloma V(D)J rearrangement and for subsequent peripheral blood tracking after treatment initiation. Positivity for cmc-/cfm-V(D)J was associated with conventional remission status (pJ (pJ despite persistent M-protein, suggesting that these markers are less inert than the M-protein, rely more on cell turnover and therefore decline more rapidly after initiation of effective treatment. Positivity for cmc- and cfm-V(D)J was associated with each other (p=0.042), but in 30% discordant. This indicated that cfm-V(D)J may not be generated entirely by circulating myeloma cells and may reflect overall tumor burden. Prospective studies need to define the predictive potential of high-sensitivity determination of circulating myeloma cells and DNA in the monitoring of multiple myeloma.

  15. Expression, stabilization and purification of membrane proteins via diverse protein synthesis systems and detergents involving cell-free associated with self-assembly peptide surfactants.

    Science.gov (United States)

    Zheng, Xuan; Dong, Shuangshuang; Zheng, Jie; Li, Duanhua; Li, Feng; Luo, Zhongli

    2014-01-01

    G-protein coupled receptors (GPCRs) are involved in regulating most of physiological actions and metabolism in the bodies, which have become most frequently addressed therapeutic targets for various disorders and diseases. Purified GPCR-based drug discoveries have become routine that approaches to structural study, novel biophysical and biochemical function analyses. However, several bottlenecks that GPCR-directed drugs need to conquer the problems including overexpression, solubilization, and purification as well as stabilization. The breakthroughs are to obtain efficient protein yield and stabilize their functional conformation which are both urgently requiring of effective protein synthesis system methods and optimal surfactants. Cell-free protein synthesis system is superior to the high yields and post-translation modifications, and early signs of self-assembly peptide detergents also emerged to superiority in purification of membrane proteins. We herein focus several predominant protein synthesis systems and surfactants involving the novel peptide detergents, and uncover the advantages of cell-free protein synthesis system with self-assembling peptide detergents in purification of functional GPCRs. This review is useful to further study in membrane proteins as well as the new drug exploration.

  16. The healing of bony defects by cell-free collagen-based scaffolds compared to stem cell-seeded tissue engineered constructs.

    LENUS (Irish Health Repository)

    Lyons, Frank G

    2010-12-01

    One of the key challenges in tissue engineering is to understand the host response to scaffolds and engineered constructs. We present a study in which two collagen-based scaffolds developed for bone repair: a collagen-glycosaminoglycan (CG) and biomimetic collagen-calcium phosphate (CCP) scaffold, are evaluated in rat cranial defects, both cell-free and when cultured with MSCs prior to implantation. The results demonstrate that both cell-free scaffolds showed excellent healing relative to the empty defect controls and somewhat surprisingly, to the tissue engineered (MSC-seeded) constructs. Immunological analysis of the healing response showed higher M1 macrophage activity in the cell-seeded scaffolds. However, when the M2 macrophage response was analysed, both groups (MSC-seeded and non-seeded scaffolds) showed significant activity of these cells which are associated with an immunomodulatory and tissue remodelling response. Interestingly, the location of this response was confined to the construct periphery, where a capsule had formed, in the MSC-seeded groups as opposed to areas of new bone formation in the non-seeded groups. This suggests that matrix deposited by MSCs during in vitro culture may adversely affect healing by acting as a barrier to macrophage-led remodelling when implanted in vivo. This study thus improves our understanding of host response in bone tissue engineering.

  17. Branched DNA-based Alu quantitative assay for cell-free plasma DNA levels in patients with sepsis or systemic inflammatory response syndrome.

    Science.gov (United States)

    Hou, Yan-Qiang; Liang, Dong-Yu; Lou, Xiao-Li; Zhang, Mei; Zhang, Zhen-huan; Zhang, Lu-rong

    2016-02-01

    Cell-free circulating DNA (cf-DNA) can be detected by various of laboratory techniques. We described a branched DNA-based Alu assay for measuring cf-DNA in septic patients. Compared to healthy controls and systemic inflammatory response syndrome (SIRS) patients, serum cf-DNA levels were significantly higher in septic patients (1426.54 ± 863.79 vs 692.02 ± 703.06 and 69.66 ± 24.66 ng/mL). The areas under the receiver operating characteristic curve of cf-DNA for normal vs sepsis and SIRS vs sepsis were 0.955 (0.884-1.025), and 0.856 (0.749-0.929), respectively. There was a positive correlation between cf-DNA and interleukin 6 or procalcitonin or Acute Physiology and Chronic Health Evaluation II. The cf-DNA concentration was higher in intensive care unit nonsurviving patients compared to surviving patients (2183.33 ± 615.26 vs 972.46 ± 648.36 ng/mL; P DNA-based Alu assays are feasible and useful to quantify serum cf-DNA levels. Increased cf-DNA levels in septic patients might complement C-reactive protein and procalcitonin in a multiple marker format. Cell-free circulating DNA might be a new marker in discrimination of sepsis and SIRS.

  18. Light splitting with imperfect wave plates.

    Science.gov (United States)

    Jackson, Jarom S; Archibald, James L; Durfee, Dallin S

    2017-02-01

    We discuss the use of wave plates with arbitrary retardances, in conjunction with a linear polarizer, to split linearly polarized light into two linearly polarized beams with an arbitrary splitting fraction. We show that for non-ideal wave plates, a much broader range of splitting ratios is typically possible when a pair of wave plates, rather than a single wave plate, is used. We discuss the maximum range of splitting fractions possible with one or two wave plates as a function of the wave plate retardances, and how to align the wave plates to achieve the maximum splitting range possible when simply rotating one of the wave plates while keeping the other one fixed. We also briefly discuss an alignment-free polarization rotator constructed from a pair of half-wave plates.

  19. Effects of a sliding plate on morphology of the epiphyseal plate in goat distal femur.

    Science.gov (United States)

    Lin, Da-sheng; Lian, Ke-jian; Hong, Jia-yuan; Ding, Zhen-qi; Zhai, Wen-liang

    2012-01-01

    The aim of this study was to observe the effects of a sliding plate on the morphology of the epiphyseal plate in goat distal femur. Eighteen premature female goats were divided randomly into sliding plate, regular plate and control groups. Radiographic analysis and histological staining were performed to evaluate the development of epiphyseal plate at 4 and 8 weeks after surgery. In the sliding plate group, the plate extended accordingly as the epiphyseal plate grows, and the epiphyseal morphology was kept essential normal. However, the phenomenon of the epiphyseal growth retardation and premature closure were very common in the regular plate group. In addition, the sliding plate group exhibited more normal histologic features and Safranin O staining compared to the regular plate group. Our results suggest that the sliding plate can provide reliable internal fixation of epiphyseal fracture without inhibiting epiphyseal growth.

  20. Effects of a Sliding Plate on Morphology of the Epiphyseal Plate in Goat Distal Femur

    Directory of Open Access Journals (Sweden)

    Da-sheng LIN, Ke-jian LIAN, Jia-yuan HONG, Zhen-qi DING, Wen-liang ZHAI

    2012-01-01

    Full Text Available The aim of this study was to observe the effects of a sliding plate on the morphology of the epiphyseal plate in goat distal femur. Eighteen premature female goats were divided randomly into sliding plate, regular plate and control groups. Radiographic analysis and histological staining were performed to evaluate the development of epiphyseal plate at 4 and 8 weeks after surgery. In the sliding plate group, the plate extended accordingly as the epiphyseal plate grows, and the epiphyseal morphology was kept essential normal. However, the phenomenon of the epiphyseal growth retardation and premature closure were very common in the regular plate group. In addition, the sliding plate group exhibited more normal histologic features and Safranin O staining compared to the regular plate group. Our results suggest that the sliding plate can provide reliable internal fixation of epiphyseal fracture without inhibiting epiphyseal growth.

  1. Comment on "Intermittent plate tectonics?".

    Science.gov (United States)

    Korenaga, Jun

    2008-06-01

    Silver and Behn (Reports, 4 January 2008, p. 85) proposed that intermittent plate tectonics may resolve a long-standing paradox in Earth's thermal evolution. However, their analysis misses one important term, which subsequently brings their main conclusion into question. In addition, the Phanerozoic eustasy record indicates that the claimed effect of intermittency is probably weak.

  2. License plate recognition using DTCNNs

    NARCIS (Netherlands)

    ter Brugge, M.H; Stevens, J.H; Nijhuis, J.A G; Spaanenburg, L; Tavsanonoglu, V

    1998-01-01

    Automatic license plate recognition requires a series of complex image processing steps. For practical use, the amount of data to he processed must be minimized early on. This paper shows that the computationally most intensive steps can be realized by DTCNNs. Moreover; high-level operations like fi

  3. Corrosion resistant metallic bipolar plate

    Science.gov (United States)

    Brady, Michael P.; Schneibel, Joachim H.; Pint, Bruce A.; Maziasz, Philip J.

    2007-05-01

    A corrosion resistant, electrically conductive component such as a bipolar plate for a PEM fuel cell includes 20 55% Cr, balance base metal such as Ni, Fe, or Co, the component having thereon a substantially external, continuous layer of chromium nitride.

  4. Structural Analysis of Plate Based Tensegrity Structures

    DEFF Research Database (Denmark)

    Hald, Frederik; Kirkegaard, Poul Henning; Damkilde, Lars

    2013-01-01

    Plate tensegrity structures combine tension cables with a cross laminated timber plate and can then form e.g. a roof structure. The topology of plate tensegrity structures is investigated through a parametric investigation. Plate tensegrity structures are investigated, and a method...... for determination of the structures pre-stresses is used. A parametric investigation is performed to determine a more optimized form of the plate based tensegrity structure. Conclusions of the use of plate based tensegrity in civil engineering and further research areas are discussed....

  5. Avionics Box Cold Plate Damage Prevention

    Science.gov (United States)

    Stambolian, Damon B.; Larchar, Steven W.; Henderson, Gena; Tran, Donald; Barth, Tim

    2012-01-01

    Problem Introduction: 1. Prevent Cold Plate Damage in Space Shuttle. 1a. The number of cold plate problems had increased from an average of 16.5 per/year between 1990 through 2000, to an average of 39.6 per year between 2001through 2005. 1b. Each complete set of 80 cold plates cost approximately $29 million, an average of $362,500 per cold plate. 1c It takes four months to produce a single cold plate. 2. Prevent Cold Plate Damage in Future Space Vehicles.

  6. Study on STR Genotyping of Cell Free DNA in Plasma%血浆游离DNA的STR分型检测研究

    Institute of Scientific and Technical Information of China (English)

    陈阳; 胡利平; 马波; 马立宇; 聂胜洁

    2014-01-01

    目的:探讨利用血浆中游离DNA进行短串联重复序列(short tandem repeat,STR)分型检测,解决法医学个体识别和亲权鉴定问题的可行性。方法采集36例无关健康个体EDTA-Na2抗凝血样,分离血浆,采用经典酚-氯仿法分别处理血浆和血细胞,对提取的DNA进行15个STR基因座常规PCR扩增和荧光标记复合扩增,采用聚丙烯酰胺凝胶电泳和毛细管电泳检测2种STR分型方法进行检测。结果常规PCR扩增银染检测和荧光标记复合扩增毛细管电泳检测两种STR分型方法的结果表明,同一个体的血浆游离DNA和血细胞DNA STR分型一致,且分型效果接近。结论血浆游离DNA可作为一种有效的生物学样本进行STR分型检测,应用于法医个体识别和亲权鉴定。%Objective The purpose of this study was to investigate the feasibility of short tandem repeat(STR) genotyping of cell free DNA in plasma for individual identification and paternity testing. Methods EDTA-Na2 DNA anti-coagulant blood samples were collected from 36 unrelated healthy volunteers,and both DNA in leukocytes and cell free DNA in plasma were extracted respectively using phenol-chloroform method. Target DNA in blood cells and plasma were amplified using regular STR typing and fluorescent multiplex STR assay separately,accordingly,the PCR products were analyzed by polyacrylamide gel electrophoresis and capillary electrophoresis. Results Using either normal PCR-STR or fluorescent multiplex STR assay,the consistent STR genotyping results were detected with similar efficiency for cell DNA and plasma DNA samples from the same individual. Conclusion Cell free DNA in plasma samples can be used as useful biological samples for STR genotyping,which can be applied to individual identification and paternity testing in forensic practice.

  7. Prenylation of a Rab1B mutant with altered GTPase activity is impaired in cell-free systems but not in intact mammalian cells.

    Science.gov (United States)

    Wilson, A L; Sheridan, K M; Erdman, R A; Maltese, W A

    1996-09-15

    Previous studies have reached differing conclusions as to whether or not guanine-nucleotide-dependent conformational changes affect the ability of Rab proteins to undergo post-translational modification by Rab:geranylgeranyltransferase (Rab-GGTase). We now show that the ability of a Rab1B mutant [Q67L (Gln-67-->Leu)] with reduced intrinsic GTPase activity to undergo geranylgeranylation in cell-free assays depends on the guanine nucleotide composition of the system. When GTP is the predominant nucleotide in the assay, Rab1BQ67L is a poor substrate. However, when GDP is present and GTP is omitted, prenylation of the Q67L mutant is comparable with that of the wild-type (WT) protein. These studies, coupled with the poor prenylation of Rab1BWT in the presence of the non-hydrolysable GTP analogue guanosine 5'-[gamma-thio]triphosphate, support the notion that Rab-GGTase prefers substrates in the GDP conformation. When the abilities of Rab1BQ67L and Rab1BWT to undergo prenylation were compared by metabolic labelling of transiently expressed proteins in cultured human 293 cells, we did not observe a decline in prenylation of the mutant protein as predicted on the basis of the cell-free assays. Moreover, the Q67L mutant was comparable with the wild-type Rab1B in its ability to associate with co-expressed Rab GDP dissociation inhibitors in 293 cells. These findings raise the possibility that unidentified proteins present in intact cells may compensate for the reduced intrinsic GTPase activity of the Q67L mutant, allowing a significant proportion of the nascent Rab1BQ67L to assume a GDP conformation. The differential prenylation of Rab1BQ67L in cell-free systems versus intact cells underscores the importance of evaluating the post-translational modification of specific Rab mutants in vivo, where poorly characterized regulatory proteins may have a significant effect on GTPase activity or nucleotide exchange rates.

  8. Earth's Decelerating Tectonic Plates

    Energy Technology Data Exchange (ETDEWEB)

    Forte, A M; Moucha, R; Rowley, D B; Quere, S; Mitrovica, J X; Simmons, N A; Grand, S P

    2008-08-22

    Space geodetic and oceanic magnetic anomaly constraints on tectonic plate motions are employed to determine a new global map of present-day rates of change of plate velocities. This map shows that Earth's largest plate, the Pacific, is presently decelerating along with several other plates in the Pacific and Indo-Atlantic hemispheres. These plate decelerations contribute to an overall, globally averaged slowdown in tectonic plate speeds. The map of plate decelerations provides new and unique constraints on the dynamics of time-dependent convection in Earth's mantle. We employ a recently developed convection model constrained by seismic, geodynamic and mineral physics data to show that time-dependent changes in mantle buoyancy forces can explain the deceleration of the major plates in the Pacific and Indo-Atlantic hemispheres.

  9. Embedded adhesive connection for laminated glass plates

    DEFF Research Database (Denmark)

    Hansen, Jens Zangenberg; Poulsen, S.H.; Bagger, A.

    2012-01-01

    The structural behavior of a new connection design, the embedded adhesive connection, used for laminated glass plates is investigated. The connection consists of an aluminum plate encapsulated in-between two adjacent triple layered laminated glass plates. Fastening between glass and aluminum...... usage in a design situation. The embedded connection shows promising potential as a future fastening system for load-carrying laminated glass plates....

  10. Modeling the hydrodynamics of Phloem sieve plates

    DEFF Research Database (Denmark)

    Jensen, Kaare Hartvig; Mullendore, Daniel Leroy; Holbrook, Noel Michele;

    2012-01-01

    Sieve plates have an enormous impact on the efficiency of the phloem vascular system of plants, responsible for the distribution of photosynthetic products. These thin plates, which separate neighboring phloem cells, are perforated by a large number of tiny sieve pores and are believed to play...... are investigated. We find that the sieve plate resistance is correlated to the cell lumen resistance, and that the sieve plate and the lumen contribute almost equally to the total hydraulic resistance of the phloem translocation pathway....

  11. Electrochemical Assay of Gold-Plating Solutions

    Science.gov (United States)

    Chiodo, R.

    1982-01-01

    Gold content of plating solution is assayed by simple method that required only ordinary electrochemical laboratory equipment and materials. Technique involves electrodeposition of gold from solution onto electrode, the weight gain of which is measured. Suitable fast assay methods are economically and practically necessary in electronics and decorative-plating industries. If gold content in plating bath is too low, poor plating may result, with consequent economic loss to user.

  12. Mathematical methods for elastic plates

    CERN Document Server

    Constanda, Christian

    2014-01-01

    Mathematical models of deformation of elastic plates are used by applied mathematicians and engineers in connection with a wide range of practical applications, from microchip production to the construction of skyscrapers and aircraft. This book employs two important analytic techniques to solve the fundamental boundary value problems for the theory of plates with transverse shear deformation, which offers a more complete picture of the physical process of bending than Kirchhoff’s classical one.   The first method transfers the ellipticity of the governing system to the boundary, leading to singular integral equations on the contour of the domain. These equations, established on the basis of the properties of suitable layer potentials, are then solved in spaces of smooth (Hölder continuous and Hölder continuously differentiable) functions.   The second technique rewrites the differential system in terms of complex variables and fully integrates it, expressing the solution as a combination of complex ana...

  13. Transfinite thin plate spline interpolation

    CERN Document Server

    Bejancu, Aurelian

    2009-01-01

    Duchon's method of thin plate splines defines a polyharmonic interpolant to scattered data values as the minimizer of a certain integral functional. For transfinite interpolation, i.e. interpolation of continuous data prescribed on curves or hypersurfaces, Kounchev has developed the method of polysplines, which are piecewise polyharmonic functions of fixed smoothness across the given hypersurfaces and satisfy some boundary conditions. Recently, Bejancu has introduced boundary conditions of Beppo Levi type to construct a semi-cardinal model for polyspline interpolation to data on an infinite set of parallel hyperplanes. The present paper proves that, for periodic data on a finite set of parallel hyperplanes, the polyspline interpolant satisfying Beppo Levi boundary conditions is in fact a thin plate spline, i.e. it minimizes a Duchon type functional.

  14. Vehicle License Plate Character Segmentation

    Institute of Scientific and Technical Information of China (English)

    Mei-Sen Pan; Jun-Biao Yan; Zheng-Hong Xiao

    2008-01-01

    Vehicle license plate (VLP) character segmentation is an important part of the vehicle license plate recognition system (VLPRS). This paper proposes a least square method (LSM) to treat horizontal tilt and vertical tilt in VLP images. Auxiliary lines are added into the image (or the tilt-corrected image) to make the separated parts of each Chinese character to be an interconnected region. The noise regions will be eliminated after two fusing images are merged according to the minimum principle of gray values.Then, the characters are segmented by projection method (PM) and the final character images are obtained. The experimental results show that this method features fast processing and good performance in segmentation.

  15. Optical Near-Field Plates

    Science.gov (United States)

    2015-04-08

    OPTICAL FREQUENCIES We designed a near field plate (NFP) structure for deep subwavelength super -focusing at optical frequencies [1]. The method used... resolution of λ/20 of the wavelength was obtained [2]. We proposed a practical design of a NFP that operates at optical frequencies by using a thin...bar is 2µm. (b) Optical microscopy image of the plasmonic spectro- scope illuminated with white light. (c) SEM image of the fabricated 2D spoke

  16. Electroless metal plating of plastics

    Science.gov (United States)

    Krause, Lawrence J.

    1984-01-01

    Process for plating main group metals on aromatic polymers is carried out by the use of a nonaqueous solution of a salt of an alkali metal in a positive valence state and a main group metal in a negative valence state with contact between the solution and polymer providing a redox reaction causing the deposition of the main group metal and the reduction of the polymer. Products from the process exhibit useful decorative and electrical properties.

  17. Moving Divertor Plates in a Tokamak

    Energy Technology Data Exchange (ETDEWEB)

    S.J. Zweben, H. Zhang

    2009-02-12

    Moving divertor plates could help solve some of the problems of the tokamak divertor through mechanical ingenuity rather than plasma physics. These plates would be passively heated on each pass through the tokamak and cooled and reprocessed outside the tokamak. There are many design options using varying plate shapes, orientations, motions, coatings, and compositions.

  18. Designing a licence plate for memorability

    NARCIS (Netherlands)

    Schraagen, J.M.C.; Dongen, C.J.G. van

    2005-01-01

    Good memorability of licence plates is important in those cases where licence plates are viewed for a brief period of time and the information is essential for police investigations. The purpose of the current study was to design a new Dutch licence plate that could be remembered well. A memory expe

  19. Episodic plate tectonics on Venus

    Science.gov (United States)

    Turcotte, Donald

    1992-01-01

    Studies of impact craters on Venus from the Magellan images have placed important constraints on surface volcanism. Some 840 impact craters have been identified with diameters ranging from 2 to 280 km. Correlations of this impact flux with craters on the Moon, Earth, and Mars indicate a mean surface age of 0.5 +/- 0.3 Ga. Another important observation is that 52 percent of the craters are slightly fractured and only 4.5 percent are embayed by lava flows. These observations led researchers to hypothesize that a pervasive resurfacing event occurred about 500 m.y. ago and that relatively little surface volcanism has occurred since. Other researchers have pointed out that a global resurfacing event that ceased about 500 MYBP is consistent with the results given by a recent study. These authors carried out a series of numerical calculations of mantle convection in Venus yielding thermal evolution results. Their model considered crustal recycling and gave rapid planetary cooling. They, in fact, suggested that prior to 500 MYBP plate tectonics was active in Venus and since 500 MYBP the lithosphere has stabilized and only hot-spot volcanism has reached the surface. We propose an alternative hypothesis for the inferred cessation of surface volcanism on Venus. We hypothesize that plate tectonics on Venus is episodic. Periods of rapid plate tectonics result in high rates of subduction that cool the interior resulting in more sluggish mantle convection.

  20. Modified tubularized incised plate urethroplasty

    Directory of Open Access Journals (Sweden)

    Shivaji Mane

    2013-01-01

    Full Text Available Aim: To share our experience of doing tubularized incised plate urethroplasty with modifications. Materials and Methods: This is a single surgeon personal series from 2004 to 2009. One hundred patients of distal hypospadias were subjected for Snodgrass urethroplasty with preputioplasty. The age range was 1 to 5 year with mean age of 2.7 years. Selection criteria were good urethral plate, without chordee and torsion needing complete degloving. Main technical modification from original Snodgrass procedure was spongioplasty, preputioplasty, and dorsal slit when inability to retract prepuce during surgery. Results: Average follow-up period is 23 months. Seven (7% patients developed fistula and one patient had complete preputial dehiscence. Phimosis developed in three (3% patients and required circumcision. Dorsal slit was required in seven patients. One patient developed meatal stenosis in postoperative period. All other patients are passing single urinary stream and have cosmesis that is acceptable. Conclusions: Modified tubularized incised plate urethroplasty with preputioplasty effectively gives cosmetically normal looking penis with low complications.

  1. Plating of proximal humeral fractures.

    Science.gov (United States)

    Martetschläger, Frank; Siebenlist, Sebastian; Weier, Michael; Sandmann, Gunther; Ahrens, Philipp; Braun, Karl; Elser, Florian; Stöckle, Ulrich; Freude, Thomas

    2012-11-01

    The optimal treatment for proximal humeral fractures is controversial. Few data exist concerning the influence of the surgical approach on the outcome. The purpose of this study was to evaluate the clinical and radiological outcomes of proximal humeral fractures treated with locking plate fixation through a deltopectoral vs an anterolateral deltoid-splitting approach. Of 86 patients who met the inclusion criteria, 70 were available for follow-up examination. Thirty-three patients were treated through a deltopectoral approach and 37 through an anterolateral deltoid-splitting approach. In all cases, open reduction and internal fixation with a PHILOS locking plate (Synthes, Umkirch, Germany) was performed. Clinical follow-up included evaluation of pain, shoulder mobility, and strength. Constant score and Disabilities of the Arm, Shoulder and Hand (DASH) score were assessed. A clinical neurological examination of the axillary nerve was also performed. Consolidation, reduction, and appearance of head necrosis were evaluated radiographically. After a mean follow-up of 33 months, Constant scores, DASH scores, and American Shoulder and Elbow Surgeons scores showed no significant differences between the groups. Clinical neurologic examination of the axillary nerve revealed no obvious damage to the nerve in either group. Deltopectoral and anterolateral detoid-splitting approaches for plate fixation of proximal humeral fractures are safe and provide similar clinical outcomes. The results of this study suggest that the approach can be chosen according to surgeon preference.

  2. Antioxidant action of SMe1EC2, the low-basicity derivative of the pyridoindole stobadine, in cell free chemical models and at cellular level.

    Science.gov (United States)

    Balcerczyk, Aneta; Bartosz, Grzegorz; Drzewinska, Joanna; Piotrowski, Łukasz; Pulaski, Łukasz; Stefek, Milan

    2014-03-01

    The aim of the study was to evaluate the antioxidant action of SMe1EC2, the structural analogue of the hexahydropyridoindole antioxidant stobadine. The antiradical activity of SMe1EC2 was found to be higher when compared to stobadine, as determined both in cell-free model systems of AAPH-induced oxidation of dihydrorhodamine 123 and 2',7'-dichloro-dihydrofluorescein diacetate, and in the cellular system of stimulated macrophages RAW264.7. Analysis of proliferation of HUVEC and HUVEC-ST cells revealed absence of cytotoxic effect of SMe1EC2 at concentrations below 100 µM. The antioxidant activity of SMe1EC2, superior to the parent drug stobadine, is accounted for by both the higher intrinsic free radical scavenging action and by the better bioavailability of the low-basicity SMe1EC2 relative to the high-basicity stobadine.

  3. Detection of Clonal and Subclonal Copy-Number Variants in Cell-Free DNA from Patients with Breast Cancer Using a Massively Multiplexed PCR Methodology

    Directory of Open Access Journals (Sweden)

    Eser Kirkizlar

    2015-10-01

    Using an in vitro model of cell-free DNA, we show that mmPCR-NGS can accurately detect CNVs with average allelic imbalances as low as 0.5%, an improvement over previously reported whole-genome sequencing approaches. Our method revealed differences in the spectrum of CNVs detected in tumor tissue subsections and matching plasma samples from 11 patients with stage II breast cancer. Moreover, we showed that liquid biopsies are able to detect subclonal mutations that may be missed in tumor tissue biopsies. We anticipate that this mmPCR-NGS methodology will have broad applicability for the characterization, diagnosis, and therapeutic monitoring of CNV-enriched cancers, such as breast, ovarian, and lung cancer.

  4. Non-invasive prenatal diagnosis of β-thalassemia by detection of the cell-free fetal DNA in maternal circulation: a systematic review and meta-analysis.

    Science.gov (United States)

    Zafari, Mandana; Kosaryan, Mehrnoush; Gill, Pooria; Alipour, Abbass; Shiran, Mohammadreza; Jalalli, Hossein; Banihashemi, Ali; Fatahi, Fatemeh

    2016-08-01

    The discovery of fetal DNA (f-DNA) opens the possibility of early non-invasive procedure for detection of paternally inherited mutation of beta-thalassemia. Since 2002, some studies have examined the sensitivity and specificity of this method for detection of paternally inherited mutation of thalassemia in pregnant women at risk of having affected babies. We conducted a systematic review of published articles that evaluated using this method for early detection of paternally inherited mutation in maternal plasma. A sensitive search of multiple databases was done in which nine studies met our inclusion criteria. The sensitivity and specificity was 99 and 99 %, respectively. The current study found that detection of paternally inherited mutation of thalassemia using analysis of cell-free fetal DNA is highly accurate. This method could replace conventional and invasive methods.

  5. Properties of the ribonucleic acid bacteriophage ZIK-1 coat protein and its synthesis in an Escherichia coli cell-free system.

    Science.gov (United States)

    Robinson, J W

    1972-07-01

    The coat protein subunit of the RNA bacteriophage ZIK/1 has a molecular weight of 12100 and does not contain histidine, methionine and cysteine. The amino acid composition of the coat protein is different from that of other RNA bacteriophage coat proteins. Bacteriophage ZIK/1 belongs to a class of RNA bacteriophages distinct from the f2 type, which lack histidine in their coat proteins, and the Qbeta type, which lack histidine and methionine. Bacteriophage ZIK/1 RNA is an efficient template in the Escherichia coli cell-free system producing coat protein as the major product and a number of non-coat proteins. This result is similar to that obtained with RNA from f2-type bacteriophages. It is probable that the genomes of RNA bacteriophages are structurally similar and that differences between the types of RNA bacteriophage arise from minor differences in RNA sequence.

  6. Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system.

    Science.gov (United States)

    Sun, Zachary Z; Yeung, Enoch; Hayes, Clarmyra A; Noireaux, Vincent; Murray, Richard M

    2014-06-20

    Accelerating the pace of synthetic biology experiments requires new approaches for rapid prototyping of circuits from individual DNA regulatory elements. However, current testing standards require days to weeks due to cloning and in vivo transformation. In this work, we first characterized methods to protect linear DNA strands from exonuclease degradation in an Escherichia coli based transcription-translation cell-free system (TX-TL), as well as mechanisms of degradation. This enabled the use of linear DNA PCR products in TX-TL. We then compared expression levels and binding dynamics of different promoters on linear DNA and plasmid DNA. We also demonstrated assembly technology to rapidly build circuits entirely in vitro from separate parts. Using this strategy, we prototyped a four component genetic switch in under 8 h entirely in vitro. Rapid in vitro assembly has future applications for prototyping multiple component circuits if combined with predictive computational models.

  7. The cell-free integration of a polytopic mitochondrial membrane protein into liposomes occurs cotranslationally and in a lipid-dependent manner.

    Directory of Open Access Journals (Sweden)

    Ashley R Long

    Full Text Available The ADP/ATP Carrier (AAC is the most abundant transporter of the mitochondrial inner membrane. The central role that this transporter plays in cellular energy production highlights the importance of understanding its structure, function, and the basis of its pathologies. As a means of preparing proteoliposomes for the study of membrane proteins, several groups have explored the use of cell-free translation systems to facilitate membrane protein integration directly into preformed unilamellar vesicles without the use of surfactants. Using AAC as a model, we report for the first time the detergent-free reconstitution of a mitochondrial inner membrane protein into liposomes using a wheat germ-based in vitro translation system. Using a host of independent approaches, we demonstrate the efficient integration of AAC into vesicles with an inner membrane-mimetic lipid composition and, more importantly, that the integrated AAC is functionally active in transport. By adding liposomes at different stages of the translation reaction, we show that this direct integration is obligatorily cotranslational, and by synthesizing stable ribosome-bound nascent chain intermediates, we show that the nascent AAC polypeptide interacts with lipid vesicles while ribosome-bound. Finally, we show that the presence of the phospholipid cardiolipin in the liposomes specifically enhances AAC translation rate as well as the efficiency of vesicle association and integration. In light of these results, the possible mechanisms of liposome-assisted membrane protein integration during cell-free translation are discussed with respect to the mode of integration and the role of specific lipids.

  8. The influence of the cell free solution of lactic acid bacteria on tyramine production by food borne-pathogens in tyrosine decarboxylase broth.

    Science.gov (United States)

    Toy, Nurten; Özogul, Fatih; Özogul, Yesim

    2015-04-15

    The function of cell-free solutions (CFSs) of lactic acid bacteria (LAB) on tyramine and other biogenic amine production by different food borne-pathogens (FBPs) was investigated in tyrosine decarboxylase broth (TDB) using HPLC. Cell free solutions were prepared from four LAB strains. Two different concentrations which were 50% (5 ml CFS+5 ml medium/1:1) and 25% (2.5 ml CFS+7.5 ml medium/1:3) CFS and the control without CFS were prepared. Both concentration of CFS of Streptococcus thermophilus and 50% CFS of Pediococcus acidophilus inhibited tyramine production up to 98% by Salmonella paratyphi A. Tyramine production by Escherichia coli was also inhibited by 50% CFS of Lactococcus lactis subsp. lactis and 25% CFS of Leuconostoc lactis. subsp. cremoris. The inhibitor effect of 50% CFS of P. acidophilus was the highest on tyramine production (55%) by Listeria monocytogenes, following Lc. lactis subsp. lactis and Leuconostoc mesenteroides subsp. cremoris (20%) whilst 25% CFS of Leu. mes. subsp. cremoris and Lc. lactis subsp. lactis showed stimulator effects (160%). The stimulation effects of 50% CFS of S. thermophilus and Lc. lactis subsp. lactis were more than 70% by Staphylococcus aureus comparing to the control. CFS of LAB strains showed statistically inhibitor effect since lactic acid inhibited microbial growth, decreased pH quickly and reduced the formation of AMN and BAs. Consequently, in order to avoid the formation of high concentrations of biogenic amines in fermented food by bacteria, it is advisable to use CFS for food and food products.

  9. Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA.

    Directory of Open Access Journals (Sweden)

    Richard B Lanman

    Full Text Available Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital Sequencing™ is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999% enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient's cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing.

  10. Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA.

    Science.gov (United States)

    Lanman, Richard B; Mortimer, Stefanie A; Zill, Oliver A; Sebisanovic, Dragan; Lopez, Rene; Blau, Sibel; Collisson, Eric A; Divers, Stephen G; Hoon, Dave S B; Kopetz, E Scott; Lee, Jeeyun; Nikolinakos, Petros G; Baca, Arthur M; Kermani, Bahram G; Eltoukhy, Helmy; Talasaz, AmirAli

    2015-01-01

    Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital Sequencing™ is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient's cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing.

  11. Plate tectonics, habitability and life

    Science.gov (United States)

    Spohn, Tilman; Breuer, Doris

    2016-04-01

    The role of plate tectonics in defining habitability of terrestrial planets is being increasingly discussed (e.g., Elkins-Tanton, 2015). Plate tectonics is a significantly evolved concept with a large variety of aspects. In the present context, cycling of material between near surface and mantle reservoirs is most important. But increased heat transport through mixing of cold lithosphere with the deep interior and formation of continental crust may also matter. An alternative mechanism of material cycling between these reservoirs is hot-spot volcanism combined with crust delamination. Hot-spot volcanism will transport volatiles to the atmosphere while delamination will mix crust, possibly altered by sedimentation and chemical reactions, with the mantle. The mechanism works as long as the stagnant lithosphere plate has not grown thicker than the crust and as long as volcanic material is added onto the crust. Thermal evolution studies suggest that the mechanism could work for the first 1-2 Ga of planetary evolution. The efficiency of the mechanism is limited by the ratio of extrusive to intrusive volcanism, which is thought to be less than 0.25. Plate tectonics would certainly have an advantage by working even for more evolved planets. A simple, most-used concept of habitability requires the thermodynamic stability of liquid water on the surface of a planet. Cycling of CO2between the atmosphere, oceans and interior through subduction and surface volcanism is an important element of the carbonate-silicate cycle, a thermostat feedback cycle that will keep the atmosphere from entering into a runaway greenhouse. Calculations for a model Earth lacking plate tectonics but degassing CO2, N, and H2O to form a surface ocean and a secondary atmosphere (Tosi et al, 2016) suggest that liquid water can be maintained on the surface for 4.5Ga. The model planet would then qualify as habitable. It is conceivable that the CO2 buffering capability of its ocean together with silicate

  12. Hierarchical self-organization of tectonic plates

    CERN Document Server

    Morra, Gabriele; Müller, R Dietmar

    2010-01-01

    The Earth's surface is subdivided into eight large tectonic plates and many smaller ones. We reconstruct the plate tessellation history and demonstrate that both large and small plates display two distinct hierarchical patterns, described by different power-law size-relationships. While small plates display little organisational change through time, the structure of the large plates oscillate between minimum and maximum hierarchical tessellations. The organization of large plates rapidly changes from a weak hierarchy at 120-100 million years ago (Ma) towards a strong hierarchy, which peaked at 65-50, Ma subsequently relaxing back towards a minimum hierarchical structure. We suggest that this fluctuation reflects an alternation between top and bottom driven plate tectonics, revealing a previously undiscovered tectonic cyclicity at a timescale of 100 million years.

  13. When Did Plate Tectonics Begin

    Science.gov (United States)

    Brown, M.

    2015-12-01

    Present-day plate tectonics on Earth is characterized by asymmetric (one-sided) subduction, but how do we recognize the imprint of subduction in the geologic record? How do we weigh global (commonly younger) vs local (commonly older) datasets or distinguish initiation from episodic from continuous subduction? How reliable are data gaps? Characteristics of the Paleozoic record of subduction include calc-alkaline magmatism, blueschist/UHP metamorphism and collisional orogenesis, and ophiolites as representatives of former ocean lithosphere. Are these characteristic rocks preserved in Proterozoic, Archean and Hadean crust? Does a hotter mantle, higher heat production and weaker lithosphere modify or eliminate these features? What preceded subduction and how do we recognize that regime? Are rock associations or geochemical fingerprints reliable? Does reworking and overprinting modify geochemical fingerprints? Proposals for the start of plate tectonics have been based on: persistence of isotope anomalies/fractionated chemical domains in the mantle; changes in chemistry of magmatic rocks, rates of crustal growth vs reworking, and sites of growth; the metamorphic record, particularly the first appearance of contrasting thermal gradients or eclogite (including evidence from mineral inclusions in diamonds) or UHP metamorphic rocks; stabilization of cratonic lithosphere and formation of supercratons, and the beginning of the Proterozoic supercontinent cycle; the end of the flat Earth, emergence of continents, development of significant topography, changes in the style of orogeny and the rise in atmospheric oxygen; and, the appearance of passive margins and changes in the style of sedimentation. Estimates of the timing have varied from the Hadean to Neoproterozoic. I will summarize evidence for a growing consensus that the late Mesoarchean to early Paleoproterozoic was a 700 Myr long period of transition to continuous (?) subduction and global (?) mobile-lid plate tectonics.

  14. Septal splint with wax plates.

    Directory of Open Access Journals (Sweden)

    Nayak D

    1995-07-01

    Full Text Available To pack or not to pack, has always been a debate, especially after septal and functional endoscopic sinus surgery. The authors have studied the symptoms of packing versus not packing in their series of 100 patients having undergone nasal surgery. They advocate the use of dental wax for the fashioning of septal splints, since they are easy to introduce, cheap and malleable. The patients postoperative comfort is greatly enhanced with the use of dental wax plate splints instead of nasal packing.

  15. Seismic link at plate boundary

    Indian Academy of Sciences (India)

    Faical Ramdani; Omar Kettani; Benaissa Tadili

    2015-06-01

    Seismic triggering at plate boundaries has a very complex nature that includes seismic events at varying distances. The spatial orientation of triggering cannot be reduced to sequences from the main shocks. Seismic waves propagate at all times in all directions, particularly in highly active zones. No direct evidence can be obtained regarding which earthquakes trigger the shocks. The first approach is to determine the potential linked zones where triggering may occur. The second step is to determine the causality between the events and their triggered shocks. The spatial orientation of the links between events is established from pre-ordered networks and the adapted dependence of the spatio-temporal occurrence of earthquakes. Based on a coefficient of synchronous seismic activity to grid couples, we derive a network link by each threshold. The links of high thresholds are tested using the coherence of time series to determine the causality and related orientation. The resulting link orientations at the plate boundary conditions indicate that causal triggering seems to be localized along a major fault, as a stress transfer between two major faults, and parallel to the geothermal area extension.

  16. Wood zone plate fishnet metalens

    Directory of Open Access Journals (Sweden)

    Orazbayev Bakhtiyar

    2015-01-01

    Full Text Available Fresnel-zone plate lenses provide focusing performance while having low profile. Unfortunately, they usually display higher reflection losses than conventional dielectric lenses. Here, we demonstrate a low-profile Wood zone plate metalens based on the fishnet metamaterial working in a near-zero regime with an equivalent refractive index less than unity (nf = 0.51. The metalens is made of alternating dielectric and fishnet metamaterial concentric rings. The use of fishnet metamaterial allows reducing the reflections from the lens, while maintaining low profile, low cost and ease of manufacturing. The lens is designed to work at the W-band of the millimeter-waves range with a focal length FL = 22.8 mm (7.5 λ0 aiming at antenna or radar system applications. The focusing performance of the lens along with its radiation characteristics in a lens antenna configuration have been studied numerically and confirmed experimentally, showing a gain improvement of ~2.5 dB with respect to a fishnet Soret metalens.

  17. Petrologic implications of plate tectonics.

    Science.gov (United States)

    Yoder, H S

    1971-07-30

    Petrologists can make significant contributions to the plate tectonic concept. Fixing the stability fields of the principal rock types involved will provide the limits of pressure and temperature of the various environments. Experimental determination of the partition coefficients of the trace elements will be helpful. Studies of the partial melting behavior of possible parental materials in the absence and presence of water, especially the undersaturated region, will contribute to the understanding of magma production. Experimental observations on the rheological properties of the peridotites below and just above the solidus will lead to a better evaluation of the convective mechanism. Measurement of the fundamental properties of rocks, such as the density of solids and liquids at high pressures and temperatures, would contribute to understanding the concepts of diapiric rise, magma segregation, and the low-velocity zone. Broader rock sampling of the oceanic areas of all environments will do much to define the petrologic provinces. The field petrologist specializing in the Paleozoic regions and Precambrian shields can contribute by examining those regions for old plate boundaries and devising new criteria for their recognition.

  18. Effect of plate roughness on the field near RPC plates

    CERN Document Server

    Jash, Abhik; Mukhopadhyay, Supratik; Chattopadhyay, Subhasis

    2016-01-01

    The inner surfaces of the electrodes encompassing the gas volume of a Resistive Plate Chamber (RPC) have been found to exhibit asperities with three kind of features grossly. The desired uniform electric field within the gas volume of RPC is expected to be affected due to the presence of these asperities, which will eventually affect the final response from the detector. In this work, an attempt has been made to model the highly complex roughness of the electrode surfaces and compute its effect on the electrostatic field within RPC gas chamber. The calculations have been performed numerically using Finite Element Method (FEM) and Boundary Element Method (BEM) and the two methods have been compared in this context.

  19. Methylation status of the APC and RASSF1A promoter in cell-free circulating DNA and its prognostic role in patients with colorectal cancer.

    Science.gov (United States)

    Matthaios, Dimitrios; Balgkouranidou, Ioanna; Karayiannakis, Anastasios; Bolanaki, Helen; Xenidis, Nikolaos; Amarantidis, Kyriakos; Chelis, Leonidas; Romanidis, Konstantinos; Chatzaki, Aikaterini; Lianidou, Evi; Trypsianis, Grigorios; Kakolyris, Stylianos

    2016-07-01

    DNA methylation is the most frequent epigenetic alteration. Using methylation-specific polymerase chain reaction (MSP), the methylation status of the adenomatous polyposis coli (APC) and Ras association domain family 1 isoform A (RASSF1A) genes was examined in cell-free circulating DNA from 155 plasma samples obtained from patients with early and advanced colorectal cancer (CRC). APC and RASSF1A hypermethylation was frequently observed in both early and advanced disease, and was significantly associated with a poorer disease outcome. The methylation status of the APC and RASSF1A promoters was investigated in cell-free DNA of patients with CRC. Using MSP, the promoter methylation status of APC and RASSF1A was examined in 155 blood samples obtained from patients with CRC, 88 of whom had operable CRC (oCRC) and 67 had metastatic CRC (mCRC). The frequency of APC methylation in patients with oCRC was 33%. Methylated APC promoter was significantly associated with older age (P=0.012), higher stage (P=0.014) and methylated RASSF1A status (P=0.050). The frequency of APC methylation in patients with mCRC was 53.7%. In these patients, APC methylation was significantly associated with methylated RASSF1A status (P=0.016). The frequency of RASSF1A methylation in patients with oCRC was 25%. Methylated RASSF1A in oCRC was significantly associated with higher stage (P=0.021). The frequency of RASSF1A methylation in mCRC was 44.8%. Methylated RASSF1A in mCRC was associated with moderate differentiation (P=0.012), high levels of carcinoembryonic antigen (P=0.023) and methylated APC status (P=0.016). Patients with an unmethylated APC gene had better survival in both early (81±5 vs. 27±4 months, PAPC. Patients with an unmethylated RASSF1A gene had better survival in both early (71±6 vs. 46±8 months, PAPC and RASSF1A promoter methylation status and survival may be indicative of a prognostic role for these genes in CRC, which requires additional testing in larger studies.

  20. Rapidly Moving Divertor Plates In A Tokamak

    Energy Technology Data Exchange (ETDEWEB)

    S. Zweben

    2011-05-16

    It may be possible to replace conventional actively cooled tokamak divertor plates with a set of rapidly moving, passively cooled divertor plates on rails. These plates would absorb the plasma heat flux with their thermal inertia for ~10-30 sec, and would then be removed from the vessel for processing. When outside the tokamak, these plates could be cooled, cleaned, recoated, inspected, and then returned to the vessel in an automated loop. This scheme could provide nearoptimal divertor surfaces at all times, and avoid the need to stop machine operation for repair of damaged or eroded plates. We describe various possible divertor plate designs and access geometries, and discuss an initial design for a movable and removable divertor module for NSTX-U.

  1. Excitation and Characterization of Chladni Plate Patterns

    Science.gov (United States)

    Bourke, Shannon; Behringer, Ernest

    2011-04-01

    When a thin metal plate with a small amount of sand on it is made to vibrate, aesthetically pleasing sand patterns can form along the nodal lines of the plate. These symmetric patterns are called Chladni Patterns. Students taking PHY 101 Physical Science in the Arts at Eastern Michigan University create these patterns by pulling a violin bow across the edge of a plate, or by using a mechanical oscillator to drive the center of a plate. These two methods only allow a small subset of all possible points on the plate to be excited. We designed and built an electronic device that allows its user to excite the plate at any point. We present patterns created with this electronic device and other methods, and describe ways to model the observed patterns.

  2. Coupling between plate vibration and acoustic radiation

    Science.gov (United States)

    Frendi, Abdelkader; Maestrello, Lucio; Bayliss, Alvin

    1993-01-01

    A detailed numerical investigation of the coupling between the vibration of a flexible plate and the acoustic radiation is performed. The nonlinear Euler equations are used to describe the acoustic fluid while the nonlinear plate equation is used to describe the plate vibration. Linear, nonlinear, and quasi-periodic or chaotic vibrations and the resultant acoustic radiation are analyzed. We find that for the linear plate response, acoustic coupling is negligible. However, for the nonlinear and chaotic responses, acoustic coupling has a significant effect on the vibration level as the loading increases. The radiated pressure from a plate undergoing nonlinear or chaotic vibrations is found to propagate nonlinearly into the far field. However, the nonlinearity due to wave propagation is much weaker than that due to the plate vibrations. As the acoustic wave propagates into the far field, the relative difference in level between the fundamental and its harmonics and subharmonics decreases with distance.

  3. Fuzzy Sliding Mode Control of Plate Vibrations

    OpenAIRE

    Manu Sharma; Singh, S. P.

    2010-01-01

    In this paper, fuzzy logic is meshed with sliding mode control, in order to control vibrations of a cantilevered plate. Test plate is instrumented with a piezoelectric sensor patch and a piezoelectric actuator patch. Finite element method is used to obtain mathematical model of the test plate. A design approach of a sliding mode controller for linear systems with mismatched time-varying uncertainties is used in this paper. It is found that chattering around the sliding surface in the sliding ...

  4. 431K/CD vehicle number plates

    CERN Multimedia

    GS Department

    2009-01-01

    The Green Plates Service, which is responsible for issuing the 431K/CD vehicle number plates , wishes to apologise for the delay in processing applications over the past weeks. The delay is outside the Service’s control, as it is due to the recent introduction of new rules governing the vehicle registration process in France. Normal service will be resumed as soon as possible. Thank you for your understanding. GS-SEM-LS – Green Plates Service

  5. Sigmoid plate dehiscence: Congenital or acquired condition?

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zhaohui, E-mail: lzhtrhos@163.com [Capital Medical University, Beijing Tongren Hospital, No 1 Dong Jiao Min Street, Dongcheng District, Beijing 100730 (China); Li, Jing, E-mail: lijingxbh@yahoo.com.cn [Capital Medical University, Beijing Tongren Hospital, No 1 Dong Jiao Min Street, Dongcheng District, Beijing 100730 (China); Zhao, Pengfei, E-mail: zhaopengf05@163.com [Capital Medical University, Beijing Friendship Hospital, No 95 Yongan Road, Xicheng District, Beijing 100050 (China); Lv, Han, E-mail: chrislvhan@126.com [Capital Medical University, Beijing Friendship Hospital, No 95 Yongan Road, Xicheng District, Beijing 100050 (China); Dong, Cheng, E-mail: derc007@sina.com [Capital Medical University, Beijing Friendship Hospital, No 95 Yongan Road, Xicheng District, Beijing 100050 (China); Liu, Wenjuan, E-mail: wenjuanliu@163.com [Jining No. 1 People' s Hospital, No. 6 Health Street, Jining 272100 (China); Wang, Zhenchang, E-mail: cjr.wzhch@vip.163.com [Capital Medical University, Beijing Friendship Hospital, No 95 Yongan Road, Xicheng District, Beijing 100050 (China)

    2015-05-15

    Highlights: • CT with multiplanar reformations can accurately display the sigmoid platet dehiscence. • The prevalence of sigmoid plate dehiscence was no significant difference among different age groups. • The size of sigmoid plate bony defects were not statistically different among different age groups. • The sigmoid plate dehiscence is more commonly a congenital than an acquired condition. - Abstract: Background and purpose: The imaging features of sigmoid plate dehiscence-induced pulsatile tinnitus have been presented. The origin of the sigmoid plate dehiscence, however, remains unclear. Our aim was to assess the prevalence and extent of sigmoid plate dehiscence on computed tomography (CT) images in multiple age groups to determine whether this condition is more likely to be congenital or acquired. Materials and methods: We retrospectively reviewed contrast-enhanced CT images of sigmoid plates of temporal bones in 504 patients. Each temporal bone was characterized as normal or dehiscent. Patients were then subcategorized into four age groups, and the prevalence and extent of dehiscent sigmoid plates in each group were calculated and compared. Results: Overall, 80 patients had sigmoid plate dehiscence, nine of whom had it bilaterally. In successively older age groups, the prevalences of sigmoid plate dehiscence were 18.9%, 20.1%, 14.5%, and 12.7%, respectively. Respective average anteroposterior bony defect diameters were 3.7 ± 1.7, 3.0 ± 1.3, 3.1 ± 1.5, and 3.0 ± 1.1 mm. Respective average vertical bony defect diameters were 3.6 ± 2.3, 2.6 ± 1.2, 3.2 ± 1.5, and 3.0 ± 1.7 mm. The prevalence and extent of sigmoid plate dehiscence were not statistically different among the four age groups. Conclusions: The similar radiologic prevalence and extent of dehiscent sigmoid plates among the age groups suggest that the dehiscence is more commonly a congenital than an acquired condition.

  6. Anisotropic magnetocapacitance in ferromagnetic-plate capacitors

    Science.gov (United States)

    Haigh, J. A.; Ciccarelli, C.; Betz, A. C.; Irvine, A.; Novák, V.; Jungwirth, T.; Wunderlich, J.

    2015-04-01

    The capacitance of a parallel-plate capacitor can depend on the applied magnetic field. Previous studies have identified capacitance changes induced via classical Lorentz force or spin-dependent Zeeman effects. Here we measure a magnetization direction-dependent capacitance in parallel-plate capacitors where one plate is a ferromagnetic semiconductor, gallium manganese arsenide. This anisotropic magnetocapacitance is due to the anisotropy in the density of states dependent on the magnetization through the strong spin-orbit interaction.

  7. Strain resolving method of composite plane plates

    Directory of Open Access Journals (Sweden)

    Ion FUIOREA

    2011-06-01

    Full Text Available The paper deals with the extension of isotropic plates problem to the case of composite plates. In order to perform it, the Kirchhoff-Love hypotheses were “softened” by some additional ones. Considering the constitutive laws for composite materials the stress functions were eliminated by using Cauchy equations. As a result a partial derivative equation in displacements was obtained. Finally the boundary condition formulation was extended for the case of complex composite plates.

  8. High performance flat plate solar collector

    Science.gov (United States)

    Lansing, F. L.; Reynolds, R.

    1976-01-01

    The potential use of porous construction is presented to achieve efficient heat removal from a power producing solid and is applied to solar air heaters. Analytical solutions are given for the temperature distribution within a gas-cooled porous flat plate having its surface exposed to the sun's energy. The extracted thermal energy is calculated for two different types of plate transparency. Results show the great improvement in performance obtained with porous flat plate collectors as compared with analogous nonporous types.

  9. Reliability assessment of different plate theories for elastic wave propagation analysis in functionally graded plates.

    Science.gov (United States)

    Mehrkash, Milad; Azhari, Mojtaba; Mirdamadi, Hamid Reza

    2014-01-01

    The importance of elastic wave propagation problem in plates arises from the application of ultrasonic elastic waves in non-destructive evaluation of plate-like structures. However, precise study and analysis of acoustic guided waves especially in non-homogeneous waveguides such as functionally graded plates are so complicated that exact elastodynamic methods are rarely employed in practical applications. Thus, the simple approximate plate theories have attracted much interest for the calculation of wave fields in FGM plates. Therefore, in the current research, the classical plate theory (CPT), first-order shear deformation theory (FSDT) and third-order shear deformation theory (TSDT) are used to obtain the transient responses of flexural waves in FGM plates subjected to transverse impulsive loadings. Moreover, comparing the results with those based on a well recognized hybrid numerical method (HNM), we examine the accuracy of the plate theories for several plates of various thicknesses under excitations of different frequencies. The material properties of the plate are assumed to vary across the plate thickness according to a simple power-law distribution in terms of volume fractions of constituents. In all analyses, spatial Fourier transform together with modal analysis are applied to compute displacement responses of the plates. A comparison of the results demonstrates the reliability ranges of the approximate plate theories for elastic wave propagation analysis in FGM plates. Furthermore, based on various examples, it is shown that whenever the plate theories are used within the appropriate ranges of plate thickness and frequency content, solution process in wave number-time domain based on modal analysis approach is not only sufficient but also efficient for finding the transient waveforms in FGM plates.

  10. Line Heat-Source Guarded Hot Plate

    Data.gov (United States)

    Federal Laboratory Consortium — Description:The 1-meter guarded hot-plate apparatus measures thermal conductivity of building insulation. This facility provides for absolute measurement of thermal...

  11. Line Heat-Source Guarded Hot Plate

    Data.gov (United States)

    Federal Laboratory Consortium — Description: The 1-meter guarded hot-plate apparatus measures thermal conductivity of building insulation. This facility provides for absolute measurement of thermal...

  12. Plate Tectonics: A Paradigm under Threat.

    Science.gov (United States)

    Pratt, David

    2000-01-01

    Discusses the challenges confronting plate tectonics. Presents evidence that contradicts continental drift, seafloor spreading, and subduction. Reviews problems posed by vertical tectonic movements. (Contains 242 references.) (DDR)

  13. Maximizing band gaps in plate structures

    DEFF Research Database (Denmark)

    Halkjær, Søren; Sigmund, Ole; Jensen, Jakob Søndergaard

    2006-01-01

    Band gaps, i.e., frequency ranges in which waves cannot propagate, can be found in elastic structures for which there is a certain periodic modulation of the material properties or structure. In this paper, we maximize the band gap size for bending waves in a Mindlin plate. We analyze an infinite...... periodic plate using Bloch theory, which conveniently reduces the maximization problem to that of a single base cell. Secondly, we construct a finite periodic plate using a number of the optimized base cells in a postprocessed version. The dynamic properties of the finite plate are investigated...

  14. Strength of Ship Plates under Combined Loading

    DEFF Research Database (Denmark)

    Cui, W.; Wang, Y.; Pedersen, Preben Terndrup

    2002-01-01

    Strength of ship plates plays a significant role in the ultimate strength analysis of ship structures. In recent years several authors have proposed simplified analytical methods to calculate the ultimate strength of unstiffened plates. The majority of these investigations deal with plates....... The obtained results indicate that the simplified analytical method is able to determine the ultimate strength of unstiffened plates with imperfections in the form of welding-induced residual stresses and geometric deflections subjected to combined loads. Comparisons with experimental results show...

  15. Strength of ship plates under combined loading

    DEFF Research Database (Denmark)

    Cui, Weiching; Wang, Yongjun; Pedersen, Preben Terndrup

    2000-01-01

    Strength of ship plates plays a significant role for the ultimate strength analysis of ship structures. In recent years several authors have proposed simplified methods to calculate the ultimate strength of unstiffened plates. The majority of these investigations deal with plates subjected...... that the simplified method is able to determine the ultimate strength of unstiffened plates with imperfections in the form of welding induced residual stresses and geometric deflections subjected to combined loads. Comparisons with experimental results show that the procedure has sufficient accuracy for practical...

  16. Using Character Recognition for Plate Localization

    Directory of Open Access Journals (Sweden)

    Lama Hamandi

    2012-10-01

    Full Text Available In this paper, the “character recognition” approach to recognizing a vehicle license plate is used for localizing Saudi license plates. The proposed algorithm filters out all possible objects from the license plate image and focuses on the resulting objects. The coordinates of the center point of the bounding box for these objects is calculated and then possible alignments between these objects are checked. After finding the aligned objects, the recognition algorithms are applied to differentiate the numbers from the letters in the plate.

  17. Composition of the continental plates

    Science.gov (United States)

    Gilluly, J.

    1954-01-01

    The structures of continental plates and of oceanic basins suggested by several seismologists are utilized to estimate the relative volumes of sial and sima in the earth's crust. It seems that sial of the composition of the average igneous rock constitutes fully 26% and perhaps as much as 43% of the total crust. This ratio is far higher than seems likely if the sial had been entirely derived through fractional crystallization of a basaltic magma. The relative paucity of intermediate rocks as compared with granite and gabbro in the crust points in the same direction. The tentative conclusion is reached that the sial owes a large part of its volume to some process other than fractional crystallization of basalt-possibly to the emanation of low-melting constituents such as water, silica, potassa, soda, and alumina directly from the mantle to the crust. ?? 1954 Springer-Verlag.

  18. An efficient rectangular plate element

    Institute of Scientific and Technical Information of China (English)

    SHI; Zhongci

    2001-01-01

    [1]Shi Zhong-ci, On the accuracy of the quasi-conforming and generalize conforming finite elements, Chin. Ann. Math., 1990, 11B: 148.[2]Shi Zhong-ci, Chen Shao-chun, Huang Hong-ci, Plate elements with high accuracy, Collec. Geom. Anal. Math. Phys. (ed. Li Ta-Tsien), Singapore: World Scientific, 1997, 155—164.[3]Chen Shao-chun, Shi Zhong-ci, Double set parameter method for the construction of the element stiffness matrix, Mathematica Numerica Sinica (in Chinese), 1991, 13: 286.[4]Ciarlet, P., The Finite Element Method for Elliptic Problems, Amsterdam: North-Holland, 1978.

  19. Development of Catalytic Cooking Plates

    Energy Technology Data Exchange (ETDEWEB)

    Hjelm, Anna-Karin; Silversand, Fredrik [CATATOR AB, Lund (Sweden); Tena, Emmanuel; Berger, Marc [Gaz de France (France)

    2004-04-01

    Gas catalytic combustion for gas stoves or cooking plates (closed catalytic burner system with ceramic plates) is a very promising technique in terms of ease of cleaning, power modulation and emissions. Previous investigations show that wire mesh catalysts, prepared and supplied by Catator AB (CAT), seem to be very well suited for such applications. Beside significantly reducing the NOx-emissions, these catalysts offer important advantages such as good design flexibility, low pressure drop and high heat transfer capacity, where the latter leads to a quick thermal response. Prior to this project, Gaz de France (GdF) made a series of measurements with CAT's wire mesh catalysts in their gas cooking plates and compared the measured performance with similar results obtained with theirs cordierite monolith catalysts. Compared to the monolith catalyst, the wire mesh catalyst was found to enable very promising results with respect to both emission levels (<10 mg NO{sub x} /kWh, <5 mg CO/kWh) and life-time (>8000 h vs. 700 h at 200 kW/m{sup 2}). It was however established that the radiation and hence, the thermal efficiency of the cooking plate, was significantly less than is usually measured in combination with the monolith (15 % vs. 32 %). It was believed that the latter could be improved by developing new burner designs based on CAT's wire mesh concept. As a consequence, a collaboration project between GdF, CAT and the Swedish Gas Technology AB was created. This study reports on the design, the construction and the evaluation of new catalytic burners, based on CAT's wire mesh catalysts, used for the combustion of natural gas in gas cooking stoves. The evaluation of the burners was performed with respect to key factors such as thermal efficiency, emission quality and pressure drop, etc, by the use of theoretical simulations and experimental tests. Impacts of parameters such as the the wire mesh number, the wire mesh structure (planar or folded), the

  20. The usage and current approaches of cell free fetal DNA (cffDNA as a prenatal diagnostic method in fetal aneuploidy screening

    Directory of Open Access Journals (Sweden)

    Hülya Erbaba

    2015-12-01

    Full Text Available Prenatal diagnosis of invasive and noninvasive tests can be done in a way (NIPT, but because of the invasive methods have risks of infection and abortion, diagnosing non-invasive procedure increasing day by day. One of the widespread cell free fetal DNA in maternal blood test (cffDNA that is increasing in clinical use has been drawing attention. The incidence of aneuploidy chromosomal anomaly of the kind in which all live births; Trisomy 21 (Down Syndrome 1/800, trisomy 13 (Patau syndrome 1 /10,000, trisomy 18 (Edwards syndrome is a form of 1/6000. Because of the high mortality and morbidity, it is vital that congenital anomalies should be diagnosed in prenatal period. Aneuploidy testing for high-risk pregnant women after the 10th week of pregnancy in terms of the blood sample is taken and free fetal DNA in maternal plasma is based on the measurement of the relative amount. Knowledge of the current criteria for use by healthcare professionals in the field test will allow the exclusion of maternal and fetal risks. In this study, it is aimed to demonstrate current international approaches related to the positive and negative sides of non-invasive that is one of the prenatal diagnostic methods of cffDNA test. J Clin Exp Invest 2015; 6 (4: 414-417

  1. Pre-analytical variables of circulating cell-free nucleosomes containing 5-methylcytosine DNA or histone modification H3K9Me3

    DEFF Research Database (Denmark)

    Rasmussen, Louise; Herzog, Marielle; Romer, Eva;

    2016-01-01

    AIM: To evaluate pre-analytical variables of circulating cell-free nucleosomes containing 5-methylcytosine DNA (5mC) or histone modification H3K9Me3 (H3K9Me3). MATERIALS AND METHODS: Six studies were designed to assess the possible influence of pre-analytical variables. Study 1: influence of stasis......3K9Me3 measurements were performed using enzyme-linked immunosorbent assays. RESULTS: Stasis, white-cell and platelet contamination, within-day variations, varying storage time before centrifugation, colonoscopy, and surgical trauma had no significant influence on levels of 5mC or H3K9Me3. Day......-to-day variations of 12.7% and 11.5% (intra-individual) and 98.1% and 60.8% (inter-individual) were shown for 5mC and H3K9Me3, respectively. Levels of 5mC or H3K9Me3 were significantly higher in samples stored at room temperature until centrifugation compared to samples stored on ice. Patients with cancer had...

  2. Impact of Cell-Free Fetal DNA Screening on Patients’ Choice of Invasive Procedures after a Positive California Prenatal Screen Result

    Directory of Open Access Journals (Sweden)

    Forum T. Shah

    2014-07-01

    Full Text Available Until recently, maternal serum analyte levels paired with sonographic fetal nuchal translucency measurement was the most accurate prenatal screen available for Trisomies 18 and 21, (91% and 94% detection and false positive rates of 0.31% and 4.5% respectively. Women with positive California Prenatal Screening Program (CPSP results have the option of diagnostic testing to determine definitively if the fetus has a chromosomal abnormality. Cell-free fetal (cff- DNA screening for Trisomies 13, 18, and 21 was first offered in 2012, allowing women with positive screens to choose additional screening before diagnostic testing. Cff-DNA sensitivity rates are as high as 99.9% and 99.1%, with false positive rates of 0.4% and 0.1%, for Trisomies 18 and 21, respectively. A retrospective chart review was performed in 2012 on 500 CPSP referrals at the University of California, San Diego Thornton Hospital. Data were collected prior to and after the introduction of cff-DNA. There was a significant increase in the number of participants who chose to pursue additional testing and a decrease in the number of invasive procedures performed after cff-DNA screening was available. We conclude that as fetal aneuploidy screening improves, the number of invasive procedures will continue to decrease.

  3. Detection of Clonal and Subclonal Copy-Number Variants in Cell-Free DNA from Patients with Breast Cancer Using a Massively Multiplexed PCR Methodology

    Science.gov (United States)

    Kirkizlar, Eser; Zimmermann, Bernhard; Constantin, Tudor; Swenerton, Ryan; Hoang, Bin; Wayham, Nicholas; Babiarz, Joshua E.; Demko, Zachary; Pelham, Robert J.; Kareht, Stephanie; Simon, Alexander L.; Jinnett, Kristine N.; Rabinowitz, Matthew; Sigurjonsson, Styrmir; Hill, Matthew

    2015-01-01

    We demonstrate proof-of-concept for the use of massively multiplexed PCR and next-generation sequencing (mmPCR-NGS) to identify both clonal and subclonal copy-number variants (CNVs) in circulating tumor DNA. This is the first report of a targeted methodology for detection of CNVs in plasma. Using an in vitro model of cell-free DNA, we show that mmPCR-NGS can accurately detect CNVs with average allelic imbalances as low as 0.5%, an improvement over previously reported whole-genome sequencing approaches. Our method revealed differences in the spectrum of CNVs detected in tumor tissue subsections and matching plasma samples from 11 patients with stage II breast cancer. Moreover, we showed that liquid biopsies are able to detect subclonal mutations that may be missed in tumor tissue biopsies. We anticipate that this mmPCR-NGS methodology will have broad applicability for the characterization, diagnosis, and therapeutic monitoring of CNV-enriched cancers, such as breast, ovarian, and lung cancer. PMID:26500031

  4. Circulating Tumor Cells (CTC) and Cell-Free DNA (cfDNA) Workshop 2016: Scientific Opportunities and Logistics for Cancer Clinical Trial Incorporation.

    Science.gov (United States)

    Lowes, Lori E; Bratman, Scott V; Dittamore, Ryan; Done, Susan; Kelley, Shana O; Mai, Sabine; Morin, Ryan D; Wyatt, Alexander W; Allan, Alison L

    2016-09-08

    Despite the identification of circulating tumor cells (CTCs) and cell-free DNA (cfDNA) as potential blood-based biomarkers capable of providing prognostic and predictive information in cancer, they have not been incorporated into routine clinical practice. This resistance is due in part to technological limitations hampering CTC and cfDNA analysis, as well as a limited understanding of precisely how to interpret emergent biomarkers across various disease stages and tumor types. In recognition of these challenges, a group of researchers and clinicians focused on blood-based biomarker development met at the Canadian Cancer Trials Group (CCTG) Spring Meeting in Toronto, Canada on 29 April 2016 for a workshop discussing novel CTC/cfDNA technologies, interpretation of data obtained from CTCs versus cfDNA, challenges regarding disease evolution and heterogeneity, and logistical considerations for incorporation of CTCs/cfDNA into clinical trials, and ultimately into routine clinical use. The objectives of this workshop included discussion of the current barriers to clinical implementation and recent progress made in the field, as well as fueling meaningful collaborations and partnerships between researchers and clinicians. We anticipate that the considerations highlighted at this workshop will lead to advances in both basic and translational research and will ultimately impact patient management strategies and patient outcomes.

  5. EGFR mutation detection in circulating cell-free DNA of lung adenocarcinoma patients: analysis of LUX-Lung 3 and 6

    Science.gov (United States)

    Wu, Yi-Long; Sequist, Lecia V; Hu, Cheng-Ping; Feng, Jifeng; Lu, Shun; Huang, Yunchao; Li, Wei; Hou, Mei; Schuler, Martin; Mok, Tony; Yamamoto, Nobuyuki; O'Byrne, Kenneth; Hirsh, Vera; Gibson, Neil; Massey, Dan; Kim, Miyoung; Yang, James Chih-Hsin

    2017-01-01

    Background: In the Phase III LUX-Lung 3/6 (LL3/LL6) trials in epidermal growth factor receptor (EGFR) mutation-positive lung adenocarcinoma patients, we evaluated feasibility of EGFR mutation detection using circulating cell-free DNA (cfDNA) and prognostic and predictive utility of cfDNA positivity (cfDNA+). Methods: Paired tumour and blood samples were prospectively collected from randomised patients. Mutations were detected using cfDNA from serum (LL3) or plasma (LL6) by a validated allele-specific quantitative real-time PCR kit. Results: EGFR mutation detection rates in cfDNA were 28.6% (serum) and 60.5% (plasma). Mutation detection in blood was associated with advanced disease characteristics, including higher performance score, number of metastatic sites and bone/liver metastases, and poorer prognosis. In patients with common EGFR mutations, afatinib improved progression-free survival vs chemotherapy in cfDNA+ (LL3: HR, 0.35; P=0.0009; LL6: HR, 0.25; Pafatinib was observed in cfDNA+ patients. Conclusions: Plasma cfDNA is a promising alternative to biopsy for EGFR testing. Detectable mutation in blood was associated with more advanced disease and poorer prognosis. Afatinib improved outcomes in EGFR mutation-positive patients regardless of blood mutation status. PMID:28006816

  6. Comparison of the quantification of KRAS mutations by digital PCR and E-ice-COLD-PCR in circulating-cell-free DNA from metastatic colorectal cancer patients.

    Science.gov (United States)

    Sefrioui, David; Mauger, Florence; Leclere, Laurence; Beaussire, Ludivine; Di Fiore, Frédéric; Deleuze, Jean-François; Sarafan-Vasseur, Nasrin; Tost, Jörg

    2017-02-01

    Circulating cell-free DNA (ccfDNA) bears great promise as biomarker for personalized medicine, but ccfDNA is present only at low levels in the plasma or serum of cancer patients. E-ice-COLD-PCR is a recently developed enrichment method to detect and identify mutations present at low-abundance in clinical samples. However, recent studies have shown the importance to accurately quantify low-abundance mutations as clinically important decisions will depend on certain mutation thresholds. The possibility for an enrichment method to accurately quantify the mutation levels remains a point of concern and might limit its clinical applicability. In the present study, we compared the quantification of KRAS mutations in ccfDNA from metastatic colorectal cancer patients by E-ice-COLD-PCR with two digital PCR approaches. For the quantification of mutations by E-ice-COLD-PCR, cell lines with known mutations diluted into WT genomic DNA were used for calibration. E-ice-COLD-PCR and the two digital PCR approaches showed the same range of the mutation level and were concordant for mutation levels below the clinical relevant threshold. E-ice-COLD-PCR can accurately detect and quantify low-abundant mutations in ccfDNA and has a shorter time to results making it compatible with the requirements of analyses in a clinical setting without the loss of quantitative accuracy.

  7. Circulating cell-free microRNA as biomarkers for screening, diagnosis and monitoring of neurodegenerative diseases and other neurologic pathologies

    Directory of Open Access Journals (Sweden)

    Kira S Sheinerman

    2013-09-01

    Full Text Available Many neurodegenerative diseases, such as Alzheimer’s disease, Parkinson disease, vascular and frontotemporal dementias, as well as other chronic neurological pathologies, are characterized by slow development with a long asymptomatic period followed by a stage with mild clinical symptoms. As a consequence, these serious pathologies are diagnosed late in the course of a disease, when massive death of neurons has already occurred and effective therapeutic intervention is problematic. Thus, the development of screening tests capable of detecting neurodegenerative diseases during early, preferably asymptomatic, stages is a high unmet need. Since such tests are to be used for screening of large populations, they should be non-invasive and relatively inexpensive. Further, while subjects identified by screening tests can be further tested with more invasive and expensive methods, e.g. analysis of cerebrospinal fluid or imaging techniques, to be of practical utility screening tests should have high sensitivity and specificity. In this review, we discuss advantages and disadvantages of various approaches to developing screening tests based on analysis of circulating cell-free miRNA. Applications of circulating miRNA-based tests for diagnosis of acute and chronic brain pathologies, for research of normal brain aging, and for disease and treatment monitoring are also discussed.

  8. Cell-free production of integral membrane aspartic acid proteases reveals zinc-dependent methyltransferase activity of the Pseudomonas aeruginosa prepilin peptidase PilD

    Science.gov (United States)

    Aly, Khaled A; Beebe, Emily T; Chan, Chi H; Goren, Michael A; Sepúlveda, Carolina; Makino, Shin-ichi; Fox, Brian G; Forest, Katrina T

    2013-01-01

    Integral membrane aspartic acid proteases are receiving growing recognition for their fundamental roles in cellular physiology of eukaryotes and prokaryotes, and may be medically important pharmaceutical targets. The Gram-negative Pseudomonas aeruginosa PilD and the archaeal Methanococcus voltae FlaK were synthesized in the presence of unilamellar liposomes in a cell-free translation system. Cosynthesis of PilD with its full-length substrate, PilA, or of FlaK with its full-length substrate, FlaB2, led to complete cleavage of the substrate signal peptides. Scaled-up synthesis of PilD, followed by solubilization in dodecyl-β-d-maltoside and chromatography, led to a pure enzyme that retained both of its known biochemical activities: cleavage of the PilA signal peptide and S-adenosyl methionine-dependent methylation of the mature pilin. X-ray fluorescence scans show for the first time that PilD is a zinc-binding protein. Zinc is required for the N-terminal methylation of the mature pilin, but not for signal peptide cleavage. Taken together, our work identifies the P. aeruginosa prepilin peptidase PilD as a zinc-dependent N-methyltransferase and provides a new platform for large-scale synthesis of PilD and other integral membrane proteases important for basic microbial physiology and virulence. PMID:23255525

  9. Wheat germ cell-free system-based production of hemagglutinin-neuraminidase protein of human parainfluenza virus type 3: generation and characterization of monoclonal antibody

    Directory of Open Access Journals (Sweden)

    Satoko eMatsunaga

    2014-05-01

    Full Text Available Human parainfluenza virus 3 (HPIV3 commonly causes respiratory disorders in infants and young children. Monoclonal antibodies (MAbs have been produced to several components of HPIV3 and commercially available. However, the utility of these antibodies for several immunological and proteomic assays for understanding the nature of HPIV3 infection remain to be characterized. Herein, we report the development and characterization of monoclonal antibodies against hemagglutinin-neuraminidase (HN of HPIV3. A recombinant full-length HPIV3-HN was successfully synthesized using the wheat-germ cell-free protein production system. After immunization and cell fusion, 36 mouse hybridomas producing MAbs to HPIV3-HN were established. The MAbs obtained were fully characterized using ELISA, immunoblotting and immunofluorescent analyses. Of the MAbs tested, single clone was found to be applicable in both flow cytometry and immunoprecipitation procedures. By utilizing the antibody, we newly identified HPIV3-HN binding host proteins via immunoprecipitation-based mass spectrometry analysis. This study provides the availability of our newly-developed MAbs as a valuable tool for the study of HPIV3 infection as well as the several diagnostic tests of this virus.

  10. Effects of heme-PrP complex on cell-free conversion and peroxidase-linked immunodetection of prions in blood-based assays.

    Science.gov (United States)

    Soutyrine, Andrei; Yogasingam, Nishandan; Huang, Hongsheng; Mitchell, Gordon

    2015-08-01

    Prion protein (PrP) binding to natural and synthetic porphyrins has been previously demonstrated but the effects of endogenous heme interactions with PrP remain uncertain. This study investigated implications of this interaction in blood-based peroxidase-linked prion immunodetection and seeded conversion of cellular prion (PrP(C)) into disease associated form (PrP(Sc)). Heme binding to recombinant PrP(C) enhanced intrinsic peroxidase activity (POD) by 2.5-fold and POD inherent to denatured blood accounted for over 84% of luminol-based substrate oxidation in a prion immunodetection assay. An immuno-capture assay showed that 75-98% of blood POD was attributable to binding of PrP(C) with endogenous heme. Additionally, 10 μM heme inhibited (PPrP(C) to PrP(Sc) through the protein misfolding cycling amplification assay. We conclude that the observed effects can interfere with cell-free conversion and peroxidase-linked immunodetection of prions in blood-based assays. These results indicate that heme-PrP interactions could modulate intrinsic POD and protect PrP(C) from conversion into PrP(Sc).

  11. Cell-free H-cluster synthesis and [FeFe] hydrogenase activation: all five CO and CN⁻ ligands derive from tyrosine.

    Directory of Open Access Journals (Sweden)

    Jon M Kuchenreuther

    Full Text Available [FeFe] hydrogenases are promising catalysts for producing hydrogen as a sustainable fuel and chemical feedstock, and they also serve as paradigms for biomimetic hydrogen-evolving compounds. Hydrogen formation is catalyzed by the H-cluster, a unique iron-based cofactor requiring three carbon monoxide (CO and two cyanide (CN⁻ ligands as well as a dithiolate bridge. Three accessory proteins (HydE, HydF, and HydG are presumably responsible for assembling and installing the H-cluster, yet their precise roles and the biosynthetic pathway have yet to be fully defined. In this report, we describe effective cell-free methods for investigating H-cluster synthesis and [FeFe] hydrogenase activation. Combining isotopic labeling with FTIR spectroscopy, we conclusively show that each of the CO and CN⁻ ligands derive respectively from the carboxylate and amino substituents of tyrosine. Such in vitro systems with reconstituted pathways comprise a versatile approach for studying biosynthetic mechanisms, and this work marks a significant step towards an understanding of both the protein-protein interactions and complex reactions required for H-cluster assembly and hydrogenase maturation.

  12. Microscale to manufacturing scale-up of cell-free cytokine production--a new approach for shortening protein production development timelines.

    Science.gov (United States)

    Zawada, James F; Yin, Gang; Steiner, Alexander R; Yang, Junhao; Naresh, Alpana; Roy, Sushmita M; Gold, Daniel S; Heinsohn, Henry G; Murray, Christopher J

    2011-07-01

    Engineering robust protein production and purification of correctly folded biotherapeutic proteins in cell-based systems is often challenging due to the requirements for maintaining complex cellular networks for cell viability and the need to develop associated downstream processes that reproducibly yield biopharmaceutical products with high product quality. Here, we present an alternative Escherichia coli-based open cell-free synthesis (OCFS) system that is optimized for predictable high-yield protein synthesis and folding at any scale with straightforward downstream purification processes. We describe how the linear scalability of OCFS allows rapid process optimization of parameters affecting extract activation, gene sequence optimization, and redox folding conditions for disulfide bond formation at microliter scales. Efficient and predictable high-level protein production can then be achieved using batch processes in standard bioreactors. We show how a fully bioactive protein produced by OCFS from optimized frozen extract can be purified directly using a streamlined purification process that yields a biologically active cytokine, human granulocyte-macrophage colony-stimulating factor, produced at titers of 700 mg/L in 10 h. These results represent a milestone for in vitro protein synthesis, with potential for the cGMP production of disulfide-bonded biotherapeutic proteins.

  13. Biosynthetic origin of gibberellins A sub 3 and A sub 7 in cell-free preparations from seeds of Marah macrocarpus and Malus domestica

    Energy Technology Data Exchange (ETDEWEB)

    Albone, K.S.; Gaskin, P.; MacMillan, J.; Willis, C.L. (Univ. of Bristol (England)); Phinney, B.O. (Univ. of California, Los Angeles (USA))

    1990-09-01

    Cell-free preparations from seeds of Marah macrocarpus L. and Malus domestica L. catalyzed the conversion of gibberellin A{sub 9} (GA{sub 9}) and 2,3-dehydroGA{sub 9} to GA{sub 7}; GA{sub 9} was also metabolized to GA{sub 4} in a branch pathway. The preparation from Marah seeds also metabolized GA{sub 5} to GA{sub 3} in high yield; GA{sub 6} was a minor product and was not metabolized to GA{sub 3}. Using substrates stereospecifically labeled with deuterium, it was shown that the metabolism of GA{sub 5} to GA{sub 3} and of 2,3-dehydroGA{sub 9} to GA{sub 7} occurs with the loss of the 1{beta}-hydrogen. In cultures of Gibberella fujikuroi, mutant B1-41a, (1{beta},2{beta}-{sup 2}H{sub 2})GA{sub 4}, was metabolized to (1,2-{sup 2}H{sub 2})GA{sub 3} with the loss of the 1{alpha}- and 2{alpha}-hydrogens. These results provide further evidence that the biosynthetic origin of GA{sub 3} and GA{sub 7} in higher plants is different from that in the fungus Gibberella fujikuroi.

  14. Evaluation of the cytotoxicity of cell free dermal substitutes using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide method

    Institute of Scientific and Technical Information of China (English)

    NING Fang-gang; ZHANG Guo-an

    2010-01-01

    Background The cytotoxicity of dermal substitutes may be increased by the very processes used to deplete the cells. The present research aimed to investigate the method for monitoring the cytotoxicity of cell-free dermal substitutes using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) method.Methods The cytotoxicity of four dermal substitutes was evaluated using the MTT method according to the standards set by the Chinese State Food and Drug Administration (SFDA). Swine acellular dermal matrix (SADM) and goat acellular dermal matrix (GADM) were produced using a repeated freeze-thaw method. Human dermal matrix glutaraldehyde composite (HADM-G) and SADM cross-linked with glutaraldehyde (SADM-G) were produced using conventional methods. Results The cytotoxicity of all dermal substitutes ranged from Grade 0 to Grade 1, meeting the standards of the Chinese FDA. The OD_(490) of both SADM and GADM was higher than that of either HADM-G or SADM-G (P<0.05). Conclusion Dermal substitutes produced by the freeze-thaw method are less cytotoxic than those produced using conventional methods.

  15. Expression regulation by a methyl-CpG binding domain in an E. coli based, cell-free TX-TL system

    Science.gov (United States)

    Schenkelberger, M.; Shanak, S.; Finkler, M.; Worst, E. G.; Noireaux, V.; Helms, V.; Ott, A.

    2017-04-01

    Cytosine methylation plays an important role in the epigenetic regulation of eukaryotic gene expression. The methyl-CpG binding domain (MBD) is common to a family of eukaryotic transcriptional regulators. How MBD, a stretch of about 80 amino acids, recognizes CpGs in a methylation dependent manner, and as a function of sequence, is only partly understood. Here we show, using an Escherichia coli cell-free expression system, that MBD from the human transcriptional regulator MeCP2 performs as a specific, methylation-dependent repressor in conjunction with the BDNF (brain-derived neurotrophic factor) promoter sequence. Mutation of either base flanking the central CpG pair changes the expression level of the target gene. However, the relative degree of repression as a function of MBD concentration remains unaltered. Molecular dynamics simulations that address the DNA B fiber ratio and the handedness reveal cooperative transitions in the promoter DNA upon MBD binding that correlate well with our experimental observations. We suggest that not only steric hindrance, but also conformational changes of the BDNF promoter as a result of MBD binding are required for MBD to act as a specific inhibitory element. Our work demonstrates that the prokaryotic transcription machinery can reproduce features of epigenetic mammalian transcriptional regulatory elements.

  16. Hetero subunit interaction and RNA recognition of yeast tRNA (m7G46) methyltransferase synthesized in a wheat germ cell-free translation system.

    Science.gov (United States)

    Muneyoshi, Yuki; Matsumoto, Keisuke; Tomikawa, Chie; Toyooka, Takashi; Ochi, Anna; Masaoka, Takashi; Endo, Yaeta; Hori, Hiroyuki

    2007-01-01

    Yeast tRNA (m(7)G46) methyltransferase contains two protein subunits (Trm8 and Trm82). The enzyme catalyzes a methyl-transfer from S-adenosyl-L-methionine to the N(7) atom of guanine at position 46 in tRNA. We deviced synthesis of active Trm8-Trm82 heterodimer in a wheat germ cell-free translation system. When Trm8 or Trm82 mRNA were used for a synthesis, Trm8 or Trm82 protein could be synthesized. Upon mixing the synthesized Trm8 and Trm82 proteins, no active Trm8-Trm82 heterodimer was produced. Active Trm8-Trm82 heterodimer was only synthesized under conditions, in which both Trm8 and Trm82 mRNAs were co-translated. To address the RNA recognition mechanism of the Trm8-Trm82 complex, we investigated methyl acceptance activities of eight truncated yeast tRNA(Phe) transcripts. In this meeting, we demonstrate that yeast Trm8-Trm82 has stricter recognition requirements for the tRNA molecule as compared to the bacterial enzyme, TrmB.

  17. An ex vivo continuous passive motion model in a porcine knee for assessing primary stability of cell-free collagen gel plugs

    Directory of Open Access Journals (Sweden)

    El-Zayat Bilal

    2010-12-01

    Full Text Available Abstract Background Primary stability of cartilage repair constructs is of the utmost importance in the clinical setting but few continuous passive motion (CPM models are available. Our study aimed to establish a novel ex vivo CPM animal model and to evaluate the required motion cycles for testing the mechanical properties of a new cell-free collagen type I gel plug (CaReS®-1S. Methods A novel ex vivo CPM device was developed. Full-thickness cartilage defects (11 mm diameter by 6 mm deep were created on the medial femoral condyle of porcine knee specimens. CaReS®-1S was implanted in 16 animals and each knee underwent continuous passive motion. After 0, 2000, 4000, 6000, and 8000 motions, standardized digital pictures of the grafts were taken, focusing on the worn surfaces. The percentage of worn surface on the total CaReS®-1S surface was evaluated with image processing software. Results Significant differences in the worn surface were recorded between 0 and 2000 motion cycles (p ®-1S with an empty defect site was recorded. Conclusion The ex vivo CPM animal model is appropriate in investigating CaReS®-1S durability under continuous passive motion. 2000 motion cycles appear adequate to assess the primary stability of type I collagen gels used to repair focal chondral defects.

  18. Evaluation of anti-malarial activity of Artemisia turcomanica and A. kopetdaghensis by cell-free β-hematin formation assay

    Directory of Open Access Journals (Sweden)

    M. Mojarrab

    2016-10-01

    Full Text Available Background and objectives:The plants of genus Artemisia (Asteraceae have been conventionally used for prevention and medication of a number of ailments. In the present research, ten extracts with different polarities from aerial parts of two Artemisia species, A. kopetdaghensis and A. turcomanica were evaluated for their potential anti-malarial properties. Methods: The plant materials were extracted successively with petroleum ether (PE, dichloromethane (DCM, ethyl acetate (EtOAC, ethanol, and ethanol-water (1:1 v/v  by cold maceration method. Cell free β-hematin formation assay were used for assessing anti-malarial activity of obtained extracts. Results: DCM extract of A. kopetdaghensis and PE extract of A. turcomanica showed remarkable anti-malarial activity with IC50 values of 1.04±0.02 mg/mL and 0.90±0.27 mg/mL, respectively, compared to positive control (chloroquine, IC50 0.04±0.01 mg/mL. Conclusion:  It seems that the anti-malarial activity of these extracts might be bound up with the presence of compounds with low or medium polarity; hence, this preliminary test indicated that these potent extracts could be considered for further investigations to find new sources of anti-malarial phytochemicals.

  19. ANALYTICAL RELATIONS BETWEEN EIGENVALUES OF CIRCULAR PLATE BASED ON VARIOUS PLATE THEORIES

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Based on the mathematical similarity of the axisymmetric eigenvalue problems of a circular plate between the classical plate theory(CPT), the first-order shear deformation plate theory(FPT) and the Reddy's third-order shear deformation plate theory(RPT), analytical relations between the eigenvalues of circular plate based on various plate theories are investigated. In the present paper, the eigenvalue problem is transformed to solve an algebra equation. Analytical relationships that are expressed explicitly between various theories are presented. Therefore, from these relationships one can easily obtain the exact RPT and FPT solutions of critical buckling load and natural frequencyfor a circular plate with CPT solutions. The relationships are useful for engineering application, and can be used to check the validity, convergence and accuracy of numerical results for the eigenvalue problem of plates.

  20. High-throughput and automated diagnosis of antimicrobial resistance using a cost-effective cellphone-based micro-plate reader

    Science.gov (United States)

    Feng, Steve; Tseng, Derek; di Carlo, Dino; Garner, Omai B.; Ozcan, Aydogan

    2016-12-01

    Routine antimicrobial susceptibility testing (AST) can prevent deaths due to bacteria and reduce the spread of multi-drug-resistance, but cannot be regularly performed in resource-limited-settings due to technological challenges, high-costs, and lack of trained professionals. We demonstrate an automated and cost-effective cellphone-based 96-well microtiter-plate (MTP) reader, capable of performing AST without the need for trained diagnosticians. Our system includes a 3D-printed smartphone attachment that holds and illuminates the MTP using a light-emitting-diode array. An inexpensive optical fiber-array enables the capture of the transmitted light of each well through the smartphone camera. A custom-designed application sends the captured image to a server to automatically determine well-turbidity, with results returned to the smartphone in ~1 minute. We tested this mobile-reader using MTPs prepared with 17 antibiotics targeting Gram-negative bacteria on clinical isolates of Klebsiella pneumoniae, containing highly-resistant antimicrobial profiles. Using 78 patient isolate test-plates, we demonstrated that our mobile-reader meets the FDA-defined AST criteria, with a well-turbidity detection accuracy of 98.21%, minimum-inhibitory-concentration accuracy of 95.12%, and a drug-susceptibility interpretation accuracy of 99.23%, with no very major errors. This mobile-reader could eliminate the need for trained diagnosticians to perform AST, reduce the cost-barrier for routine testing, and assist in spatio-temporal tracking of bacterial resistance.

  1. Steel plate reinforcement of orthotropic bridge decks

    NARCIS (Netherlands)

    Teixeira de Freitas, S.

    2012-01-01

    The PhD research is focused on the reinforcement of fatigue cracked orthotropic steel bridge decks (OBD) by adding a second steel plate to the existing deck. The main idea is to stiffen the existing deck plate, which will reduce the stresses at the fatigue sensitive details and extend the fatigue li

  2. Roll-forming tubes to header plates

    Science.gov (United States)

    Kramer, K.

    1976-01-01

    Technique has been developed for attaching and sealing tubes to header plates using a unique roll-forming tool. Technique is useful for attaching small tubes which are difficult to roll into conventional grooves in header plate tube holes, and for attaching when welding, brazing, or soldering is not desirable.

  3. Novel Algorithms for Astronomical Plate Analyses

    Indian Academy of Sciences (India)

    Rene Hudec; Lukas Hudec

    2011-03-01

    Powerful computers and dedicated software allow effective data mining and scientific analyses in astronomical plate archives. We give and discuss examples of newly developed algorithms for astronomical plate analyses, e.g., searches for optical transients, as well as for major spectral and brightness changes.

  4. 49 CFR 230.46 - Badge plates.

    Science.gov (United States)

    2010-10-01

    ... TRANSPORTATION STEAM LOCOMOTIVE INSPECTION AND MAINTENANCE STANDARDS Boilers and Appurtenances Steam Gauges § 230.46 Badge plates. A metal badge plate showing the allowed steam pressure shall be attached to the boiler backhead in the cab. If boiler backhead is lagged, the lagging and jacket shall be cut away...

  5. UNSYMMETRICAL LARGE DEFORMATION PROBLEM OF ORTHOTROPIC PLATES

    Institute of Scientific and Technical Information of China (English)

    王新志; 赵永刚; 叶开沅; 黄达文

    2002-01-01

    Based upon the theory of anisotropic plates, the unsymmetrical large deformation equations of orthotropic circular plates were derived. By using Fourier series, the partial differential equations of this problem can be transformed into sets of nonlinear differential equations. And the procedure to solve the problem using the iterative method is given.

  6. Modelling of CMUTs with Anisotropic Plates

    DEFF Research Database (Denmark)

    la Cour, Mette Funding; Christiansen, Thomas Lehrmann; Jensen, Jørgen Arendt;

    2012-01-01

    Traditionally, CMUTs are modelled using the isotropic plate equation and this leads to deviations between analytical calculations and FEM simulations. In this paper, the deflection profile and material parameters are calculated using the anisotropic plate equation. It is shown that the anisotropic...

  7. Crane Scheduling for a Plate Storage

    DEFF Research Database (Denmark)

    Hansen, Jesper; Clausen, Jens

    2002-01-01

    Odense Steel Shipyard produces the worlds largest container ships. The first process of producing the steel ships is handling arrival and storage of steel plates until they are needed in production. This paper considers the problem of scheduling two cranes that carry out the movements of plates...

  8. Micromachined silicon plates for sensing molecular interactions

    NARCIS (Netherlands)

    Carlen, E.T.; Weinberg, M.S.; Dube, C.E.; Zapata, A.M.; Borenstein, J.T.

    2006-01-01

    A micromachined surface stress sensor based on a thin suspended crystalline silicon circular plate measures differential surface stress changes associated with vapor phase chemisorption of an alkanethiol self-assembled monolayer. The isolated face of the suspended silicon plate serves as the sensing

  9. Precision Plate Plan View Pattern Predictive Model

    Institute of Scientific and Technical Information of China (English)

    ZHAO Yang; YANG Quan; HE An-rui; WANG Xiao-chen; ZHANG Yun

    2011-01-01

    According to the rolling features of plate mill, a 3D elastic-plastic FEM (finite element model) based on full restart method of ANSYS/LS-DYNA was established to study the inhomogeneous plastic deformation of multipass plate rolling. By analyzing the simulation results, the difference of head and tail ends predictive models was found and modified. According to the numerical simulation results of 120 different kinds of conditions, precision plate plan view pattern predictive model was established. Based on these models, the sizing MAS (mizushima automatic plan view pattern control system) method was designed and used on a 2 800 mm plate mill. Comparing the rolled plates with and without PVPP (plan view pattern predictive) model, the reduced width deviation indicates that the olate !olan view Dattern predictive model is preeise.

  10. Mixed boundary conditions for piezoelectric plates

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    For plate bending and stretching problems in piezoelectric materials,the reciprocal theorem and the general solution of piezoelasticity are applied in a novel way to obtain the appropriate mixed boundary conditions accurate to all order.A decay analysis technique is used to establish necessary conditions that the prescribed data on the edge of the plate must satisfy in order that it should generate a decaying state within the plate.For the case of axisymmetric bending and stretching of a circular plate,these decaying state conditions are obtained explicitly for the first time when the mixed conditions are imposed on the plate edge.They are then used for the correct formulation of boundary conditions for the interior solution.

  11. Chaotic Motion of Corrugated Circular Plates

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Large deflection theory of thin anisotropic circular plates was used to analyze the bifurcation behavior and chaotic phenomena of a corrugated thin circular plate with combined transverse periodic excitation and an in-plane static boundary load. The nonlinear dynamic equation for the corrugated plate was derived by employing Galerkin's technique. The critical conditions for occurrence of the homoclinic and subharmonic bifurcations as well as chaos were studied theoretically using the Melnikov function method. The chaotic motion was also simulated numerically using Maple, with the Poincaré map and phase curve used to evaluate when chaotic motion appears. The results indicate some chaotic motion in the corrugated plate. The method is directly applicable to chaotic analysis of an isotropic circular plate.

  12. Plate shell structures - statics and stability

    DEFF Research Database (Denmark)

    Almegaard, Henrik

    2008-01-01

    This paper describes the basic structural system, statics and spatial stability of plate shells. The structural system can be considered as a single layer of planar elements, where each element only transfers in-plane (membrane) forces to its neighbouring elements. External out-of-plane loads...... are carried into the structure as in-plane forces by plate action in each element. These in-plane forces are then carried through the plate structure to the supports as in-plane forces by membrane action. The consequence is that the spatial stability of the structure can be simply analysed by considering...... the plate system as only subject to in-plane loads. The stability of such systems is based on the fact that each plane element is held fixed in space by three fixed support lines and that these support lines can be provided by three plane neighbour elements. This means that the spatial stability of a plate...

  13. Is There Really A North American Plate?

    Science.gov (United States)

    Krill, A.

    2011-12-01

    Lithospheric plates are typically identified from earthquake epicenters and evidence such as GPS movements. But no evidence indicates a plate boundary between the North American and South American Plates. Some plate maps show them separated by a transform boundary, but it is only a fracture zone. Other maps show an "undefined plate boundary" or put no boundary between these two plates (check Google images). Early plate maps showed a single large American Plate, quite narrow east of the Caribbean Plate (Le Pichon 1968, Morgan 1968). The North and South American Plates became established by the leading textbook Earth (Press & Siever 1974). On their map, from a Scientific American article by John Dewey (1972), these new plates were separated by an "uncertain plate boundary." The reasons for postulating a North American Plate were probably more psychological than geological. Each of the other continents of the world had its own plate, and North American geologists naturally wanted theirs. Similarly, European geographers used to view Europe as its own continent. A single large plate should again be hypothesized. But the term American Plate would now be ambiguous ("Which plate, North or South?") Perhaps future textbook authors could call it the "Two-American Plate." Textbook authors ultimately decide such global-tectonic matters. I became aware of textbook authors' opinions and influence from my research into the history of Alfred Wegener's continental drift (see Fixists vs. Mobilists by Krill 2011). Leading textbook author Charles Schuchert realized that continental drift would abolish his cherished paleogeographic models of large east-west continents (Eria, Gondwana) and small oceans (Poseiden, Nereis). He and his junior coauthors conspired to keep drift evidence out of their textbooks, from the 1934-editions until the 1969-editions (Physical Geology by Longwell et al. 1969, Historical Geology by Dunbar & Waage 1969). Their textbooks ruled in America. Textbooks

  14. Plain carbon steel bipolar plates for PEMFC

    Institute of Scientific and Technical Information of China (English)

    WANG Jianli; SUN Juncai; TIAN Rujin; XU Jing

    2006-01-01

    Bipolar plates are a multifunctional component of PEMFC. Comparing with the machined graphite and stainless steels, the plain carbon steel is a very cheap commercial metal material. In this paper, the possibility of applying the plain carbon steels in the bipolar plate for PEMFC was exploited. In order to improve the corrosion resistance of the low carbon steel in the PEMFCs' environments,two surface modification processes was developed and then the electrochemical performances and interfacial contact resistance (ICR) of the surface modified plate of plain carbon steel were investigated. The results show that the surface modified steel plates have good corrosion resistance and relatively low contact resistance, and it may be a candidate material as bipolar plate of PEMFC.

  15. Tectonic Evolution of the Jurassic Pacific Plate

    Science.gov (United States)

    Nakanishi, M.; Ishihara, T.

    2015-12-01

    We present the tectonic evolution of the Jurassic Pacific plate based on magnetic anomly lineations and abyssal hills. The Pacific plate is the largest oceanic plate on Earth. It was born as a microplate aroud the Izanagi-Farallon-Phoenix triple junction about 192 Ma, Early Jurassic [Nakanishi et al., 1992]. The size of the Pacific plate at 190 Ma was nearly half that of the present Easter or Juan Fernandez microplates in the East Pacific Rise [Martinez et at, 1991; Larson et al., 1992]. The plate boundary surrounding the Pacific plate from Early Jurassic to Early Cretaceous involved the four triple junctions among Pacific, Izanagi, Farallon, and Phoenix plates. The major tectonic events as the formation of oceanic plateaus and microplates during the period occurred in the vicinity of the triple junctions [e.g., Nakanishi and Winterer, 1998; Nakanishi et al., 1999], implying that the study of the triple junctions is indispensable for understanding the tectonic evolution of the Pacific plate. Previous studies indicate instability of the configuration of the triple junctions from Late Jurassic to Early Cretaceous (155-125 Ma). On the other hand, the age of the birth of the Pacific plate was determined assuming that all triple junctions had kept their configurations for about 30 m.y. [Nakanishi et al., 1992] because of insufficient information of the tectonic history of the Pacific plate before Late Jurassic.Increase in the bathymetric and geomagnetic data over the past two decades enables us to reveal the tectonic evolution of the Pacific-Izanagi-Farallon triple junction before Late Jurassic. Our detailed identication of magnetic anomaly lineations exposes magnetic bights before anomaly M25. We found the curved abyssal hills originated near the triple junction, which trend is parallel to magnetic anomaly lineations. These results imply that the configuration of the Pacific-Izanagi-Farallon triple junction had been RRR before Late Jurassic.

  16. Collaborative study comparing the spiral plate and aerobic plate count methods.

    Science.gov (United States)

    Gilchrist, J E; Donnelly, C B; Peeler, J T; Campbell, J E

    1977-07-01

    The spiral plate count method is a semiautomated plating technique that greatly reduces manpower and material costs normally associated with the pour plating technique. In this collaborative study, 8 laboratories compared the spiral and pour plating techniques, using 4 samples each of 3 products: frozen pumpkin pie, frozen chicken pot pie, and shampoo. The results show that 10 of the 12 comparisons of means of the pour and spiral methods were not significantly different; 2 values were significant at alpha = 0.01. Overall, the components of variance were less than that of the current milk standard, and the replicate per cent coefficient of variation was satisfactory. This study indicates that the spiral plate method is an acceptable alternative to the pour plate method; the spiral plate method has been adopted as official first action.

  17. Comparison of real-time reverse transcriptase polymerase chain reaction of peripheral blood mononuclear cells, serum and cell-free body cavity effusion for the diagnosis of feline infectious peritonitis.

    Science.gov (United States)

    Doenges, Stephanie J; Weber, Karin; Dorsch, Roswitha; Fux, Robert; Hartmann, Katrin

    2017-04-01

    Objectives Diagnosis of feline infectious peritonitis (FIP) remains challenging, especially in cats without effusions. The objective of this study was to evaluate the sensitivity and specificity of a real-time reverse transcriptase polymerase chain reaction (RT-PCR) detecting feline coronavirus (FCoV) RNA in peripheral blood mononuclear cells (PBMCs) and serum in comparison with the same real-time RT-PCR in cell-free body cavity effusion. Methods This prospective case-control study included 92 cats. Forty-three cats had a definitive diagnosis of FIP, established either by histopathological examination (n = 28) or by positive immunofluorescence staining of FCoV antigen in macrophages of effusions (n = 11), or by both methods (n = 4). Forty-nine control cats had other diseases but similar clinical signs. Real-time RT-PCR was performed on PBMCs of 37 cats (21 cats with FIP, 16 controls), on serum of 51 cats (26 cats with FIP, 25 controls) and on cell-free body cavity effusion of 69 cats (36 cats with FIP, 33 controls). Sensitivity, specificity, positive and negative predictive value, including 95% confidence intervals (CI), were calculated. Results Real-time RT-PCR of PBMCs, serum and cell-free body cavity effusion showed a specificity of 100% (95% CI 79.4-100% in PBMCs, 86.3-100% in serum, 89.4-100% in cell-free body cavity effusion) and a sensitivity of 28.6% (95% CI 11.3-52.2%) in PBMCs, 15.4% (95% CI 4.4-34.9%) in serum and 88.9% (95% CI 73.9-96.9%) in cell-free body cavity effusion to diagnose FIP. Conclusions and relevance Although it is known that RT-PCR can often provide false-positive results in healthy cats, this real-time RT-PCR was shown to be a specific tool for the diagnosis of FIP when applied in a clinical setting. Sensitivity in cell-free body cavity effusion was high but low in PBMCs and serum. PBMC samples showed a higher sensitivity than serum samples, and are therefore a better choice if no effusion is present.

  18. Quantitative and Qualitative Analysis of Circulating Cell-Free DNA Can Be Used as an Adjuvant Tool for Prostate Cancer Screening: A Meta-Analysis.

    Science.gov (United States)

    Yin, Changqing; Luo, Changliang; Hu, Wei; Ding, Xu; Yuan, Chunhui; Wang, Fubing

    2016-01-01

    As part of "liquid biopsy," lots of literature indicated the potential diagnostic value of circulating cell-free DNA (cfDNA) in the management of prostate cancer (PCa). However, the literature on the accuracy of cfDNA detection in PCa has been inconsistent. Hence, we performed this meta-analysis to assess the diagnostic value of cfDNA in PCa. A total of 19 articles were included in this analysis according to the inclusion and exclusion criteria. We then investigated two main subgroups in this meta-analysis, including qualitative analysis of abnormal level of cfDNA and qualitative analysis of single-gene methylation alterations. Overall, the results of quantitative analysis showed sensitivity of 0.73 (95% CI, 0.62-0.82) and specificity of 0.80 (95% CI, 0.70-0.87), with an area under the curve (AUC) of 0.83 (95% CI, 0.80-0.86). For qualitative assessment, the values were 0.34 (95% CI, 0.22-0.48), 0.99 (95% CI, 0.97-1.00), and 0.91 (95% CI, 0.88-0.93), respectively. Our results suggest the pooled specificity of each subgroup is much higher than the specificity of prostate-specific antigen (PSA). However, they are not recommended for PCa screening alone, because their sensitivities are not higher than the conventional serum biomarkers PSA. We conclude that analysis of cfDNA can be used as an adjuvant tool for PCa screening.

  19. Highly Efficient In Vitro Production of Bovine Blastocyst in Cell-Free Sequential Synthetic Oviductal Fluid vs. TCM199 Vero Cell Co-Culture System

    Directory of Open Access Journals (Sweden)

    Sayyed Morteza Hosseini

    2008-01-01

    Full Text Available Background: The aim of this study was to establish a cell-free sequential culture system that cansupport high levels of in vitro embryo development and blastocyst formation from bovine zygotes.To this end, this investigation was carried out to evaluate the effects of glucose, serum and EDTAon bovine zygote in vitro development.Materials and Methods: Bovine presumptive zygotes were derived from oocytes matured, andfertilized in vitro and cultured in synthetic oviductal fluid sequential medium in a two-steps manner;SOF 1 for the first 3 days and SOF 2 for the second 5-6 days of in vitro embryo development. Inorder to evaluate the effect of different modifications of the basic medium on embryo development,glucose was added to the second phase (SOF A, serum was added to the first phase (SOF C andEDTA alone (SOF D or in combination with serum (SOF E was added into the first phase of invitro embryo culture. The results of each composition were compared with each other and with theresults of embryo development in TCM199 vero cell co-culture system.Results: Glucose addition to the second phase of embryo culture, improved the developmentalcompetency; however, the differences were not significant. Serum addition to the first phase ofembryo culture, significantly improved the developmental competency of embryos beyond thecleavage stage, compared to all the treatment and TCM199 co-culture groups. EDTA supplementationof culture medium, either alone or in combination with serum, significantly inhibits the embryodevelopment beyond the morula stage.Conclusion: The results indicated that culture of bovine presumptive zygotes in two steps cell-freeculture system, can support embryo development, and addition of serum throughout the culture andglucose to the second step significantly increased overall developmental competency compared toTCM199 co-culture system.

  20. Prostaglandin E2 reduces the release and infectivity of new cell-free virions and cell-to-cell HIV-1 transfer.

    Directory of Open Access Journals (Sweden)

    María Isabel Clemente

    Full Text Available BACKGROUND: The course of human immunodeficiency virus type-1 (HIV-1 infection is influenced by a complex interplay between viral and host factors. HIV infection stimulates several proinflammatory genes, such as cyclooxigense-2 (COX-2, which leads to an increase in prostaglandin (PG levels in the plasma of HIV-1-infected patients. These genes play an indeterminate role in HIV replication and pathogenesis. The effect of prostaglandin E2 (PGE2 on HIV infection is quite controversial and even contradictory, so we sought to determine the role of PGE2 and the signal transduction pathways involved in HIV infection to elucidate possible new targets for antiretrovirals. RESULTS: Our results suggest that PGE2 post-infection treatment acts in the late stages of the viral cycle to reduce HIV replication. Interestingly, viral protein synthesis was not affected, but a loss of progeny virus production was observed. No modulation of CD4 CXCR4 and CCR5 receptor expression, cell proliferation, or activation after PGE2 treatment was detected. Moreover, PGE2 induced an increase in intracellular cAMP (cyclic AMP levels through the EP2/EP4 receptors. PGE2 effects were mimicked by dbcAMP and by a specific Epac (exchange protein directly activated by cyclic AMP agonist, 8-Cpt-cAMP. Treatment with PGE2 increased Rap1 activity, decreased RhoA activity and subsequently reduced the polymerization of actin by approximately 30% compared with untreated cells. In connection with this finding, polarized viral assembly platforms enriched in Gag were disrupted, altering HIV cell-to-cell transfer and the infectivity of new virions. CONCLUSIONS: Our results demonstrate that PGE2, through Epac and Rap activation, alters the transport of newly synthesized HIV-1 components to the assembly site, reducing the release and infectivity of new cell-free virions and cell-to-cell HIV-1 transfer.

  1. Fatal outcome in bacteremia is characterized by high plasma cell free DNA concentration and apoptotic DNA fragmentation: a prospective cohort study.

    Directory of Open Access Journals (Sweden)

    Reetta Huttunen

    Full Text Available INTRODUCTION: Recent studies have shown that apoptosis plays a critical role in the pathogenesis of sepsis. High plasma cell free DNA (cf-DNA concentrations have been shown to be associated with sepsis outcome. The origin of cf-DNA is unclear. METHODS: Total plasma cf-DNA was quantified directly in plasma and the amplifiable cf-DNA assessed using quantitative PCR in 132 patients with bacteremia caused by Staphylococcus aureus, Streptococcus pneumoniae, ß-hemolytic streptococcae or Escherichia coli. The quality of cf-DNA was analyzed with a DNA Chip assay performed on 8 survivors and 8 nonsurvivors. Values were measured on days 1-4 after positive blood culture, on day 5-17 and on recovery. RESULTS: The maximum cf-DNA values on days 1-4 (n = 132 were markedly higher in nonsurvivors compared to survivors (2.03 vs 1.26 ug/ml, p1.52 ug/ml remained an independent risk factor for case fatality in a logistic regression model. Qualitative analysis of cf-DNA showed that cf-DNA displayed a predominating low-molecular-weight cf-DNA band (150-200 bp in nonsurvivors, corresponding to the size of the apoptotic nucleosomal DNA. cf-DNA concentration showed a significant positive correlation with visually graded apoptotic band intensity (R = 0.822, p<0.001. CONCLUSIONS: Plasma cf-DNA concentration proved to be a specific independent prognostic biomarker in bacteremia. cf-DNA displayed a predominating low-molecular-weight cf-DNA band in nonsurvivors corresponding to the size of apoptotic nucleosomal DNA.

  2. Cell-free culture supernatant of Bifidobacterium breve CNCM I-4035 decreases pro-inflammatory cytokines in human dendritic cells challenged with Salmonella typhi through TLR activation.

    Science.gov (United States)

    Bermudez-Brito, Miriam; Muñoz-Quezada, Sergio; Gomez-Llorente, Carolina; Matencio, Esther; Bernal, Maria J; Romero, Fernando; Gil, Angel

    2013-01-01

    Dendritic cells (DCs) constitute the first point of contact between gut commensals and our immune system. Despite growing evidence of the immunomodulatory effects of probiotics, the interactions between the cells of the intestinal immune system and bacteria remain largely unknown. Indeed,, the aim of this work was to determine whether the probiotic Bifidobacterium breve CNCM I-4035 and its cell-free culture supernatant (CFS) have immunomodulatory effects in human intestinal-like dendritic cells (DCs) and how they respond to the pathogenic bacterium Salmonella enterica serovar Typhi, and also to elucidate the molecular mechanisms involved in these interactions. Human DCs were directly challenged with B. breve/CFS, S. typhi or a combination of these stimuli for 4 h. The expression pattern of genes involved in Toll-like receptor (TLR) signaling pathway and cytokine secretion was analyzed. CFS decreased pro-inflammatory cytokines and chemokines in human intestinal DCs challenged with S. typhi. In contrast, the B. breve CNCM I-4035 probiotic strain was a potent inducer of the pro-inflammatory cytokines and chemokines tested, i.e., TNF-α, IL-8 and RANTES, as well as anti-inflammatory cytokines including IL-10. CFS restored TGF-β levels in the presence of Salmonella. Live B.breve and its supernatant enhanced innate immune responses by the activation of TLR signaling pathway. These treatments upregulated TLR9 gene transcription. In addition, CFS was a more potent inducer of TLR9 expression than the probiotic bacteria in the presence of S. typhi. Expression levels of CASP8 and IRAK4 were also increased by CFS, and both treatments induced TOLLIP gene expression. Our results indicate that the probiotic strain B. breve CNCM I-4035 affects the intestinal immune response, whereas its supernatant exerts anti-inflammatory effects mediated by DCs. This supernatant may protect immune system from highly infectious agents such as Salmonella typhi and can down-regulate pro

  3. Pyrrhocoricin, a proline-rich antimicrobial peptide derived from insect, inhibits the translation process in the cell-free Escherichia coli protein synthesis system.

    Science.gov (United States)

    Taniguchi, Masayuki; Ochiai, Akihito; Kondo, Hiroshi; Fukuda, Shun; Ishiyama, Yohei; Saitoh, Eiichi; Kato, Tetsuo; Tanaka, Takaaki

    2016-05-01

    Previous studies have shown that pyrrhocoricin, a proline-rich antimicrobial peptide (PrAMP), killed sensitive species in a dose-dependent manner by specifically binding to DnaK. Here, on the basis of the finding that DnaK-deficient Escherichia coli strains are susceptible to PrAMPs, we used pyrrhocoricin to investigate internal targets other than DnaK. Using conventional antibiotics (bleomycin, streptomycin, and fosfomycin) that have known modes of action, first, we validated the availability of an assay using a cell-free rapid translation system (RTS), which is an in vitro protein synthesis system based on E. coli lysate, for evaluating inhibition of protein synthesis. We found that, similarly to bleomycin and streptomycin, pyrrhocoricin inhibited GFP synthesis in RTS in a concentration-dependent manner. In addition, blockage of transcription and translation steps in RTS was individually estimated using RT-PCR after gene expression to determine mRNA products and using sodium dodecyl sulfate-polyacrylamide gel electrophoresis to determine the amounts of GFP expressed from purified mRNA, respectively. The results demonstrated that this inhibition of GFP synthesis by pyrrhocoricin did not occur at the transcription step but rather at the translation step, in a manner similar to that of GFP synthesis by streptomycin, an inhibitor of the translation step by causing misreading of tRNA. These results suggest that RTS is a powerful assay system for determining if antimicrobial peptides inhibit protein synthesis and its transcription and/or translation steps. This is the first study to have shown that pyrrhocoricin inhibited protein synthesis by specifically repressing the translation step.

  4. PVP-coated silver nanoparticles block the transmission of cell-free and cell-associated HIV-1 in human cervical culture

    Directory of Open Access Journals (Sweden)

    Rodriguez-Padilla Cristina

    2010-07-01

    Full Text Available Abstract Background Previous in vitro studies have demonstrated that polyvinylpyrrolidone coated silver nanoparticles (PVP-coated AgNPs have antiviral activity against HIV-1 at non-cytotoxic concentrations. These particles also demonstrate broad spectrum virucidal activity by preventing the interaction of HIV-1 gp120 and cellular CD4, thereby inhibiting fusion or entry of the virus into the host cell. In this study, we evaluated the antiviral activity of PVP-coated AgNPs as a potential topical vaginal microbicide to prevent transmission of HIV-1 infection using human cervical culture, an in vitro model that simulates in vivo conditions. Results When formulated into a non-spermicidal gel (Replens at a concentration of 0.15 mg/mL, PVP-coated AgNPs prevented the transmission of cell-associated HIV-1 and cell-free HIV-1 isolates. Importantly, PVP-coated AgNPs were not toxic to the explant, even when the cervical tissues were exposed continuously to 0.15 mg/mL of PVP-coated AgNPs for 48 h. Only 1 min of PVP-coated AgNPs pretreatment to the explant was required to prevent transmission of HIV-1. Pre-treatment of the cervical explant with 0.15 mg/mL PVP-coated AgNPs for 20 min followed by extensive washing prevented the transmission of HIV-1 in this model for 48 h. Conclusions A formulation of PVP-coated AgNPs homogenized in Replens gel acts rapidly to inhibit HIV-1 transmission after 1 min and offers long-lasting protection of the cervical tissue from infection for 48 h, with no evidence of cytotoxicity observed in the explants. Based on this data, PVP-coated AgNPs are a promising microbicidal candidate for use in topical vaginal/cervical agents to prevent HIV-1 transmission, and further research is warranted.

  5. BRAF Mutation Testing in Cell-Free DNA from the Plasma of Patients with Advanced Cancers Using a Rapid, Automated Molecular Diagnostics System.

    Science.gov (United States)

    Janku, Filip; Huang, Helen J; Claes, Bart; Falchook, Gerald S; Fu, Siqing; Hong, David; Ramzanali, Nishma M; Nitti, Giovanni; Cabrilo, Goran; Tsimberidou, Apostolia M; Naing, Aung; Piha-Paul, Sarina A; Wheler, Jennifer J; Karp, Daniel D; Holley, Veronica R; Zinner, Ralph G; Subbiah, Vivek; Luthra, Rajyalakshmi; Kopetz, Scott; Overman, Michael J; Kee, Bryan K; Patel, Sapna; Devogelaere, Benoit; Sablon, Erwin; Maertens, Geert; Mills, Gordon B; Kurzrock, Razelle; Meric-Bernstam, Funda

    2016-06-01

    Cell-free (cf) DNA from plasma offers an easily obtainable material for BRAF mutation analysis for diagnostics and response monitoring. In this study, plasma-derived cfDNA samples from patients with progressing advanced cancers or malignant histiocytosis with known BRAF(V600) status from formalin-fixed paraffin-embedded (FFPE) tumors were tested using a prototype version of the Idylla BRAF Mutation Test, a fully integrated real-time PCR-based test with turnaround time about 90 minutes. Of 160 patients, BRAF(V600) mutations were detected in 62 (39%) archival FFPE tumor samples and 47 (29%) plasma cfDNA samples. The two methods had overall agreement in 141 patients [88%; κ, 0.74; SE, 0.06; 95% confidence interval (CI), 0.63-0.85]. Idylla had a sensitivity of 73% (95% CI, 0.60-0.83) and specificity of 98% (95% CI, 0.93-1.00). A higher percentage, but not concentration, of BRAF(V600) cfDNA in the wild-type background (>2% vs. ≤ 2%) was associated with shorter overall survival (OS; P = 0.005) and in patients with BRAF mutations in the tissue, who were receiving BRAF/MEK inhibitors, shorter time to treatment failure (TTF; P = 0.001). Longitudinal monitoring demonstrated that decreasing levels of BRAF(V600) cfDNA were associated with longer TTF (P = 0.045). In conclusion, testing for BRAF(V600) mutations in plasma cfDNA using the Idylla BRAF Mutation Test has acceptable concordance with standard testing of tumor tissue. A higher percentage of mutant BRAF(V600) in cfDNA corresponded with shorter OS and in patients receiving BRAF/MEK inhibitors also with shorter TTF. Mol Cancer Ther; 15(6); 1397-404. ©2016 AACR.

  6. A Method to Quantify Cell-Free Fetal DNA Fraction in Maternal Plasma Using Next Generation Sequencing: Its Application in Non-Invasive Prenatal Chromosomal Aneuploidy Detection.

    Directory of Open Access Journals (Sweden)

    Xu-Ping Xu

    Full Text Available The fraction of circulating cell-free fetal (cff DNA in maternal plasma is a critical parameter for aneuploidy screening with non-invasive prenatal testing, especially for those samples located in equivocal zones. We developed an approach to quantify cff DNA fractions directly with sequencing data, and increased cff DNAs by optimizing library construction procedure.Artificial DNA mixture samples (360, with known cff DNA fractions, were used to develop a method to determine cff DNA fraction through calculating the proportion of Y chromosomal unique reads, with sequencing data generated by Ion Proton. To validate our method, we investigated cff DNA fractions of 2,063 pregnant women with fetuses who were diagnosed as high risk of fetal defects. The z-score was calculated to determine aneuploidies for chromosomes 21, 18 and 13. The relationships between z-score and parameters of pregnancies were also analyzed. To improve cff DNA fractions in our samples, two groups were established as follows: in group A, the large-size DNA fragments were removed, and in group B these were retained, during library construction.A method to determine cff DNA fractions was successfully developed using 360 artificial mixture samples in which cff DNA fractions were known. A strong positive correlation was found between z-score and fetal DNA fraction in the artificial mixture samples of trisomy 21, 18 and 13, as well as in clinical maternal plasma samples. There was a positive correlation between gestational age and the cff DNA fraction in the clinical samples, but no correlation for maternal age. Moreover, increased fetal DNA fractions were found in group A compared to group B.A relatively accurate method was developed to determine the cff DNA fraction in maternal plasma. By optimizing, we can improve cff DNA fractions in sequencing samples, which may contribute to improvements in detection rate and reliability.

  7. Early Fetal Gender Determination Using Real-Time PCR Analysis of Cell-free Fetal DNA During 6th-10th Weeks of Gestation

    Directory of Open Access Journals (Sweden)

    Hamid Reza Khorram Khorshid

    2013-04-01

    Full Text Available Nowadays, new advances in the use of cell free fetal DNA (cffDNA in maternal plasma of pregnant women has provided the possibility of applying cffDNA in prenatal diagnosis as a non-invasive method. In contrary to the risks of invasive methods that affect both mother and fetus, applying cffDNA is proven to be highly effective with lower risk. One of the applications of prenatal diagnosis is fetal gender determination, which is important in fetuses at risk of sex-linked genetic diseases. In such cases by obtaining the basic information of the gender, necessary time management can be taken in therapeutic to significantly reduce the necessity of applying the invasive methods. Therefore in this study, the probability of detecting sequences on the human Y-chromosome in pregnant women has been evaluated to identify the gender of fetuses. Peripheral blood samples were obtained from 80 pregnant women with gestational age between 6th to 10th weeks and the fetal DNA was extracted from the plasma. Identification of SRY, DYS14 & DAZ sequences, which are not presentin the maternal genome, was performed using Real-Time PCR. All the obtained results were compared with the actual gender of the newborns to calculate the test accuracy. Considerable 97.3% sensitivity and 97.3% specificity were obtained in fetal gender determination which is significant in the first trimester of pregnancy. Only in one case, false positive result was obtained. Using non-invasive method of cffDNAs in the shortest time possible, as well as avoiding invasive tests for early determination of fetal gender, provides the opportunity of deciding and employing early treatment for fetuses at risk of genetic diseases

  8. Identification of Human N-Myristoylated Proteins from Human Complementary DNA Resources by Cell-Free and Cellular Metabolic Labeling Analyses

    Science.gov (United States)

    Takamitsu, Emi; Otsuka, Motoaki; Haebara, Tatsuki; Yano, Manami; Matsuzaki, Kanako; Kobuchi, Hirotsugu; Moriya, Koko; Utsumi, Toshihiko

    2015-01-01

    To identify physiologically important human N-myristoylated proteins, 90 cDNA clones predicted to encode human N-myristoylated proteins were selected from a human cDNA resource (4,369 Kazusa ORFeome project human cDNA clones) by two bioinformatic N-myristoylation prediction systems, NMT-The MYR Predictor and Myristoylator. After database searches to exclude known human N-myristoylated proteins, 37 cDNA clones were selected as potential human N-myristoylated proteins. The susceptibility of these cDNA clones to protein N-myristoylation was first evaluated using fusion proteins in which the N-terminal ten amino acid residues were fused to an epitope-tagged model protein. Then, protein N-myristoylation of the gene products of full-length cDNAs was evaluated by metabolic labeling experiments both in an insect cell-free protein synthesis system and in transfected human cells. As a result, the products of 13 cDNA clones (FBXL7, PPM1B, SAMM50, PLEKHN, AIFM3, C22orf42, STK32A, FAM131C, DRICH1, MCC1, HID1, P2RX5, STK32B) were found to be human N-myristoylated proteins. Analysis of the role of protein N-myristoylation on the intracellular localization of SAMM50, a mitochondrial outer membrane protein, revealed that protein N-myristoylation was required for proper targeting of SAMM50 to mitochondria. Thus, the strategy used in this study is useful for the identification of physiologically important human N-myristoylated proteins from human cDNA resources. PMID:26308446

  9. Non-invasive prenatal diagnostic test accuracy for fetal sex using cell-free DNA a review and meta-analysis

    Directory of Open Access Journals (Sweden)

    Wright Caroline F

    2012-09-01

    Full Text Available Abstract Background Cell-free fetal DNA (cffDNA can be detected in maternal blood during pregnancy, opening the possibility of early non-invasive prenatal diagnosis for a variety of genetic conditions. Since 1997, many studies have examined the accuracy of prenatal fetal sex determination using cffDNA, particularly for pregnancies at risk of an X-linked condition. Here we report a review and meta-analysis of the published literature to evaluate the use of cffDNA for prenatal determination (diagnosis of fetal sex. We applied a sensitive search of multiple bibliographic databases including PubMed (MEDLINE, EMBASE, the Cochrane library and Web of Science. Results Ninety studies, incorporating 9,965 pregnancies and 10,587 fetal sex results met our inclusion criteria. Overall mean sensitivity was 96.6% (95% credible interval 95.2% to 97.7% and mean specificity was 98.9% (95% CI = 98.1% to 99.4%. These results vary very little with trimester or week of testing, indicating that the performance of the test is reliably high. Conclusions Based on this review and meta-analysis we conclude that fetal sex can be determined with a high level of accuracy by analyzing cffDNA. Using cffDNA in prenatal diagnosis to replace or complement existing invasive methods can remove or reduce the risk of miscarriage. Future work should concentrate on the economic and ethical considerations of implementing an early non-invasive test for fetal sex.

  10. Early fetal gender determination using real-time PCR analysis of cell-free fetal DNA during 6th-10th weeks of gestation.

    Science.gov (United States)

    Khorram Khorshid, Hamid Reza; Zargari, Maryam; Sadeghi, Mohammad Reza; Edallatkhah, Haleh; Shahhosseiny, Mohammad Hassan; Kamali, Koorosh

    2013-05-07

    Nowadays, new advances in the use of cell free fetal DNA (cffDNA) in maternal plasma of pregnant women has provided the possibility of applying cffDNA in prenatal diagnosis as a non-invasive method. In contrary to the risks of invasive methods that affect both mother and fetus, applying cffDNA is proven to be highly effective with lower risk. One of the applications of prenatal diagnosis is fetal gender determination, which is important in fetuses at risk of sex-linked genetic diseases. In such cases by obtaining the basic information of the gender, necessary time management can be taken in therapeutic to significantly reduce the necessity of applying the invasive methods. Therefore in this study, the probability of detecting sequences on the human Y-chromosome in pregnant women has been evaluated to identify the gender of fetuses. Peripheral blood samples were obtained from 80 pregnant women with gestational age between 6th to 10th weeks and the fetal DNA was extracted from the plasma. Identification of SRY, DYS14 & DAZ sequences, which are not presentin the maternal genome, was performed using Real-Time PCR. All the obtained results were compared with the actual gender of the newborns to calculate the test accuracy. Considerable 97.3% sensitivity and 97.3% specificity were obtained in fetal gender determination which is significant in the first trimester of pregnancy. Only in one case, false positive result was obtained. Using non-invasive method of cffDNAs in the shortest time possible, as well as avoiding invasive tests for early determination of fetal gender, provides the opportunity of deciding and employing early treatment for fetuses at risk of genetic diseases.

  11. Arthroscopic Fixation of Cell Free Polymer-Based Cartilage Implants with a Bioinspired Polymer Surface on the Hip Joint: A Cadaveric Pilot Study

    Directory of Open Access Journals (Sweden)

    Matthias Lahner

    2014-01-01

    Full Text Available This study investigates the adhesion capacity of a polyglycolic acid- (PGA- hyaluronan scaffold with a structural modification based on a planar polymer (PM surface in a cadaver cartilage defect model. Two cadaver specimens were used to serially test multiple chondral matrices. In a cadaver hip model, cell free polymer-based cartilage implants with a planar bioinspired PM surface (PGA-PM-scaffolds were implanted arthroscopically on 10 mm × 15 mm full-thickness femoral hip cartilage lesions. Unprocessed cartilage implants without a bioinspired PM surface were used as control group. The cartilage implants were fixed without and with the use of fibrin glue on femoral hip cartilage defects. After 50 movement cycles and removal of the distraction, a rearthroscopy was performed to assess the outline attachment and integrity of the scaffold. The fixation techniques without and with fibrin fixation showed marginal differences for outline attachment, area coverage, scaffold integrity, and endpoint fixation after 50 cycles. The PGA-PM-scaffolds with fibrin fixation achieved a higher score in terms of the attachment, integrity, and endpoint fixation than the PGA-scaffold on the cartilage defect. Relating to the outline attachment, area coverage, scaffold integrity, and endpoint fixation, the fixation with PGA-PM-scaffolds accomplished significantly better results compared to the PGA-scaffolds (P=0.03752, P=0.03078, P=0.00512, P=0.00512. PGA-PM-scaffolds demonstrate increased observed initial fixation strength in cadaver femoral head defects relative to PGA-scaffold, particularly when fibrin glue is used for fixation.

  12. Early Change in FDG-PET Signal and Plasma Cell-Free DNA Level Predicts Erlotinib Response in EGFR Wild-Type NSCLC Patients

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    Anne Winther-Larsen

    2016-12-01

    Full Text Available INTRODUCTION: Epidermal growth factor receptor (EGFR tyrosine kinase inhibitors (TKIs are a treatment option in the second- or third-line palliative setting in EGFR wild-type (wt non–small cell lung cancer (NSCLC patients. However, response rates are low, and only approximately 25% will achieve disease control. Early prediction of treatment resistance could accelerate discontinuation of ineffective treatment and reduce unnecessary toxicity. In this study, we evaluated early changes on 18F-fluoro-D-glucose (F-18-FDG positron emission tomography/computed tomography (PET/CT and in total plasma cell-free DNA (cfDNA as markers of erlotinib response in EGFR-wt patients. METHODS: F-18-FDG-PET/CT scans and blood samples were obtained prior to erlotinib initiation and were repeated after 1 week (PET/CT and 1 to 4 weeks (blood sample of treatment. Level of cfDNA was measured by droplet digital polymerase chain reaction. Percentage change (%∆ in SULpeak and total lesion glycolysis (TLG on FDG-PET/CT and in plasma cfDNA was correlated to radiological response, progression-free survival (PFS, and overall survival (OS. RESULTS: Fifty patients were prospectively enrolled. A significant correlation was found between CT response and %∆TLG (P = .003. All patients with early metabolic progression showed radiological progression. Increased %∆TLG and %∆cfDNA were significantly correlated with shorter PFS (P = .002 and P = .004, respectively and OS (P = .009 and P = .009, respectively. Multivariate analysis indicated %∆cfDNA to be the strongest predictor of OS. CONCLUSION: Early increase in TLG on F-18-FDG-PET/CT correlates with radiological progression, and shorter PFS and OS. Early increase in cfDNA predicts shorter PFS and OS. Both assessments are promising tools for early detection of nonresponders and reduced OS in TKI-treated EGFR-wt NSCLC patients.

  13. Lipid-protein nanodiscs for cell-free production of integral membrane proteins in a soluble and folded state: comparison with detergent micelles, bicelles and liposomes.

    Science.gov (United States)

    Lyukmanova, E N; Shenkarev, Z O; Khabibullina, N F; Kopeina, G S; Shulepko, M A; Paramonov, A S; Mineev, K S; Tikhonov, R V; Shingarova, L N; Petrovskaya, L E; Dolgikh, D A; Arseniev, A S; Kirpichnikov, M P

    2012-03-01

    Production of integral membrane proteins (IMPs) in a folded state is a key prerequisite for their functional and structural studies. In cell-free (CF) expression systems membrane mimicking components could be added to the reaction mixture that promotes IMP production in a soluble form. Here lipid-protein nanodiscs (LPNs) of different lipid compositions (DMPC, DMPG, POPC, POPC/DOPG) have been compared with classical membrane mimicking media such as detergent micelles, lipid/detergent bicelles and liposomes by their ability to support CF synthesis of IMPs in a folded and soluble state. Three model membrane proteins of different topology were used: homodimeric transmembrane (TM) domain of human receptor tyrosine kinase ErbB3 (TM-ErbB3, 1TM); voltage-sensing domain of K(+) channel KvAP (VSD, 4TM); and bacteriorhodopsin from Exiguobacterium sibiricum (ESR, 7TM). Structural and/or functional properties of the synthesized proteins were analyzed. LPNs significantly enhanced synthesis of the IMPs in a soluble form regardless of the lipid composition. A partial disintegration of LPNs composed of unsaturated lipids was observed upon co-translational IMP incorporation. Contrary to detergents the nanodiscs resulted in the synthesis of ~80% active ESR and promoted correct folding of the TM-ErbB3. None of the tested membrane mimetics supported CF synthesis of correctly folded VSD, and the protocol of the domain refolding was developed. The use of LPNs appears to be the most promising approach to CF production of IMPs in a folded state. NMR analysis of (15)N-Ile-TM-ErbB3 co-translationally incorporated into LPNs shows the great prospects of this membrane mimetics for structural studies of IMPs produced by CF systems.

  14. Prospective blinded study of somatic mutation detection in cell-free DNA utilizing a targeted 54-gene next generation sequencing panel in metastatic solid tumor patients.

    Science.gov (United States)

    Kim, Seung Tae; Lee, Won-Suk; Lanman, Richard B; Mortimer, Stefanie; Zill, Oliver A; Kim, Kyoung-Mee; Jang, Kee Taek; Kim, Seok-Hyung; Park, Se Hoon; Park, Joon Oh; Park, Young Suk; Lim, Ho Yeong; Eltoukhy, Helmy; Kang, Won Ki; Lee, Woo Yong; Kim, Hee-Cheol; Park, Keunchil; Lee, Jeeyun; Talasaz, AmirAli

    2015-11-24

    Sequencing of the mutant allele fraction of circulating cell-free DNA (cfDNA) derived from tumors is increasingly utilized to detect actionable genomic alterations in cancer. We conducted a prospective blinded study of a comprehensive cfDNA sequencing panel with 54 cancer genes. To evaluate the concordance between cfDNA and tumor DNA (tDNA), sequencing results were compared between cfDNA from plasma and genomic tumor DNA (tDNA). Utilizing next generation digital sequencing technology (DST), we profiled approximately 78,000 bases encoding 512 complete exons in the targeted genes in cfDNA from plasma. Seventy-five patients were prospectively enrolled between February 2013 and March 2014, including 61 metastatic cancer patients and 14 clinical stage II CRC patients with matched plasma and tissue samples. Using the 54-gene panel, we detected at least one somatic mutation in 44 of 61 tDNA (72.1%) and 29 of 44 (65.9%) cfDNA. The overall concordance rate of cfDNA to tDNA was 85.9%, when all detected mutations were considered. We collected serial cfDNAs during cetuximab-based treatment in 2 metastatic KRAS wild-type CRC patients, one with acquired resistance and one with primary resistance. We demonstrate newly emerged KRAS mutation in cfDNA 1.5 months before radiologic progression. Another patient had a newly emerged PIK3CA H1047R mutation on cfDNA analysis at progression during cetuximab/irinotecan chemotherapy with gradual increase in allele frequency from 0.8 to 2.1%. This blinded, prospective study of a cfDNA sequencing showed high concordance to tDNA suggesting that the DST approach may be used as a non-invasive biopsy-free alternative to conventional sequencing using tumor biopsy.

  15. Relations between plate kinematics, slab geometry and overriding plate deformation in subduction zones: insights from statistical observations and laboratory modelling

    Science.gov (United States)

    Heuret, A.; Funiciello, F.; Faccenna, C.; Lallemand, S.

    2005-12-01

    3-D laboratory models have been performed in order to investigate the way plates kinematics (subducting and overriding plate absolute motions and the resulting plate convergence rate) influences the geometry of the slab and the overriding plate deformation in subduction zones. In the experiments a viscous plate of silicone (subducting plate) is pushed beneath another plate, which is itself pushed toward or pulled away from the trench (overriding plate), and sinks into a viscous layer of glucose syrup (upper mantle). The subducting and overriding plate velocities explored the variability field of natural subduction plates kinematics. The overriding plate motion exerts a primary role in the control of slab geometries and overriding plate deformation rates. The experiments have revealed two different subduction behaviours: (Style I) the overriding plate moves toward the trench and shortens at high rates, the slab is flat and deflected when reaching the bottom of the box in a forward direction; (Style II) the overriding plates moves away from the trench and shortens at low rates the slab is steep and deflected on the box bottom in a backward direction. To a lesser extent, increasing subducting plate motion is associated to increasing slab dips and overriding plate shortening. Slab geometry and overriding plate deformation are less sensitive to the overall plate convergence rate. These laboratory models behaviours are consistent with statistical analysis performed on natural subduction zones, and enlighten the first order control exerted by the overriding plate absolute motion, on the geometry adopted by the slab and the way the overriding plate deforms.

  16. Global Plate Driving Forces at 50Ma

    Science.gov (United States)

    Butterworth, N. P.; Quevedo, L. E.; Müller, R. D.

    2011-12-01

    We apply a novel workflow utilising the BEM-Earth geodynamic software to analyse the global coupled plate-mantle dynamics at 50 Ma. A subduction history model based on kinematic data going as far back as 80 Ma was developed using the GPlates software. Advection of the plates into the mantle takes into account the absolute plate motions and lithospheric thickness derived from its age to produce an estimated density heterogeneity initial model condition in the upper mantle. The resulting global model consists of regions of a mantle viscosity and density structure that is post-processed to ensure smooth non-overlapping 3D surfaces. BEM-Earth is then free to evolve the model toward the 50 Ma solution. The evolution of the model is driven by self-consistent buoyancy driven mantle dynamics. We use the model velocity output to quantify changes in forces driving the plates before and after 50 Ma. We analyse the rapid change in plate motion of India, Africa and plates in the Pacific Ocean basin by considering slab-pull, ridge-push and mantle drag/suction forces that naturally result from such top-down driven mantle flow. We compare the results with plate kinematic reconstructions and other geological observations.

  17. Effusion plate using additive manufacturing methods

    Science.gov (United States)

    Johnson, Thomas Edward; Keener, Christopher Paul; Ostebee, Heath Michael; Wegerif, Daniel Gerritt

    2016-04-12

    Additive manufacturing techniques may be utilized to construct effusion plates. Such additive manufacturing techniques may include defining a configuration for an effusion plate having one or more internal cooling channels. The manufacturing techniques may further include depositing a powder into a chamber, applying an energy source to the deposited powder, and consolidating the powder into a cross-sectional shape corresponding to the defined configuration. Such methods may be implemented to construct an effusion plate having one or more channels with a curved cross-sectional geometry.

  18. Enhanced-transmission metamaterials as anisotropic plates

    Science.gov (United States)

    Baida, F. I.; Boutria, M.; Oussaid, R.; van Labeke, D.

    2011-07-01

    We present an original design of anisotropic metamaterial plates exhibiting extraordinary transmission through perfectly conductor metallic screens perforated by a subwavelength double-pattern rectangular aperture array. The polarization properties of the fundamental guided mode inside the apertures are at the origin of the anisotropy. The metal thickness is a key parameter that is adjusted in order to get the desired value of the phase difference between the two transversal electromagnetic field components. As an example, we treat the case of a half-wave plate having 92% transmission coefficient. Such a study can be easily extended to design anisotropic plates operating in terahertz or microwave domains.

  19. Buckling analysis of a laminate plate

    Directory of Open Access Journals (Sweden)

    Mamuzić, I.

    2008-04-01

    Full Text Available The paper deals with a modeling of laminate plates and with their buckling analysis. To predict the inception of buckling for plates in plane resultant forces must be included. The buckling analysis is made by the help of finite element method in program COSMOS/M. For rectangular laminate plate consisting of 4 layers with symmetric and antisymmetric stacking sequence a buckling analysis is carried out. In the illustrative example there are depicted buckling modes for symmetric laminates [30/-30]s, [45/-45]s, [60/-60]s, [90/-90]s and results of the buckling analysis for the symmetric and antisymmetric laminates.

  20. Ion plating with an induction heating source

    Science.gov (United States)

    Spalvins, T.; Brainard, W. A.

    1976-01-01

    Induction heating is introduced as an evaporation heat source in ion plating. A bare induction coil without shielding can be directly used in the glow discharge region with no arcing. The only requirement is to utilize an rf inductive generator with low operating frequency of 75 kHz. Mechanical simplicity of the ion plating apparatus and ease of operation is a great asset for industrial applications; practically any metal such as nickel, iron, and the high temperature refractories can be evaporated and ion plated.

  1. Modeling the hydrodynamics of Phloem sieve plates

    DEFF Research Database (Denmark)

    Jensen, Kaare Hartvig; Mullendore, Daniel Leroy; Holbrook, Noel Michele

    2012-01-01

    understood. We propose a theoretical model for quantifying the effect of sieve plates on the phloem in the plant, thus unifying and improving previous work in the field. Numerical simulations of the flow in real and idealized phloem channels verify our model, and anatomical data from 19 plant species...... are investigated. We find that the sieve plate resistance is correlated to the cell lumen resistance, and that the sieve plate and the lumen contribute almost equally to the total hydraulic resistance of the phloem translocation pathway....

  2. Problem of Electromagnetoviscoelasticity for Multiply Connected Plates

    Science.gov (United States)

    Kaloerov, S. A.; Samodurov, A. A.

    2015-11-01

    A method for solving the problem of electromagnetoviscoelasticity for multiply connected plates is proposed. The small-parameter method is used to reduce this problem to a recursive sequence of problems of electromagnetoelasticity, which are solved by using complex potentials. A procedure is developed to determine, using complex potentials, approximations of the basic characteristics (stresses, electromagnetic-field strength, electromagnetic-flux density) of the electromagnetoelastic state at any time after application of a load. A plate with an elliptic hole is considered as an example. The variation in the electromagnetoelastic state of the multiply connected plate with time is studied

  3. Improvements in Cold-Plate Fabrication

    Science.gov (United States)

    Zaffetti, Mark A.; Taddey, Edmund P.; Laurin, Michael B.; Chabebe, Natalia

    2012-01-01

    Five improvements are reported in cold-plate fabrication. This cold plate is part of a thermal control system designed to serve on space missions. The first improvement is the merging of the end sheets of the cold plate with the face sheets of the structural honeycomb panel. The cold plate, which can be a brazed assembly, uses the honeycomb face sheet as its end sheet. Thus, when the honeycomb panel is fabricated, the face sheet that is used is already part of the cold plate. In addition to reducing weight, costs, and steps, the main benefit of this invention is that it creates a more structurally sound assembly. The second improvement involves incorporation of the header into the closure bar to pass the fluid to a lower layer. Conventional designs have used a separate header, which increases the geometry of the system. The improvement reduces the geometry, thus allowing the cold plate to fit into smaller area. The third improvement eliminates the need of hose, tube, or manifold to supply the cooling fluid externally. The external arrangement can be easily damaged and is vulnerable to leakage. The new arrangement incorporates an internal fluid transfer tube. This allows the fluid to pass from one cold plate to the other without any exposed external features. The fourth improvement eliminates separate fabrication of cold plate(s) and structural members followed by a process of attaching them to each other. Here, the structural member is made of material that can be brazed just as that of the cold plate. Now the structural member and the cold plate can be brazed at the same time, creating a monolithic unit, and thus a more structurally sound assembly. Finally, the fifth improvement is the elimination of an additional welding step that can damage the braze joints. A tube section, which is usually welded on after the braze process, is replaced with a more structurally sound configuration that can be brazed at the same time as the rest of the cold plate.

  4. FLEXURAL WAVE PROPAGATION IN NARROW MINDLIN'S PLATE

    Institute of Scientific and Technical Information of China (English)

    HU Chao; HAN Gang; FANG Xue-qian; HUANG Wen-hu

    2006-01-01

    Appling Mindlin's theory of thick plates and Hamilton system to propagation of elastic waves under free boundary condition, a solution of the problem was given.Dispersion equations of propagation mode of strip plates were deduced from eigenfunction expansion method. It was compared with the dispersion relation that was gained through solution of thick plate theory proposed by Mindlin. Based on the two kinds of theories,the dispersion curves show great difference in the region of short waves, and the cutoff frequencies are higher in Hamiltonian systems. However, the dispersion curves are almost the same in the region of long waves.

  5. Well-plate freeze-drying

    DEFF Research Database (Denmark)

    Trnka, Hjalte; Rantanen, Jukka; Grohganz, Holger

    2015-01-01

    , cake collapse and reconstitution time. Results: Samples freeze-dried in well-plates had an acceptable visual cake appearance. Solid form analysis by high throughput X-ray powder diffraction indicated comparable polymorphic outcome independent of the container. The expected increase in moisture level...... due to increasing amount of amorphous matter in the samples was observed in both vials and well plates. Cake collapse was found to be representative in well plates and could be effectively quantified using image analysis. Reconstitution time was also found to be equal in all three platforms. Finally...

  6. The dynamics of Cenozoic and Mesozoic plate motions

    OpenAIRE

    Lithgow-Bertelloni, C.; Richards, M. A.

    1998-01-01

    Our understanding of the dynamics of plate motions is based almost entirely upon modeling of present-day plate motions. A fuller understanding, however, can be derived from consideration of the history of plate motions. Here we investigate the kinematics of the last 120 Myr of plate motions and the dynamics of Cenozoic motions, paying special attention to changes in the character of plate motions and plate-driving forces. We analyze the partitioning of the observed surface velocity field into...

  7. Biparental Inheritance of γ-Tubulin during Human Fertilization: Molecular Reconstitution of Functional Zygotic Centrosomes in Inseminated Human Oocytes and in Cell-free Extracts Nucleated by Human Sperm

    OpenAIRE

    Simerly, Calvin; Zoran, Sara S.; Payne, Chris; Dominko, Tanja; Sutovsky, Peter; Christopher S. Navara; Salisbury, Jeffery L.; Schatten, Gerald

    1999-01-01

    Human sperm centrosome reconstitution and the parental contributions to the zygotic centrosome are examined in mammalian zygotes and after exposure of spermatozoa to Xenopus laevis cell-free extracts. The presence and inheritance of the conserved centrosomal constituents γ-tubulin, centrin, and MPM-2 (which detects phosphorylated epitopes) are traced, as is the sperm microtubule-nucleating capability on reconstituted centrosomes. γ-Tubulin is biparentally inherited in humans (maternal >> than...

  8. Design of carrier tRNAs and selection of four-base codons for efficient incorporation of various nonnatural amino acids into proteins in Spodoptera frugiperda 21 (Sf21) insect cell-free translation system.

    Science.gov (United States)

    Taki, Masumi; Tokuda, Yasunori; Ohtsuki, Takashi; Sisido, Masahiko

    2006-12-01

    Spodoptera frugiperda 21 (Sf21) insect cell-free protein synthesizing system was expanded to include nonnatural amino acids. Orthogonal tRNAs that work as carriers of nonnatural amino acids in the insect system were explored. Four-base codons for assigning the positions of nonnatural amino acids were also selected. Mutated streptavidin mRNAs that contained different four-base codons were prepared and added to the insect cell-free system in the presence of various tRNAs possessing the corresponding four-base anticodons. The tRNAs were chemically aminoacylated with various types of nonnatural amino acids to examine their incorporation efficiencies. Using p-nitrophenylalanine as the nonnatural amino acid and streptavidin as the target protein, tRNA sequences and the types of four-base codons were optimized to maximize the yield of the nonnatural mutant and to minimize production of full-length proteins that do not contain the nonnatural amino acid. Among the tRNA sequences taken from a variety of tRNAs of nonstandard structures, the tRNA derived from Methanosarcina acetivorans tRNA(Pyl) was the most efficient and orthogonal tRNA. Of the CGGN-type four-base codons, CGGA and CGGG were the most efficient ones for assigning the positions of nonnatural amino acids. p-Nitrophenylalanine and 2-naphthylalanine were efficiently incorporated as in the case of Escherichia coli and rabbit reticulocyte cell-free systems. Much less efficient incorporation was observed, however, for other nonnatural amino acids, indicating that the insect system is less tolerant to the structural diversity of amino acids than the E. coli cell-free system.

  9. Cell-Free versus Cell-to-Cell Infection by Human Immunodeficiency Virus Type 1 and Human T-Lymphotropic Virus Type 1: Exploring the Link among Viral Source, Viral Trafficking, and Viral Replication.

    Science.gov (United States)

    Dutartre, Hélène; Clavière, Mathieu; Journo, Chloé; Mahieux, Renaud

    2016-09-01

    Human immunodeficiency virus type 1 (HIV-1) and human T-lymphotropic virus type 1 (HTLV-1) are complex retroviruses mainly infecting CD4(+) T lymphocytes. In addition, antigen-presenting cells such as dendritic cells (DCs) are targeted in vivo by both viruses, although to a lesser extent. Interaction of HIV-1 with DCs plays a key role in viral dissemination from the mucosa to CD4(+) T lymphocytes present in lymphoid organs. While similar mechanisms may occur for HTLV-1 as well, most HTLV-1 data were obtained from T-cell studies, and little is known regarding the trafficking of this virus in DCs. We first compared the efficiency of cell-free versus cell-associated viral sources of both retroviruses at infecting DCs. We showed that both HIV-1 and HTLV-1 cell-free particles are poorly efficient at productively infecting DCs, except when DC-SIGN has been engaged. Furthermore, while SAMHD-1 accounts for restriction of cell-free HIV-1 infection, it is not involved in HTLV-1 restriction. In addition, cell-free viruses lead mainly to a nonproductive DC infection, leading to trans-infection of T-cells, a process important for HIV-1 spread but not for that of HTLV-1. Finally, we show that T-DC cell-to-cell transfer implies viral trafficking in vesicles that may both increase productive infection of DCs ("cis-infection") and allow viral escape from immune surveillance. Altogether, these observations allowed us to draw a model of HTLV-1 and HIV-1 trafficking in DCs.

  10. A Study of the Effect of Gold Thickness Distribution in the Jet Plating Process to Optimize Gold Usage and Plating Voltage Using Design of Experiments

    OpenAIRE

    Aramphongphun Chuckaphun; Nampanya Chalermpol

    2016-01-01

    A gold plating process in the electronics industry can be classified as (i) all surface plating or (ii) selective plating. Selective plating is more widely used than all surface plating because it can save more gold used in the plating process and takes less plating time. In this research, the selective plating process called jet plating was studied. Factors that possibly affected the gold usage and plating voltage were also studied to reduce the production cost. These factors included (a) pl...

  11. Suppression of isotope scrambling in cell-free protein synthesis by broadband inhibition of PLP enymes for selective {sup 15}N-labelling and production of perdeuterated proteins in H{sub 2}O

    Energy Technology Data Exchange (ETDEWEB)

    Su Xuncheng; Loh, Choy-Theng; Qi Ruhu; Otting, Gottfried, E-mail: gottfried.otting@anu.edu.au [Australian National University, Research School of Chemistry (Australia)

    2011-05-15

    Selectively isotope labelled protein samples can be prepared in vivo or in vitro from selectively labelled amino acids but, in many cases, metabolic conversions between different amino acids result in isotope scrambling. The best results are obtained by cell-free protein synthesis, where metabolic enzymes are generally less active, but isotope scrambling can never be suppressed completely. We show that reduction of E. coli S30 extracts with NaBH{sub 4} presents a simple and inexpensive way to achieve cleaner selective isotope labelling in cell-free protein synthesis reactions. The purpose of the NaBH{sub 4} is to inactivate all pyridoxal-phosphate (PLP) dependent enzymes by irreversible reduction of the Schiff bases formed between PLP and lysine side chains of the enzymes or amino groups of free amino acids. The reduced S30 extracts retain their activity of protein synthesis, can be stored as well as conventional S30 extracts and effectively suppress conversions between different amino acids. In addition, inactivation of PLP-dependent enzymes greatly stabilizes hydrogens bound to {alpha}-carbons against exchange with water, minimizing the loss of {alpha}-deuterons during cell-free production of proteins from perdeuterated amino acids in H{sub 2}O solution. This allows the production of highly perdeuterated proteins that contain protons at all exchangeable positions, without having to back-exchange labile deuterons for protons as required for proteins that have been synthesized in D{sub 2}O.

  12. Suppression of isotope scrambling in cell-free protein synthesis by broadband inhibition of PLP enymes for selective 15N-labelling and production of perdeuterated proteins in H2O.

    Science.gov (United States)

    Su, Xun-Cheng; Loh, Choy-Theng; Qi, Ruhu; Otting, Gottfried

    2011-05-01

    Selectively isotope labelled protein samples can be prepared in vivo or in vitro from selectively labelled amino acids but, in many cases, metabolic conversions between different amino acids result in isotope scrambling. The best results are obtained by cell-free protein synthesis, where metabolic enzymes are generally less active, but isotope scrambling can never be suppressed completely. We show that reduction of E. coli S30 extracts with NaBH(4) presents a simple and inexpensive way to achieve cleaner selective isotope labelling in cell-free protein synthesis reactions. The purpose of the NaBH(4) is to inactivate all pyridoxal-phosphate (PLP) dependent enzymes by irreversible reduction of the Schiff bases formed between PLP and lysine side chains of the enzymes or amino groups of free amino acids. The reduced S30 extracts retain their activity of protein synthesis, can be stored as well as conventional S30 extracts and effectively suppress conversions between different amino acids. In addition, inactivation of PLP-dependent enzymes greatly stabilizes hydrogens bound to α-carbons against exchange with water, minimizing the loss of α-deuterons during cell-free production of proteins from perdeuterated amino acids in H(2)O solution. This allows the production of highly perdeuterated proteins that contain protons at all exchangeable positions, without having to back-exchange labile deuterons for protons as required for proteins that have been synthesized in D(2)O.

  13. White Light Photorefractive Phase Zone Plates

    Institute of Scientific and Technical Information of China (English)

    GAO Yuan-Mei; LIU Si-Min

    2008-01-01

    Incoherent white light from an incandescent source is employed to Fabricate volume phase zone plates in LiNbO3:Fe,for the first time to our knowledge,which can guide and modulate the input white light or laser light.The diffractive efficiency of the white light volume phase zone plates fabricated can reach as high as 12%.In addition,we test the volume phase zone plates by a probe beam and find that the volume phase zone plate is present in the direction perpendicular to the c-axis and absent in the direction parallel to the c-axis.This directly proves the existence of photovoltalc photorefractive anisotropy of white light.

  14. Characterization of Tri-lab Tantalum Plate.

    Energy Technology Data Exchange (ETDEWEB)

    Buchheit, Thomas E.; Cerreta, Ellen K.; Deibler, Lisa Anne; Chen, Shu-Rong; Michael, Joseph R.

    2014-09-01

    This report provides a detailed characterization Tri-lab Tantalum (Ta) plate jointly purchased from HCStark Inc. by Sandia, Los Alamos and Lawrence Livermore National Laboratories. Data in this report was compiled from series of material and properties characterization experiments carried out at Sandia (SNL) and Los Alamos (LANL) Laboratories through a leveraged effort funded by the C2 campaign. Results include microstructure characterization detailing the crystallographic texture of the material and an increase in grain size near the end of the rolled plate. Mechanical properties evaluations include, compression cylinder, sub-scale tension specimen, micohardness and instrumented indentation testing. The plate was found to have vastly superior uniformity when compare with previously characterized wrought Ta material. Small but measurable variations in microstructure and properties were noted at the end, and at the top and bottom edges of the plate.

  15. 46 CFR 169.665 - Name plates.

    Science.gov (United States)

    2010-10-01

    ... Electrical Electrical Installations Operating at Potentials of Less Than 50 Volts on Vessels of Less Than 100 Gross Tons § 169.665 Name plates. Each generator, motor and other major item f power equipment must...

  16. Accuracy of MRI in Growth Plate Measurement

    DEFF Research Database (Denmark)

    Shiguetomi Medina, Juan Manuel; Rahbek, Ole; Ringgaard, Steffen

    2013-01-01

    was measured and compared to histology. Results. Histology measurements showed a mean growth plate thickness of 467 μm (SD = 82.2). The mean growth plate thickness measured in the 7T MR images was 465 μm (SD = 62.2) and 1325 μm (SD=183.5) on 1.5 MRI measurements. We found a better correlation between...... the growth plate thickness measured on the 7T MRI and histology samples compared to 1.5T, where the accuracy was poor. Conclusion. The growth plate can be identified and measured with high accuracy using 7T MRI. 1.5T MRI can only describe some morphological characteristics; its poor resolution impedes to do...

  17. Origin of the Caribbean Plate Conference

    Institute of Scientific and Technical Information of China (English)

    Keith H. James; Maria Antonieta Lorente

    2006-01-01

    @@ An international research conference, entitled "Geology of the area between North and South America, with focus on the origin of the Caribbean Plate", took place in Siguenza, Spain, from May 29-June 2, 2006.

  18. Theories for Elastic Plates via Orthogonal Polynomials

    DEFF Research Database (Denmark)

    Krenk, Steen

    1981-01-01

    A complementary energy functional is used to derive an infinite system of two-dimensional differential equations and appropriate boundary conditions for stresses and displacements in homogeneous anisotropic elastic plates. Stress boundary conditions are imposed on the faces a priori...

  19. Aeroheating model advancements featuring electroless metallic plating

    Science.gov (United States)

    Stalmach, C. J., Jr.; Goodrich, W. D.

    1976-01-01

    Discussed are advancements in wind tunnel model construction methods and hypersonic test data demonstrating the methods. The general objective was to develop model fabrication methods for improved heat transfer measuring capability at less model cost. A plated slab model approach was evaluated with cast models containing constantan wires that formed single-wire-to-plate surface thermocouple junctions with a seamless skin of electroless nickel alloy. The surface of a space shuttle orbiter model was selectively plated with scaled tiles to simulate, with high fidelity, the probable misalignments of the heatshield tiles on a flight vehicle. Initial, Mach 8 heating results indicated a minor effect of tile misalignment roughness on boundary layer transition, implying a possible relaxation of heatshield manufacturing tolerances. Some loss of the plated tiles was experienced when the model was tested at high heating rates.

  20. Energy transfer in double plate system dynamics

    Institute of Scientific and Technical Information of China (English)

    Katica (Stevanovic) Hedrih

    2008-01-01

    The study of energy transfer between coupled subsystems in a hybrid system is very important for applications. This paper presents an analytical analysis of energy transfer between plates of a visco-elastically connected double-plate system in free transversal vibrations. The analytical analysis shows that the visco-elastic connection between plates is responsible for the appearance of two-frequency regime in the time function, which corresponds to one eigen amplitude function of one mode, and also that time functions of different vibration modes are uncoupled, but energy transfer between plates in one eigen mode appears. It was shown for each shape of vibrations. Series of the two Lyapunov exponents corresponding to the one eigen amplitude mode are expressed by using the energy of the corresponding eigen amplitude time component.