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Various Lengths (various + length)
Selected AbstractsFrequency-volume chart: The minimum number of days required to obtain reliable resultsNEUROUROLOGY AND URODYNAMICS, Issue 2 2003Erik Schick Abstract Aims There is wide variation in the number of days necessary to maintain a diary and still furnish reliable data on which to base a sound clinical assessment. Estimates range from 1 day to 2 weeks, 7 days probably being the criterion standard. The goal of this retrospective study was to evaluate how much the 7-day period could be shortened without compromising the reliability of data. Methods Various lengths of frequency-volume (FV) charts (from 1 day to 6 days) were compared with the standard 7-day charts on 14 FV parameters. Results Overall results show that a 4-day dairy is nearly identical to the 7-day chart (most r ,,0.95). Results of the 1-, 2-, and 3-day charts were frequently different statistically from the 7-day chart, whereas comparison of the 4-day chart with the 7-day chart showed no statistically significant differences. In addition, results of 4-day FV charts from a new control cohort showed no significant differences from the 7-day charts of the main cohort. Conclusions In conclusion, our study indicates that the 4-day chart is as reliable as the 7-day chart. This reduction in the length of time, although easier for the patients, does not compromise the diagnostic value of the FV charts. Neurourol. Urodynam. 22:92,96, 2003. © 2003 Wiley-Liss, Inc. [source] Interface Structure between Immiscible Reactive Polymers under Transreaction: a Monte Carlo SimulationMACROMOLECULAR THEORY AND SIMULATIONS, Issue 5 2005Xuehao He Abstract Summary: The interface structure between two immiscible melts, a polycondensate polymer A (e.g., polycarbonate, polyester or polyamide) and a polymer B, was studied by means of Monte Carlo simulations using the bond fluctuation model. Polymer B contained a reactive end group (e.g., OH, NH2 or COOH). Copolymers were generated in-situ at the interfaces by transreactions (alcoholysis, aminolysis or acidolysis), composing of various length of block A, depending on the position of transreaction in the polycondensate chain A. The content of copolymer at the interface increased with the time, particular fast at the early stage. Fragments of polymers A were released with an end group, reactive to polymers A. This resulted in the proceeding of internal transreactions. An asymmetric interface structure was formed. The simulation also showed that copolymers generated by interfacial transreactions increased the compatibility of the two polymers and enhanced the adhesion strength at the interfaces. [source] Important Factors in Bubble Coalescence Modeling in Stirred Tank ReactorsTHE CANADIAN JOURNAL OF CHEMICAL ENGINEERING, Issue 3-4 2003Rahman Sudiyo Abstract Bubble coalescence has been studied in a 2.6 L stirred tank. Instantaneous velocity fields were measured using PIV and corresponding turbulent kinetic energy, dissipation rate, various length and timescales were estimated. All of these data, combined with data of local gas hold-up, bubble size and coalescence rate obtained with shadowgraph were used to assess bubble coalescence at different positions. Results show that bubble coalescence takes place mostly near the tank wall, especially on the leeward side of baffles. The most important factors affecting coalescence are gas hold-up, fluctuation of liquid velocity, different rise velocities of bubbles, and trapping of bubbles in stationary and turbulent eddies. On a étudié la coalescence des bulles dans un réservoir agité de 2,6 L. Les champs de vitesse instantanée ont été mesurés par vélocimétrie à imagerie de particules (PIV), et l'énergie cinétique turbulente correspondante, la vitesse de dissipation et diverses échelles de longueur et de temps ont été estimés. Toutes ces données, combinées à des données de rétention de gaz locale, de taille des bulles et de vitesse de coalescence obtenues avec le projecteur de profils, ont permis d'évaluer la coalescence des bulles à différentes positions. Les résultats montrent que la coalescence des bulles se produit principalement près de la paroi du réservoir, spécialement sur la face aval des chicanes. Les principaux facteurs qui influent la coalescence sont la rétention de gaz, la fluctuation de la vitesse de liquide, les différentes vitesses d'ascension des bulles et le piégeage des bulles dans des tourbillons stationnaires et turbulents. [source] Gliding movement in Peranema trichophorum is powered by flagellar surface motilityCYTOSKELETON, Issue 4 2003Akira Saito Abstract A colorless euglenoid flagellate Peranema trichophorum shows unique unidirectional gliding cell locomotion on the substratum at velocities up to 30 ,m/s by an as yet unexplained mechanism. In this study, we found that (1) treatment with NiCl2 inhibited flagellar beating without any effect on gliding movement; (2) water currents applied to a gliding cell from opposite sides caused detachment of the cell body from the substratum. With only the anterior flagellum adhering to the substratum, gliding movement continued along the direction of the anterior flagellum; (3) gentle pipetting induced flagellar severance into various lengths. In these cells, gliding velocity was proportional to the flagellar length; and (4) Polystyrene beads were translocated along the surface of the anterior flagellum. All of these results indicate that a cell surface motility system is present on the anterior flagellum, which is responsible for cell gliding in P. trichophorum. Cell Motil. Cytoskeleton 55:244,253, 2003. © 2003 Wiley-Liss, Inc. [source] Human and pig SRY 5, flanking sequences can direct reporter transgene expression to the genital ridge and to migrating neural crest cellsDEVELOPMENTAL DYNAMICS, Issue 3 2006Alexandre Boyer Abstract Mechanisms for sex determination vary greatly between animal groups, and include chromosome dosage and haploid,diploid mechanisms as seen in insects, temperature and environmental cues as seen in fish and reptiles, and gene-based mechanisms as seen in birds and mammals. In eutherian mammals, sex determination is genetic, and SRY is the Y chromosome located gene representing the dominant testes determining factor. How SRY took over this function from ancestral mechanisms is not known, nor is it known what those ancestral mechanisms were. What is known is that SRY is haploid and thus poorly protected from mutations, and consequently is poorly conserved between mammalian species. To functionally compare SRY promoter sequences, we have generated transgenic mice with fluorescent reporter genes under the control of various lengths of human and pig SRY 5, flanking sequences. Human SRY 5, flanking sequences (5 Kb) supported reporter transgene expression within the genital ridge of male embryos at the time of sex determination and also supported expression within migrating truncal neural crest cells of both male and female embryos. The 4.6 Kb of pig SRY 5, flanking sequences supported reporter transgene expression within the male genital ridge but not within the neural crest; however, 2.6 Kb and 1.6 Kb of pig SRY 5, flanking sequences retained male genital ridge expression and now supported extensive expression within cells of the neural crest in embryos of both sexes. When 2 Kb of mouse SRY 5, flanking sequences (,3 to ,1 Kb) were placed in front of the 1.6 Kb of pig SRY 5, flanking sequences and this transgene was introduced into mice, reporter transgene expression within the male genital ridge was retained but neural crest expression was lost. These observations suggest that SRY 5, flanking sequences from at least two mammalian species contain elements that can support transgene expression within cells of the migrating neural crest and that additional SRY 5, flanking sequences can extinguish this expression. Developmental Dynamics 235:623,632, 2006. © 2006 Wiley-Liss, Inc. [source] An examination of the relationship between dyslexia and offending in young people and the implications for the training systemDYSLEXIA, Issue 2 2001Jane Kirk Abstract A screening study was undertaken which involved 50 young offenders, serving sentences of various lengths, all from the largest young offenders' institution in Scotland. All 50 were screened for dyslexia and a number received a more detailed follow-up assessment. The results of the screening showed that 25 of the young offenders (50%) were dyslexic to some degree. This finding has implications for professionals, particularly in respect of follow-up assessment and support, and for politicians in relation to issues such as school experience, prison education and staff training. These issues are discussed here in relation to the background and results of the study. Copyright © 2001 John Wiley & Sons, Ltd. [source] A microfluidic study of mechanisms in the electrophoresis of supercoiled DNAELECTROPHORESIS, Issue 12 2008Dammika P. Manage Abstract In this work, microfluidic chips were used to study the electrophoresis of supercoiled DNA (SC DNA) in agarose. This system allowed us to study the electrophoretic and trapping behaviours of SC DNA of various lengths, at various fields and separation distances. Near a critical electric field the DNA is trapped such that the concentration falls exponentially with distance. The trapping of such circular DNA has been explained in terms of the ,lobster trap' or ,impalement' model where shorter fibres become trapping sites at higher fields, leading to an ongoing (and gradual) increase in trapping with increasing field. By contrast, the present study suggests that under some circumstances the traps have a barrier such that only when the DNA has sufficient energy (at high enough fields) can it become trapped, leading to a sudden transition in behaviours at the critical field. We propose an ,activated impalement' mechanism of trapping in which only at sufficiently high fields is the SC DNA impaled and trapped for long times. The critical electric field appears to be inversely proportional to the length of the DNA molecule, suggesting that the force required to impale the SC DNA is constant. [source] Genomic structure and expression analysis of the RNase , family ortholog gene in the insect Ceratitis capitataFEBS JOURNAL, Issue 24 2008Theodoros N. Rampias Cc RNase is the founding member of the recently identified RNase , family, which is represented by a single ortholog in a wide range of animal taxonomic groups. Although the precise biological role of this protein is still unknown, it has been shown that the recombinant proteins isolated so far from the insect Ceratitis capitata and from human exhibit ribonucleolytic activity. In this work, we report the genomic organization and molecular evolution of the RNase , gene from various animal species, as well as expression analysis of the ortholog gene in C. capitata. The high degree of amino acid sequence similarity, in combination with the fact that exon sizes and intronic positions are extremely conserved among RNase , orthologs in 15 diverse genomes from sea anemone to human, imply a very significant biological function for this enzyme. In C. capitata, two forms of RNase , mRNA (0.9 and 1.5 kb) with various lengths of 3, UTR were identified as alternative products of a single gene, resulting from the use of different polyadenylation signals. Both transcripts are expressed in all insect tissues and developmental stages. Sequence analysis of the extended region of the longer transcript revealed the existence of three mRNA instability motifs (AUUUA) and five poly(U) tracts, whose functional importance in RNase , mRNA decay remains to be explored. [source] Structure and promoter analysis of the mouse membrane-bound transferrin-like protein (MTf) geneFEBS JOURNAL, Issue 5 2001Kazuko Nakamasu Recently, we purified membrane-bound transferrin-like protein (MTf) from the plasma membrane of rabbit chondrocytes and showed that the expression levels of MTf protein and mRNA were much higher in cartilage than in other tissues [Kawamoto T, Pan, H., Yan, W., Ishida, H., Usui, E., Oda, R., Nakamasu, K., Noshiro, M., Kawashima-Ohya, Y., Fujii, M., Shintani, H., Okada, Y. & Kato, Y. (1998) Eur. J. Biochem.256, 503,509]. In this study, we isolated the MTf gene from a constructed mouse genomic library. The mouse MTf gene was encoded by a single-copy gene spanning ,,26 kb and consisting of 16 exons. The transcription-initiation site was located 157 bp upstream from the translation-start codon, and a TATA box was not found in the 5, flanking region. The mouse MTf gene was mapped on the B3 band of chromosome 16 by fluorescence in situ hybridization. Using primary chondrocytes, SK-MEL-28 (melanoma cell line), ATDC5 (chondrogenic cell line) and NIH3T3 (fibroblast cell line) cells, we carried out transient expression studies on various lengths of the 5, flanking region of the MTf gene fused to the luciferase reporter gene. Luciferase activity in SK-MEL-28 cells was higher than in primary chondrocytes. Although no luciferase activity was detectable in NIH3T3 cells, it was higher in chondrocytes than in ATDC5 chondrogenic cells. These findings were consistent with the levels of expression of MTf mRNA in these cells cultured under similar conditions. The patterns of increase and decrease in the luciferase activity in chondrocytes transfected with various 5, deleted constructs of the MTf promoter were similar to that in ATDC5 cells, but differed from that in SK-MEL-28 cells. The findings obtained with primary chondrocytes suggest that the regions between ,693 and ,444 and between ,1635 and ,1213 contain positive and negative cis -acting elements, respectively. The chondrocyte-specific expression of the MTf gene could be regulated via these regulatory elements in the promoter region. [source] Uniform Head in Horizontal and Vertical WellsGROUND WATER, Issue 1 2006David R. Steward The steady-state head within a fully penetrating well may be estimated by evaluating the Thiem equation at the radius of the well. A method is presented here to extend results from the Thiem equation to horizontal wells and to partially penetrating wells. The particular model used in this investigation is based upon the analytic element method; it accurately reproduces a boundary condition of uniform head along the cylindrical surface at the perforated face of the well. This model is exercised over a representative range of parameters including the well's length, radius, and pumping rate, and the aquifer's hydraulic conductivity and thickness. Results are presented in a set of figures and tables that compare the well's drawdown to the drawdown that would have been obtained using the Thiem solution with the same pumping rate and radius. A methodology is presented to estimate the head within a horizontal or partially penetrating well by adding a correction term to results that can be readily obtained from computer models of vertical fully penetrating wells. This approach may also be used to contrast the differences in head between horizontal and vertical wells of various lengths, radii, and placement elevations. [source] Unusual Sb,Sb bonding in high temperature thermoelectric materialsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2008Jianxiao Xu Abstract The emerging families of advanced thermoelectrics are dominated by antimonides and tellurides. Because the structures of the tellurides are mostly composed of NaCl-related motifs, they do not contain any Te,Te bonds, and all of the antimonide structures exhibit Sb,Sb bonds of various lengths. Taking all Sb,Sb distances shorter than 3.2 Å into account, the Sb atom substructures are Sb24, pairs in ,-Zn4Sb3, linear Sb37, units in Yb14MnSb11, planar Sb44, rectangles in the skutterudites, for example, LaFe3CoSb12, and Sb8 cubes interconnected via short Sb,Sb bonds to a three-dimensional network in Mo3Sb5Te2. These interactions have a significant impact on the band gap size as well as on the effective mass around the Fermi level, for the bottom of the conduction band is in all cases predominated by antibonding Sb,Sb interactions, and,in some cases,the top of the valence band by bonding Sb,Sb interactions. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008 [source] Thermal Inactivation of Salmonella on Cantaloupes Using Hot WaterJOURNAL OF FOOD SCIENCE, Issue 2 2006Ethan B. Solomon ABSTRACT The inactivation of Salmonella on cantaloupes using hot water was investigated. Whole melons, inoculated with a cocktail of Salmonella isolates, were subjected to thermal treatments of various lengths in water at 65 °C, 75 °C, and 85 °C. Treatment with water at 85 °C for 60 and 90 s resulted in reductions of up to 4.7 log colony forming units (CFU) per square centimeter of rind. However, the rind of melons treated at 85 °C for 90 s were noticeably softer than the rind of melons treated for 60 s. Thermal penetration profiles were measured and computer simulations were conducted to verify the effect of hot water treatment conditions on the internal temperatures of cantaloupe melons. Experimental and simulation data indicated that the internal temperature of melons treated with hot water did not increase rapidly compared with the rind temperature. Regardless of the process temperature used, the temperature of the edible flesh, 10 mm from the surface of the rind, remained at least 40 °C cooler than the surface temperature of cantaloupe melons. These results demonstrate the utility of hot water for the inactivation of Salmonella on cantaloupes and provide a framework to producers of fresh-cut melon for the potential use of hot water as an intervention treatment. [source] The effects of 1.5T magnetic resonance imaging on early murine in-vitro embryo developmentJOURNAL OF MAGNETIC RESONANCE IMAGING, Issue 3 2001MMed (O&G), MRACOG, Stephen Chew MBBS Abstract Although no ionizing radiation is involved, patients undergoing magnetic resonance imaging (MRI) are exposed to powerful static magnetic fields, magnetic field gradients, and radio-frequency fields that may be potentially damaging. Our study aims to document the effect of MRI imaging sequences on early murine embryo development (two-cell to blastocyst stage) in vitro. Two-cell murine embryos were exposed to various lengths of MRI using pulse sequences employed in present day clinical imaging. Early murine embryo development was documented in vitro, and blastocyst development rates were computed for both the control and exposed groups. There were no significant differences detected in the rate of blastocyst formation between the control groups and the embryos exposed to MRI. J. Magn. Reson. Imaging 2001;13:417,420. © 2001 Wiley-Liss, Inc. [source] Process induced disorder in crystalline materials: Differentiating defective crystals from the amorphous form of griseofulvinJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 8 2008Tao Feng Abstract This research investigates milling induced disorder in crystalline griseofulvin. Griseofulvin was subjected to cryogenic milling for various lengths of time. For comparison, the amorphous form of griseofulvin was also prepared by the quench melt method. Different analytical techniques were used to study the differences between the cryomilled, amorphous and crystalline forms of the drug. Cryogenic milling of griseofulvin progressively reduces the crystallinity of the drug by inducing crystal defects, rather than amorphous materials. Raman analysis provides evidence of structural differences between the two. The differences between the defective crystals produced by milling and the amorphous form are significant enough as to be measurable in their bulk thermal properties. Defective crystals show significant decrease in the heat of fusion as a function of milling time but do not exhibit a glass transition nor recrystallization from the amorphous form. Crystal defects undergo recrystallization upon heating at temperatures well below the glass transition temperature (Tg) in a process that is separate and completely independent from the crystallization of the amorphous griseofulvin, observed above Tg. Physical mixtures of defective crystals and amorphous drug demonstrate that the thermal events associated with each form persist in the mixtures, unaffected by the presence of the other form. © 2007 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 97: 3207,3221, 2008 [source] The effect of ligand on the rate of propagation of Cu(0)-wire catalyzed SET-LRP of MA in DMSO at 25 °CJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 21 2009Nga H. Nguyen Abstract The effect of initial ligand concentration on the apparent rate constant of propagation of single-electron transfer living radical polymerization (SET-LRP) of MA in DMSO at 25 °C was examined using various lengths of Cu(0) wire as catalyst. It was determined that unlike other parameters such as initiator concentration, solvent concentration, and deactivator concentration, no simple external rate-order for the ligand concentration could be determined. Rather, the response of the rate of SET-LRP to initial ligand concentration is complex and is likely determined by a competition of ligand-dependent extent of disproportionation as well as the role of ligand concentration in the surface mediated activation process. Results suggest that a minimum concentration of ligand is needed to achieve both acceptable reaction rate and reaction control, and therefore, ligand concentration must be considered in designing experimental conditions for SET-LRP. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 5629,5638, 2009 [source] Synthesis and self-assembly of helical polypeptide-random coil amphiphilic diblock copolymerJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 9 2008Shiao-Wei Kuo Abstract Three amphiphilic rod-coil diblock copolymers, poly(2-ethyl-2-oxazoline- b -,-benzyl- L -glutamate) (PEOz- b -PBLG), incorporating the same-length PEOz block length and various lengths of their PBLG blocks, were synthesized through a combining of living cationic and N -carboxyanhydride (NCA) ring-opening polymerizations. In the bulk, these block copolymers display thermotropic liquid crystalline behavior. The self-assembled aggregates that formed from these diblock copolymers in aqueous solution exhibited morphologies that differed from those obtained in ,-helicogenic solvents, that is, solvents in which the PBLG blocks adopt rigid ,-helix conformations. In aqueous solution, the block copolymers self-assembled into spherical micelles and vesicular aggregates because of their amphiphilic structures. In helicogenic solvents (in this case, toluene and benzyl alcohol), the PEOz- b -PBLG copolymers exhibited rod-coil chain properties, which result in a diverse array of aggregate morphologies (spheres, vesicles, ribbons, and tube nanostructures) and thermoreversible gelation behavior. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 3108,3119, 2008 [source] Synthesis of hydroxy-terminated, oligomeric poly(silarylene disiloxane)s via rhodium-catalyzed dehydrogenative coupling and their use in the aminosilane,disilanol polymerization reaction,JOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 9 2002Craig L. Homrighausen Abstract A series of oligomeric, hydroxy-terminated silarylene,siloxane prepolymers of various lengths were prepared via dehydrogenative coupling between 1,4-bis(dimethylsilyl)benzene [H(CH3)2SiC6H4Si(CH3)2H] and excess 1,4-bis(hydroxydimethylsilyl)benzene [HO(CH3)2SiC6H4Si(CH3)2OH] in the presence of a catalytic amount of Wilkinson's catalyst [(Ph3P)3RhCl]. Attempts to incorporate the diacetylene units via dehydrogenative coupling polymerization between 1,4-bis(dimethylsilyl)butadiyne [H(CH3)2SiCCCCSi(CH3)2H] and the hydroxy-terminated prepolymers were unsuccessful. The diacetylene units were incorporated into the polymer main chain via aminosilane,disilanol polycondensation between 1,4-bis(dimethylaminodimethylsilyl)butadiyne [(CH3)2NSi(CH3)2CCCC(CH3)2SiN(CH3)2] and the hydroxy-terminated prepolymers. Linear polymers were characterized by Fourier transform infrared, 1H and 13C NMR, gel permeation chromatography, differential scanning calorimetry, and thermogravimetric analysis, and they were thermally crosslinked through the diacetylene units, producing networked polymeric systems. The thermooxidative stability of the networked polymers is discussed. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1334,1341, 2002 [source] Effect of thermal processing on genistein, daidzein and glycitein content in soymilkJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 7 2006Huihua Huang Abstract Soymilk was subjected to various heat treatments at 95, 121 and 140 °C for various lengths of time. The contents of the aglycones of isoflavone (daidzein, glycitein and genistein) of the soymilk were determined using C18 reversed-phase high-performance liquid chromatography. Genistein showed greater stability to heat treatment than daidzein and glycitein. Both the daidzein and glycitein contents decreased rapidly during the early stage of heating, but on continued heating the rates of decrease were much slower. Heating may cause an increase or decrease in the genistein content of soymilk depending on the temperature and time used. Upon heating at 95 and 121 °C, there was an increase in the genistein content in the early stage of heating, possibly due the conversion of genistin to genistein. Heating at 140 °C for more than 15 s and prolonged heating at 95 and 121 °C, however, caused a slow decline in the genistein content. Copyright © 2006 Society of Chemical Industry [source] Study on Superabsorbent Composite, 14MACROMOLECULAR MATERIALS & ENGINEERING, Issue 12 2006Preparation of Poly(acrylic acid)/Organo-attapulgite Composite Hydrogels, Swelling Behaviors in Aqueous Electrolyte Solution Abstract Summary: Organo-attapulgite (organo-APT) was prepared by modifying APT using four quaternary ammonium salts with various lengths of the alkyl group, including (octyl)trimethylammonium bromide (OTMABr) and (stearyl)trimethylammonium chloride (STMACl), etc. A series of composite hydrogels, poly(acrylic acid)/organo-APT, from acrylic acid (AA), and organo-APT was prepared by aqueous polymerization, using N,N, -methylenebisacrylamide (MBA) as a crosslinker and ammonium persulfate (APS) as an initiator. The organification and organification degree of APT as well as the corresponding composites were characterized by FTIR, TGA, and XRD. The effects of the length of the alkyl group for different quaternary ammonium salts, organification degree of APT, and organo-APT content on water absorbency and swelling behaviors in various electrolyte solutions were investigated in this study. Equilibrium water absorbency strongly depends on chain length of the alkyl group of quaternary ammonium salts, organification degree of APT as well as organo-APT content. Longer alkyl group, higher organification degree, and proper organo-APT content are of benefit for the improvement of equilibrium water absorbency. Equilibrium water absorbency in distilled water for PAA/APT was enhanced from 350.1 to 562.1 g,·,g,1 after 10 wt.-% organo-APT, modified with STMACl for the highest degree, was introduced. The kind of cation is the key factor influencing equilibrium water absorbency of these composite hydrogels in electrolyte solutions. Organification of APT could enhance responsiveness of the corresponding composite hydrogel to electrolyte solutions. Schematic structure of PAA/organo-APT composite in a dry state (left) and in a swollen state (right). [source] Protein Sequences as Literature TextMACROMOLECULAR THEORY AND SIMULATIONS, Issue 5 2006Valentina V. Vasilevskaya Abstract Summary: We have performed analysis of protein sequences treating them as texts written in a "protein" language. We have shown that repeating patterns (words) of various lengths can be identified in these sequences. It was found that the maximum word lengths are different for proteins belonging to different classes; therefore, the corresponding values can be used to characterize the protein type. The suggested technique was first applied to analyze (decompose into words) normal (literature) texts written as a gapless symbolic sequence without spaces and punctuation marks. The tests using fiction, scientific, and popular scientific English texts proved the relative efficiency of the technique. Maximum word length for various proteins: ,fibrillar proteins, ,globular proteins, ,membrane proteins. [source] BARCODING: Assessing the effect of varying sequence length on DNA barcoding of fungiMOLECULAR ECOLOGY RESOURCES, Issue 3 2007XIANG JIA MIN Abstract DNA barcoding shows enormous promise for the rapid identification of organisms at the species level. There has been much recent debate, however, about the need for longer barcode sequences, especially when these sequences are used to construct molecular phylogenies. Here, we have analysed a set of fungal mitochondrial sequences , of various lengths , and we have monitored the effect of reducing sequence length on the utility of the data for both species identification and phylogenetic reconstruction. Our results demonstrate that reducing sequence length has a profound effect on the accuracy of resulting phylogenetic trees, but surprisingly short sequences still yield accurate species identifications. We conclude that the standard short barcode sequences (,600 bp) are not suitable for inferring accurate phylogenetic relationships, but they are sufficient for species identification among the fungi. [source] Conferring cadmium resistance to mature tobacco plants through metal-adsorbing particles of tomato mosaic virus vectorPLANT BIOTECHNOLOGY JOURNAL, Issue 3 2006Yoshinori Shingu Summary Tomato mosaic virus vectors were designed that produced, by a translational readthrough, a fusion protein consisting of coat protein and metal-binding peptide, as a result of which particles were expected to present the metal-binding peptides on their surface. When inoculated in plants, they were expected to replicate and form a metal-adsorbing artificial sink in the cytoplasm, so as to reduce metal toxicity. Vectors were constructed harbouring sequences encoding various lengths of polyhistidine as a metal-binding peptide. One of the vectors, TLRT6His, which contains a 6 × histidine sequence, moved systemically in tobacco plants, and its particles were shown to retain cadmium ions by an in vitro assay. When a toxic amount of cadmium was applied, the toxic effect was much reduced in TLRT6His-inoculated tobacco plants, probably as a result of cadmium adsorption by TLRT6His particles in the cytosol. This shows the possible use of an artificial sink for metal tolerance and the advantage of employing a plant viral vector for phytoremediation. [source] An experimental study of GFP-based FRET, with application to intrinsically unstructured proteinsPROTEIN SCIENCE, Issue 7 2007Tomoo Ohashi Abstract We have experimentally studied the fluorescence resonance energy transfer (FRET) between green fluorescent protein (GFP) molecules by inserting folded or intrinsically unstructured proteins between CyPet and Ypet. We discovered that most of the enhanced FRET signal previously reported for this pair was due to enhanced dimerization, so we engineered a monomerizing mutation into each. An insert containing a single fibronectin type III domain (3.7 nm end-to-end) gave a moderate FRET signal while a two-domain insert (7.0 nm) gave no FRET. We then tested unstructured proteins of various lengths, including the charged-plus-PQ domain of ZipA, the tail domain of ,-adducin, and the C-terminal tail domain of FtsZ. The structures of these FRET constructs were also studied by electron microscopy and sedimentation. A 12 amino acid linker and the N-terminal 33 amino acids of the charged domain of the ZipA gave strong FRET signals. The C-terminal 33 amino acids of the PQ domain of the ZipA and several unstructured proteins with 66,68 amino acids gave moderate FRET signals. The 150 amino acid charged-plus-PQ construct gave a barely detectable FRET signal. FRET efficiency was calculated from the decreased donor emission to estimate the distance between donor and acceptor. The donor,acceptor distance varied for unstructured inserts of the same length, suggesting that they had variable stiffness (persistence length). We conclude that GFP-based FRET can be useful for studying intrinsically unstructured proteins, and we present a range of calibrated protein inserts to experimentally determine the distances that can be studied. [source] Analysis of vitamin D-regulated gene expression in LNCaP human prostate cancer cells using cDNA microarraysTHE PROSTATE, Issue 3 2004Aruna V. Krishnan Abstract BACKGROUND 1,25-dihydroxyvitamin D3 [1,25(OH)2D3] exerts growth inhibitory, pro-differentiating, and pro-apoptotic effects on prostate cells. To better understand the molecular mechanisms underlying these actions, we employed cDNA microarrays to study 1,25(OH)2D3 -regulated gene expression in the LNCaP human prostate cancer cells. METHODS mRNA isolated from LNCaP cells treated with vehicle or 50 nM 1,25(OH)2D3 for various lengths of time were hybridized to microarrays carrying approximately 23,000 genes. Some of the putative target genes revealed by the microarray analysis were verified by real-time PCR assays. RESULTS 1,25(OH)2D3 most substantially increased the expression of the insulin-like growth factor binding protein-3 (IGFBP-3) gene. Our analysis also revealed several novel 1,25(OH)2D3 -responsive genes. Interestingly, some of the key genes regulated by 1,25(OH)2D3 are also androgen-responsive genes. 1,25(OH)2D3 also down-regulated genes that mediate androgen catabolism. CONCLUSIONS The putative 1,25(OH)2D3 target genes appear to be involved in a variety of cellular functions including growth regulation, differentiation, membrane transport, cell,cell and cell,matrix interactions, DNA repair, and inhibition of metastasis. The up-regulation of IGFBP-3 gene has been shown to be crucial in 1,25(OH)2D3 -mediated inhibition of LNCaP cell growth. 1,25(OH)2D3 regulation of androgen-responsive genes as well as genes involved in androgen catabolism suggests that there are interactions between 1,25(OH)2D3 and androgen signaling pathways in LNCaP cells. Further studies on the role of these genes and others in mediating the anti-cancer effects of 1,25(OH)2D3 may lead to better approaches to the prevention and treatment of prostate cancer. © 2004 Wiley-Liss, Inc. [source] Optimization of a novel headspace,solid-phase microextraction,gas chromatographic method by means of a Doehlert uniform shell design for the analysis of trace level ethylene oxide residuals in sterilized medical devicesBIOMEDICAL CHROMATOGRAPHY, Issue 6 2009Michael P. DiCicco Abstract Medical devices sterilized by ethylene oxide (EtO) retain trace quantities of EtO residuals, which may irritate patients' tissue. Reliably quantifying trace level EtO residuals in small medical devices requires an extremely sensitive analytical method. In this research, a Doehlert uniform shell design was utilized in obtaining a response surface to optimize a novel headspace,solid-phase microextraction,gas chromatographic (HS-SPME-GC) method developed for analyzing trace levels of EtO residuals in sterilized medical devices, by evaluating sterilized, polymer-coated, drug-eluting cardiovascular stents. The effects of four independent experimental variables (HS-SPME desorption time, extraction temperature, GC inlet temperature and extraction time) on GC peak area response of EtO were investigated simultaneously and the most influential experimental variables determined were extraction temperature and GC inlet temperature, with the fitted model showing no evidence of lack-of-fit. The optimized HS-SPME-GC method demonstrated overall good linearity/linear range, accuracy, repeatability, reproducibility, absolute recovery and high sensitivity. This novel method was successfully applied to analysis of trace levels of EtO residuals in sterilized/aerated cardiovascular stents of various lengths and internal diameter, where, upon heating, trace EtO residuals fully volatilized into HS for extraction, thereby nullifying matrix effects. As an alternative, this novel HS-SPME-GC method can offer higher sensitivity compared with conventional headspace analyzer-based sampling. Copyright © 2009 John Wiley & Sons, Ltd. [source] The presence of rRNA sequences in polyadenylated RNA and its potential functionsBIOTECHNOLOGY JOURNAL, Issue 8 2008Qiongman Kong Abstract Accumulating evidence has shown that various lengths of ribosomal RNA (rRNA) sequences are widely present in polyadenylated RNA. This review article will discuss these polyadenylated rRNAcontaining transcripts (PART). PART are highly abundant and widely expressed in various tissues. It appears that there may be two types of PART. One type, type I, contains the rRNA segments (from ,10 nucleotides up to several hundred nucleotides) located within the transcripts. It has been demonstrated that short rRNA sequences within type I PART may function as cis-regulatory elements that regulate translational efficiency. The other type, type II, contains large portions or almost entire sequences of rRNA with a cap at the 5' end and poly(A) at 3' end. Recent work has shown that some type II PART have functional significance for some neurodegenerative disease processes and may play an important role in the pathogenesis of diseases. Further investigation in this area is critical to understanding the basic biology of PART and the potential role of PART in diseases. [source] Stabilization of invertase by molecular engineeringBIOTECHNOLOGY PROGRESS, Issue 1 2010Pattamawadee Tananchai Abstract Extracellular invertase (EC 3.2.1.26) of Saccharomyces cerevisiae was stabilized against thermal denaturation by intermolecular and intramolecular crosslinking of the surface nucleophilic functional groups with diisocyanate homobifunctional reagents (OCN(CH2)nNCO) of various lengths (n = 4, 6, 8). Crosslinking with 1,4-diisocyanatobutane (n = 4) proved most effective in enhancing thermostability. Stability was improved dramatically by crosslinking 0.5 mg/mL of protein with 30 ,mol/mL of the reagent. Molecular engineering by crosslinking reduced the first-order thermal denaturation constant at 60°C from 1.567 min,1 (for the native enzyme) to 0.437 min,1 (for the stabilized enzyme). Similarly, the best crosslinking treatment increased the activation energy for denaturation from 391 kJ mol,1 (for the native protein) to 466 kJ mol,1 (for the stabilized enzyme). Crosslinking was confirmed by sodium dodecyl sulfate polyacrylamide gel electrophoresis. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010 [source] Functional Characterization of the Recombinant N -Methyltransferase Domain from the Multienzyme Enniatin SynthetaseCHEMBIOCHEM, Issue 9 2007Till Hornbogen Dr. Abstract A 51 kDa fusion protein incorporating the N -methyltransferase domain of the multienzyme enniatin synthetase from Fusarium scirpi was expressed in Saccharomyces cerevisiae. The protein was purified and found to bind S -adenosyl methionine (AdoMet) as demonstrated by cross-linking experiments with 14C-methyl-AdoMet under UV irradiation. Cofactor binding at equilibrium conditions was followed by saturation transfer difference (STD) NMR spectroscopy, and the native conformation of the methyltransferase was assigned. STD NMR spectroscopy yielded significant signals for H2 and H8 of the adenine moiety, H1' of D -ribose, and SCH3 group of AdoMet. Methyl group transfer catalyzed by the enzyme was demonstrated by using aminoacyl- N -acetylcysteamine thioesters (aminoacyl-SNACs) of L -Val, L -Ile, and L -Leu, which mimic the natural substrate amino acids of enniatin synthetase presented by the enzyme bound 4,-phosphopantetheine arm. In these experiments the enzyme was incubated in the presence of the corresponding aminoacyl-SNAC and 14C-methyl-AdoMet for various lengths of time, for up to 30 min. N -[14C-Methyl]-aminoacyl-SNAC products were extracted with EtOAc and separated by TLC. Acid hydrolysis of the isolated labeled compounds yielded the corresponding N -[14C-methyl] amino acids. Further proof for the formation of N - 14C-methyl-aminoacyl-SNACs came from MALDI-TOF mass spectrometry which yielded 23,212 Da for N -methyl-valyl-SNAC, accompanied by the expected postsource decay (PSD) pattern. Interestingly, L -Phe, which is not a substrate amino acid of enniatin synthetase, also proved to be a methyl group acceptor. D -Val was not accepted as a substrate; this indicates selectivity for the L isomer. [source] Synthesis and Stability in Biological Media of 1H -Imidazole-1-carboxylates of ROS203, an Antagonist of the Histamine H3 ReceptorCHEMISTRY & BIODIVERSITY, Issue 1 2008Mirko Rivara Abstract A series of carbamate derivatives of the H3 antagonist ROS203 (1) were prepared, and their lipophilicity and steric hindrance were modulated by introducing linear or branched alkyl chains of various lengths. In vitro stability studies were conducted to evaluate how structural modulations affect the intrinsic reactivity of the carbamoyl moiety and its recognition by metabolic enzymes. Linear alkyl carbamates were the most susceptible to enzymatic hydrolysis, with bioconversion rates being higher in rat liver and plasma. Chain ramification significantly enhanced the enzymatic stability of the set, with two derivatives (1g and 1h) being more stable by a factor of 8,40 than the ethyl carbamate 1a. Incubation with bovine serum albumin (BSA) showed a protective role of proteins on chemical and porcine-liver esterase (PLE)-catalyzed hydrolysis. Ex vivo binding data after i.v. administration of 1h revealed prolonged displacement of the labeled ligand [3H]-(R)- , -methylhistamine ([3H]RAMHA) from rat-brain cortical membranes, when compared to 1. However, the high rates of bioconversion in liver, as well as the chemical instability of 1h, suggest that further work is needed to optimize the enzymatic and chemical stability of these compounds. [source] Synthesis and Pharmacological Evaluation of Dimeric Follicle-Stimulating Hormone Receptor AntagonistsCHEMMEDCHEM, Issue 12 2009Kimberly Abstract A series of homo- and heterodimeric compounds encompassing the follicle-stimulating hormone receptor (FSHR) antagonist (R)- 1 and its inactive conformer (S)- 1 connected through ethylene glycol spacers of various lengths is described. Evaluation of these compounds reveals that dimeric compounds, with a spacer of sufficient length, bearing two active copies of the antagonist are more potent relative to dimeric compounds in which one of the active pharmacophores is replaced by an inactive conformer. Interestingly, the opposite trend is observed if a short spacer is used, indicating that these compounds may be valuable tools to study FSHR dimerization in greater detail. [source] | |||||||||||||||||||||||||||||||